^SERIES = GSE282551
!Series_title = Long-read RNA sequencing reveals synaptic genes with differential isoform usage in schizophrenia [long-read RNAseq ]
!Series_geo_accession = GSE282551
!Series_status = Public on Dec 01 2025
!Series_submission_date = Nov 21 2024
!Series_last_update_date = Dec 01 2025
!Series_summary = Over the past 15+ years, genetic studies have been notably successful in revealing the architecture of multiple psychiatric disorders, including schizophrenia. It is now widely acknowledged that schizophrenia is highly polygenic, consisting of both common variants of unknown significance, identified through genome-wide association studies (GWAS), and rare CNVs and coding variants. Despite these advances, the underlying mechanisms of specific genes implicated by GWAS are not well understood. Multiple lines of evidence implicate alternative splicing in the pathophysiology of schizophrenia. Single-nucleotide polymorphisms (SNPs) within implicated schizophrenia loci could alter isoform diversity and abundances which may not be reflected in a typical differential expression study. Hence, we generated a comprehensive isoform survey of postmortem human dorsolateral prefrontal cortex (DLPFC) from schizophrenia cases and neurotypical controls to identify case-control isoform-level differences. We developed an analysis pipeline that combines the strengths of PacBio SMRT long-read RNA sequencing in conducting a detailed isoform census with the capacity of short-read RNA sequencing for the quantification of isoform abundances. From several hundred thousand discovered long-read isoforms we curated a transcriptome with tens of thousands of high confidence novel isoforms. We then identified differential isoform usage (DIU) genes using a combination of established and in-house pipelines that enables case-control comparisons. Many of these novel isoforms are differentially expressed in schizophrenia DLPFC vs neurotypical controls. Differentially expressed genes are enriched in gene sets related to synaptic structure and function, RNA binding and splicing, as well as cell types previously implicated in schizophrenia, including cortical excitatory neurons, medium spiny neurons, and pyramidal CA1 neurons. Publicly available splicing data, genotyping, proteomics, and single nucleus sequencing results verify and support our results.
!Series_overall_design = pacbio long read RNA-seq data from human post mortem DLPFC tissue in schizophrenic and healthy control subjects
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Anthony,,Abrantes
!Series_contributor = Lisa,,Bast
!Series_contributor = Fatima,,Memic
!Series_contributor = Shuyang,,Yao
!Series_contributor = NaEshia,,Ancalade
!Series_contributor = Shadia,,Sekle
!Series_contributor = Anke A.,,Dijkstra
!Series_contributor = Elizabeth,,Tseng
!Series_contributor = George,,Jurjus
!Series_contributor = James,,Overholser
!Series_contributor = Gouri,,Mahajan
!Series_contributor = Craig A.,,Stockmeier
!Series_contributor = Gloria,,Sheynkman
!Series_contributor = Jens,,Hjerling-Leffler
!Series_contributor = Guus,,Smit
!Series_contributor = Patrick F.,,Sullivan
!Series_contributor = Paola,,Giusti-Rodriguez
!Series_sample_id = GSM8645872
!Series_sample_id = GSM8645873
!Series_sample_id = GSM8645874
!Series_sample_id = GSM8645875
!Series_sample_id = GSM8645876
!Series_sample_id = GSM8645877
!Series_sample_id = GSM8645878
!Series_sample_id = GSM8645879
!Series_sample_id = GSM8645880
!Series_sample_id = GSM8645881
!Series_sample_id = GSM8645882
!Series_sample_id = GSM8645883
!Series_sample_id = GSM8645884
!Series_sample_id = GSM8645885
!Series_sample_id = GSM8645886
!Series_sample_id = GSM8645887
!Series_sample_id = GSM8645888
!Series_sample_id = GSM8645889
!Series_sample_id = GSM8645890
!Series_sample_id = GSM8645891
!Series_sample_id = GSM8645892
!Series_sample_id = GSM8645893
!Series_sample_id = GSM8645894
!Series_sample_id = GSM8645895
!Series_sample_id = GSM8645896
!Series_sample_id = GSM8645897
!Series_sample_id = GSM8645898
!Series_sample_id = GSM8645899
!Series_sample_id = GSM8645900
!Series_sample_id = GSM8645901
!Series_contact_name = anthony,shawn,abrantes
!Series_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Series_contact_phone = 9196194107
!Series_contact_laboratory = sullivan
!Series_contact_department = genetic medicine
!Series_contact_institute = unc-chapel hill
!Series_contact_address = 402 Paunack st apt 1
!Series_contact_city = Madison
!Series_contact_state = WI
!Series_contact_zip/postal_code = 53726
!Series_contact_country = USA
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE282nnn/GSE282551/suppl/GSE282551_SQANTI3_results_classification.txt.gz
!Series_platform_id = GPL28352
!Series_platform_id = GPL34678
!Series_platform_organism = Homo sapiens
!Series_platform_taxid = 9606
!Series_sample_organism = Homo sapiens
!Series_sample_taxid = 9606
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1189125

^SAMPLE = GSM8645872
!Sample_title = humanDLPFC_Schizophrenia_1
!Sample_geo_accession = GSM8645872
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Schizophrenia
!Sample_characteristics_ch1 = batch: "007"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_007_001
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL28352
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel II
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860823
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806062
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645873
!Sample_title = humanDLPFC_Schizophrenia_2
!Sample_geo_accession = GSM8645873
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Schizophrenia
!Sample_characteristics_ch1 = batch: "007"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_007_002
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL28352
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel II
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860822
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806063
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645874
!Sample_title = humanDLPFC_Control_1
!Sample_geo_accession = GSM8645874
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Control
!Sample_characteristics_ch1 = batch: "007"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_007_003
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL28352
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel II
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860821
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806064
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645875
!Sample_title = humanDLPFC_Control_2
!Sample_geo_accession = GSM8645875
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Control
!Sample_characteristics_ch1 = batch: "007"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_007_004
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL28352
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel II
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860820
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806065
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645876
!Sample_title = humanDLPFC_Schizophrenia_3
!Sample_geo_accession = GSM8645876
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Schizophrenia
!Sample_characteristics_ch1 = batch: "007"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_007_005
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL28352
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel II
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860819
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806066
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645877
!Sample_title = humanDLPFC_Schizophrenia_4
!Sample_geo_accession = GSM8645877
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Schizophrenia
!Sample_characteristics_ch1 = batch: "007"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_007_006
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL28352
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel II
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860818
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806067
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645878
!Sample_title = humanDLPFC_Schizophrenia_5
!Sample_geo_accession = GSM8645878
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Schizophrenia
!Sample_characteristics_ch1 = batch: "007"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_007_007
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL28352
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel II
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860817
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806068
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645879
!Sample_title = humanDLPFC_Control_3
!Sample_geo_accession = GSM8645879
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Control
!Sample_characteristics_ch1 = batch: "007"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_007_008
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL28352
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel II
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860816
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806069
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645880
!Sample_title = humanDLPFC_Control_4
!Sample_geo_accession = GSM8645880
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Control
!Sample_characteristics_ch1 = batch: "007"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_007_009
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL28352
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel II
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860815
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806070
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645881
!Sample_title = humanDLPFC_Control_5
!Sample_geo_accession = GSM8645881
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Control
!Sample_characteristics_ch1 = batch: "007"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_007_011
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL28352
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel II
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860814
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806071
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645882
!Sample_title = humanDLPFC_Schizophrenia_6
!Sample_geo_accession = GSM8645882
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Schizophrenia
!Sample_characteristics_ch1 = batch: "043"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_043_001
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL34678
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel IIe
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860813
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806072
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645883
!Sample_title = humanDLPFC_Schizophrenia_7
!Sample_geo_accession = GSM8645883
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Schizophrenia
!Sample_characteristics_ch1 = batch: "043"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_043_002
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL34678
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel IIe
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860812
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806073
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645884
!Sample_title = humanDLPFC_Schizophrenia_8
!Sample_geo_accession = GSM8645884
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Schizophrenia
!Sample_characteristics_ch1 = batch: "043"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_043_003
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL34678
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel IIe
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860811
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806074
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645885
!Sample_title = humanDLPFC_Schizophrenia_9
!Sample_geo_accession = GSM8645885
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Schizophrenia
!Sample_characteristics_ch1 = batch: "043"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_043_004
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL34678
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel IIe
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860810
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806075
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645886
!Sample_title = humanDLPFC_Schizophrenia_10
!Sample_geo_accession = GSM8645886
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Schizophrenia
!Sample_characteristics_ch1 = batch: "043"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_043_005
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL34678
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel IIe
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860809
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806076
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645887
!Sample_title = humanDLPFC_Schizophrenia_11
!Sample_geo_accession = GSM8645887
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Schizophrenia
!Sample_characteristics_ch1 = batch: "043"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_043_006
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL34678
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel IIe
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860808
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806077
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645888
!Sample_title = humanDLPFC_Schizophrenia_12
!Sample_geo_accession = GSM8645888
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Schizophrenia
!Sample_characteristics_ch1 = batch: "043"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_043_007
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL34678
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel IIe
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860807
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806078
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645889
!Sample_title = humanDLPFC_Control_6
!Sample_geo_accession = GSM8645889
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Control
!Sample_characteristics_ch1 = batch: "043"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_043_009
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL34678
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel IIe
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860806
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806079
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645890
!Sample_title = humanDLPFC_Control_7
!Sample_geo_accession = GSM8645890
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Control
!Sample_characteristics_ch1 = batch: "043"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_043_010
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL34678
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel IIe
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860805
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806080
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645891
!Sample_title = humanDLPFC_Control_8
!Sample_geo_accession = GSM8645891
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Control
!Sample_characteristics_ch1 = batch: "052"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_052_001
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL34678
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel IIe
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860804
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806081
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645892
!Sample_title = humanDLPFC_Control_9
!Sample_geo_accession = GSM8645892
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Control
!Sample_characteristics_ch1 = batch: "052"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_052_002
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL34678
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
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!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
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!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806082
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!Sample_series_id = GSE282551
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!Sample_geo_accession = GSM8645893
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
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!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
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!Sample_characteristics_ch1 = disease state: Control
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!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_052_003
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL34678
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
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!Sample_contact_country = USA
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!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806083
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^SAMPLE = GSM8645894
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!Sample_geo_accession = GSM8645894
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
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!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_052_004
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL34678
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
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!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806084
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^SAMPLE = GSM8645895
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!Sample_geo_accession = GSM8645895
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
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!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_052_005
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
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!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL34678
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
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^SAMPLE = GSM8645896
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!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
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!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
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!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL34678
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
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^SAMPLE = GSM8645897
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!Sample_status = Public on Dec 01 2025
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!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
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!Sample_data_processing = SQANTI3 QC filtering
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!Sample_platform_id = GPL34678
!Sample_contact_name = anthony,shawn,abrantes
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^SAMPLE = GSM8645898
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!Sample_contact_name = anthony,shawn,abrantes
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^SAMPLE = GSM8645899
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!Sample_last_update_date = Dec 01 2025
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!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
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!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
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!Sample_platform_id = GPL34678
!Sample_contact_name = anthony,shawn,abrantes
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!Sample_contact_country = USA
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!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806089
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
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^SAMPLE = GSM8645900
!Sample_title = humanDLPFC_Schizophrenia_13
!Sample_geo_accession = GSM8645900
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Schizophrenia
!Sample_characteristics_ch1 = batch: "052"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_052_011
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL34678
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel IIe
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860795
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806090
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
^SAMPLE = GSM8645901
!Sample_title = humanDLPFC_Schizophrenia_14
!Sample_geo_accession = GSM8645901
!Sample_status = Public on Dec 01 2025
!Sample_submission_date = Nov 21 2024
!Sample_last_update_date = Dec 01 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)
!Sample_characteristics_ch1 = disease state: Schizophrenia
!Sample_characteristics_ch1 = batch: "052"
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
!Sample_extract_protocol_ch1 = Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.
!Sample_description = FL.pt_052_012
!Sample_data_processing = SMRTLink (v8.0.0)
!Sample_data_processing = removed primers using Lima (v2.0.0).
!Sample_data_processing = clustered using IsoSeq3
!Sample_data_processing = aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
!Sample_data_processing = Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
!Sample_data_processing = SQANTI3 QC filtering
!Sample_data_processing = Assembly: GRCh38.p13
!Sample_data_processing = Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts
!Sample_platform_id = GPL34678
!Sample_contact_name = anthony,shawn,abrantes
!Sample_contact_email = abrantes@live.unc.edu, abrantes@wisc.edu, antshaabr@gmail.com
!Sample_contact_phone = 9196194107
!Sample_contact_laboratory = sullivan
!Sample_contact_department = genetic medicine
!Sample_contact_institute = unc-chapel hill
!Sample_contact_address = 402 Paunack st apt 1
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53726
!Sample_contact_country = USA
!Sample_instrument_model = Sequel IIe
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN44860794
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX26806091
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE282551
!Sample_data_row_count = 0
