^SERIES = GSE310554
!Series_title = Paired Vascular-Parenchymal Single Nuclei Sequencing Reveals Perturbed Endothelial-to-Mesenchymal Transition in Alzheimer’s Disease
!Series_geo_accession = GSE310554
!Series_status = Public on Nov 28 2025
!Series_submission_date = Nov 19 2025
!Series_last_update_date = Nov 28 2025
!Series_summary = The neurovascular unit (NVU) plays a crucial role in maintaining brain functions by integrating vascular cells, neurons, and glia to ensure metabolic support and blood-brain barrier integrity. While vascular dysfunction has been implicated in Alzheimer's disease (AD), the specific contributions of various vascular cell types remain understudied, partly due to challenges in isolating these cells from post-mortem tissue. In this study, we analyzed prefrontal cortex tissue from AD patients and control subjects using single-nuclei RNA sequencing to create a high-resolution atlas capturing major vascular and parenchymal cell types. Our findings reveal distinct associations between AD risk and gene expression profiles specific to pericytes, perivascular fibroblasts, and activated microglia. Functional analyses indicate that these genes converge on amyloid-related pathways, suggesting that perivascular compartments and immune modulators play significant roles in the early stages of AD pathobiology. Additionally, we identified a new endothelial-mesenchymal transition population that is diminished in AD, indicating a potential disruption in endothelial plasticity that may contribute to vascular dysfunction. Key ligand-receptor interactions between vascular and parenchymal cell types, such as ANGPT2, were found to be markedly dysregulated, highlighting potential targets that could drive NVU breakdown in AD. These findings provide a comprehensive framework for evaluating NVU cells in human disease and underscore novel links between vascular dynamics and AD pathogenesis. The study offers valuable insights into disease mechanisms and suggests new therapeutic avenues aimed at protecting and restoring the brain's neurovascular interface.
!Series_overall_design = Post-mortem pre-frontal cortex from 20 controls and 20 AD brain donors were collected from The Oxford Brain Bank. Vasculature and parenchyma fractions were sequenced seperately, giving 2 samples from each donor for a total of 80 samples. 3 donors were excluded in QC and of the remaining 37 donors, 23 were female and 14 were male with a median age of 87 (range 48-101).
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Gabriel Mateus,,Bernardo Harrington
!Series_contributor = Jimena,,Monzón-Sandoval
!Series_contributor = Gabriel,,Rocha
!Series_contributor = Lara,,Robinson
!Series_contributor = Michal,,Rokicki
!Series_contributor = Joanne,,Morgan
!Series_contributor = Ngoc-Nga,,Vinh
!Series_contributor = Hannah,,Sleven
!Series_contributor = Quenten,,Schwarz
!Series_contributor = Caleb,,Webber
!Series_contributor = Zameel,,Cader
!Series_sample_id = GSM9303433
!Series_sample_id = GSM9303434
!Series_sample_id = GSM9303435
!Series_sample_id = GSM9303436
!Series_sample_id = GSM9303437
!Series_sample_id = GSM9303438
!Series_sample_id = GSM9303439
!Series_sample_id = GSM9303440
!Series_sample_id = GSM9303441
!Series_sample_id = GSM9303442
!Series_sample_id = GSM9303443
!Series_sample_id = GSM9303444
!Series_sample_id = GSM9303445
!Series_sample_id = GSM9303446
!Series_sample_id = GSM9303447
!Series_sample_id = GSM9303448
!Series_sample_id = GSM9303449
!Series_sample_id = GSM9303450
!Series_sample_id = GSM9303451
!Series_sample_id = GSM9303452
!Series_sample_id = GSM9303453
!Series_sample_id = GSM9303454
!Series_sample_id = GSM9303455
!Series_sample_id = GSM9303456
!Series_sample_id = GSM9303457
!Series_sample_id = GSM9303458
!Series_sample_id = GSM9303459
!Series_sample_id = GSM9303460
!Series_sample_id = GSM9303461
!Series_sample_id = GSM9303462
!Series_sample_id = GSM9303463
!Series_sample_id = GSM9303464
!Series_sample_id = GSM9303465
!Series_sample_id = GSM9303466
!Series_sample_id = GSM9303467
!Series_sample_id = GSM9303468
!Series_sample_id = GSM9303469
!Series_sample_id = GSM9303470
!Series_sample_id = GSM9303471
!Series_contact_name = Gabriel Mateus,,Bernardo Harrington
!Series_contact_email = bernardo-harringtong@cardiff.ac.uk
!Series_contact_laboratory = Webber Lab
!Series_contact_institute = UK Dementia Research Institute at Cardiff University
!Series_contact_address = 52 Maindy Road
!Series_contact_city = Cardiff
!Series_contact_zip/postal_code = CF24 4HQ
!Series_contact_country = United Kingdom
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE310nnn/GSE310554/suppl/GSE310554_cell_metadata.tsv.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE310nnn/GSE310554/suppl/GSE310554_processed_seurat_obj.qs.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE310nnn/GSE310554/suppl/GSE310554_raw_counts_matrix.tsv.gz
!Series_gp_id = PRJNA1307833
!Series_platform_id = GPL24676
!Series_platform_organism = Homo sapiens
!Series_platform_taxid = 9606
!Series_sample_organism = Homo sapiens
!Series_sample_taxid = 9606

^SAMPLE = GSM9303433
!Sample_title = Parenchymal fraction, Control, donor 21
!Sample_geo_accession = GSM9303433
!Sample_status = Public on Nov 28 2025
!Sample_submission_date = Nov 19 2025
!Sample_last_update_date = Nov 28 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Prefrontal cortex
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Prefrontal cortex
!Sample_characteristics_ch1 = batch: 3
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = 1g of cortical tissue per sample was isolated, meninges removed, and fine dissection performed at -80⁰C and tissue stored at -80⁰C prior to the experiment. On the experimental day tissue was homogenised using a hand-held motorised homogeniser followed by a 7ml Dounce. The vascular fraction was enriched using differential centrifugation and purified using multi-layer dextran centrifugations. Large vessels were removed using 100um filter and small contaminants using a 40um filter. Finally vessels were digested at 4⁰C using 5mg/ml collagenase II to break down the basement membrane and ground on a 20um filter to obtain a vascular nuclei suspension. Nuclei were purified using FACS prior to 10x loading.
!Sample_extract_protocol_ch1 = Library preparation was performed according to the manufacturer's instructions (Chromium Next GEM Single Cell 3' v3.1 kit, Chromium Next GEM Chip G, 10X Genomics) with the Dual Index Plate TT Set A. Libraries were sequenced on one or multiple lanes of an S4 flow cell of the Illumina NovaSeq 6000 system (300 cycles, R1 with 28bp or 150bp, R2 with 150bp or 151bp, dual sample index reads I1 and I2 with 10bp cycles).
!Sample_description = Library name: P_21
!Sample_data_processing = The raw sequencing data was processed using CellRanger (version 7.1.0, 10X Genomics), which performed initial alignment, filtering, barcode counting, and UMI counting. An updated reference genome (Ensembl version 109 and Gencode version 43 annotations for GRCh38) was generated for use with CellRanger. The resulting gene-barcode matrices were then further processed using the scFlow pipeline implemented in Nextflow
!Sample_data_processing = Assembly: GRCh38
!Sample_data_processing = Supplementary files format and content: processed_seurat_obj.qs is an R Seurat object, details of format here: https://github.com/qsbase/qs. The object contains the processed post-QC data with celltype annotations and relevant sample metadata.
!Sample_data_processing = Supplementary files format and content: raw_counts_matrix.tsv.gz is a gzip tsv file with the raw count data
!Sample_data_processing = Supplementary files format and content: cell_metadata.tsv is a tsv file with the cell metadata
!Sample_platform_id = GPL24676
!Sample_contact_name = Gabriel Mateus,,Bernardo Harrington
!Sample_contact_email = bernardo-harringtong@cardiff.ac.uk
!Sample_contact_laboratory = Webber Lab
!Sample_contact_institute = UK Dementia Research Institute at Cardiff University
!Sample_contact_address = 52 Maindy Road
!Sample_contact_city = Cardiff
!Sample_contact_zip/postal_code = CF24 4HQ
!Sample_contact_country = United Kingdom
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN50676161
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX30148745
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE310554
!Sample_data_row_count = 0
^SAMPLE = GSM9303434
!Sample_title = Vascular fraction, Control, donor 21
!Sample_geo_accession = GSM9303434
!Sample_status = Public on Nov 28 2025
!Sample_submission_date = Nov 19 2025
!Sample_last_update_date = Nov 28 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Prefrontal cortex
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Prefrontal cortex
!Sample_characteristics_ch1 = batch: 3
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = 1g of cortical tissue per sample was isolated, meninges removed, and fine dissection performed at -80⁰C and tissue stored at -80⁰C prior to the experiment. On the experimental day tissue was homogenised using a hand-held motorised homogeniser followed by a 7ml Dounce. The vascular fraction was enriched using differential centrifugation and purified using multi-layer dextran centrifugations. Large vessels were removed using 100um filter and small contaminants using a 40um filter. Finally vessels were digested at 4⁰C using 5mg/ml collagenase II to break down the basement membrane and ground on a 20um filter to obtain a vascular nuclei suspension. Nuclei were purified using FACS prior to 10x loading.
!Sample_extract_protocol_ch1 = Library preparation was performed according to the manufacturer's instructions (Chromium Next GEM Single Cell 3' v3.1 kit, Chromium Next GEM Chip G, 10X Genomics) with the Dual Index Plate TT Set A. Libraries were sequenced on one or multiple lanes of an S4 flow cell of the Illumina NovaSeq 6000 system (300 cycles, R1 with 28bp or 150bp, R2 with 150bp or 151bp, dual sample index reads I1 and I2 with 10bp cycles).
!Sample_description = Library name: V_21
!Sample_data_processing = The raw sequencing data was processed using CellRanger (version 7.1.0, 10X Genomics), which performed initial alignment, filtering, barcode counting, and UMI counting. An updated reference genome (Ensembl version 109 and Gencode version 43 annotations for GRCh38) was generated for use with CellRanger. The resulting gene-barcode matrices were then further processed using the scFlow pipeline implemented in Nextflow
!Sample_data_processing = Assembly: GRCh38
!Sample_data_processing = Supplementary files format and content: processed_seurat_obj.qs is an R Seurat object, details of format here: https://github.com/qsbase/qs. The object contains the processed post-QC data with celltype annotations and relevant sample metadata.
!Sample_data_processing = Supplementary files format and content: raw_counts_matrix.tsv.gz is a gzip tsv file with the raw count data
!Sample_data_processing = Supplementary files format and content: cell_metadata.tsv is a tsv file with the cell metadata
!Sample_platform_id = GPL24676
!Sample_contact_name = Gabriel Mateus,,Bernardo Harrington
!Sample_contact_email = bernardo-harringtong@cardiff.ac.uk
!Sample_contact_laboratory = Webber Lab
!Sample_contact_institute = UK Dementia Research Institute at Cardiff University
!Sample_contact_address = 52 Maindy Road
!Sample_contact_city = Cardiff
!Sample_contact_zip/postal_code = CF24 4HQ
!Sample_contact_country = United Kingdom
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN50676162
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX30148744
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE310554
!Sample_data_row_count = 0
^SAMPLE = GSM9303435
!Sample_title = Parenchymal fraction, AD, donor 22
!Sample_geo_accession = GSM9303435
!Sample_status = Public on Nov 28 2025
!Sample_submission_date = Nov 19 2025
!Sample_last_update_date = Nov 28 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Prefrontal cortex
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Prefrontal cortex
!Sample_characteristics_ch1 = batch: 3
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = 1g of cortical tissue per sample was isolated, meninges removed, and fine dissection performed at -80⁰C and tissue stored at -80⁰C prior to the experiment. On the experimental day tissue was homogenised using a hand-held motorised homogeniser followed by a 7ml Dounce. The vascular fraction was enriched using differential centrifugation and purified using multi-layer dextran centrifugations. Large vessels were removed using 100um filter and small contaminants using a 40um filter. Finally vessels were digested at 4⁰C using 5mg/ml collagenase II to break down the basement membrane and ground on a 20um filter to obtain a vascular nuclei suspension. Nuclei were purified using FACS prior to 10x loading.
!Sample_extract_protocol_ch1 = Library preparation was performed according to the manufacturer's instructions (Chromium Next GEM Single Cell 3' v3.1 kit, Chromium Next GEM Chip G, 10X Genomics) with the Dual Index Plate TT Set A. Libraries were sequenced on one or multiple lanes of an S4 flow cell of the Illumina NovaSeq 6000 system (300 cycles, R1 with 28bp or 150bp, R2 with 150bp or 151bp, dual sample index reads I1 and I2 with 10bp cycles).
!Sample_description = Library name: P_22
!Sample_data_processing = The raw sequencing data was processed using CellRanger (version 7.1.0, 10X Genomics), which performed initial alignment, filtering, barcode counting, and UMI counting. An updated reference genome (Ensembl version 109 and Gencode version 43 annotations for GRCh38) was generated for use with CellRanger. The resulting gene-barcode matrices were then further processed using the scFlow pipeline implemented in Nextflow
!Sample_data_processing = Assembly: GRCh38
!Sample_data_processing = Supplementary files format and content: processed_seurat_obj.qs is an R Seurat object, details of format here: https://github.com/qsbase/qs. The object contains the processed post-QC data with celltype annotations and relevant sample metadata.
!Sample_data_processing = Supplementary files format and content: raw_counts_matrix.tsv.gz is a gzip tsv file with the raw count data
!Sample_data_processing = Supplementary files format and content: cell_metadata.tsv is a tsv file with the cell metadata
!Sample_platform_id = GPL24676
!Sample_contact_name = Gabriel Mateus,,Bernardo Harrington
!Sample_contact_email = bernardo-harringtong@cardiff.ac.uk
!Sample_contact_laboratory = Webber Lab
!Sample_contact_institute = UK Dementia Research Institute at Cardiff University
!Sample_contact_address = 52 Maindy Road
!Sample_contact_city = Cardiff
!Sample_contact_zip/postal_code = CF24 4HQ
!Sample_contact_country = United Kingdom
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN50676163
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX30148743
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE310554
!Sample_data_row_count = 0
^SAMPLE = GSM9303436
!Sample_title = Vascular fraction, AD, donor 22
!Sample_geo_accession = GSM9303436
!Sample_status = Public on Nov 28 2025
!Sample_submission_date = Nov 19 2025
!Sample_last_update_date = Nov 28 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Prefrontal cortex
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Prefrontal cortex
!Sample_characteristics_ch1 = batch: 3
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = 1g of cortical tissue per sample was isolated, meninges removed, and fine dissection performed at -80⁰C and tissue stored at -80⁰C prior to the experiment. On the experimental day tissue was homogenised using a hand-held motorised homogeniser followed by a 7ml Dounce. The vascular fraction was enriched using differential centrifugation and purified using multi-layer dextran centrifugations. Large vessels were removed using 100um filter and small contaminants using a 40um filter. Finally vessels were digested at 4⁰C using 5mg/ml collagenase II to break down the basement membrane and ground on a 20um filter to obtain a vascular nuclei suspension. Nuclei were purified using FACS prior to 10x loading.
!Sample_extract_protocol_ch1 = Library preparation was performed according to the manufacturer's instructions (Chromium Next GEM Single Cell 3' v3.1 kit, Chromium Next GEM Chip G, 10X Genomics) with the Dual Index Plate TT Set A. Libraries were sequenced on one or multiple lanes of an S4 flow cell of the Illumina NovaSeq 6000 system (300 cycles, R1 with 28bp or 150bp, R2 with 150bp or 151bp, dual sample index reads I1 and I2 with 10bp cycles).
!Sample_description = Library name: V_22
!Sample_data_processing = The raw sequencing data was processed using CellRanger (version 7.1.0, 10X Genomics), which performed initial alignment, filtering, barcode counting, and UMI counting. An updated reference genome (Ensembl version 109 and Gencode version 43 annotations for GRCh38) was generated for use with CellRanger. The resulting gene-barcode matrices were then further processed using the scFlow pipeline implemented in Nextflow
!Sample_data_processing = Assembly: GRCh38
!Sample_data_processing = Supplementary files format and content: processed_seurat_obj.qs is an R Seurat object, details of format here: https://github.com/qsbase/qs. The object contains the processed post-QC data with celltype annotations and relevant sample metadata.
!Sample_data_processing = Supplementary files format and content: raw_counts_matrix.tsv.gz is a gzip tsv file with the raw count data
!Sample_data_processing = Supplementary files format and content: cell_metadata.tsv is a tsv file with the cell metadata
!Sample_platform_id = GPL24676
!Sample_contact_name = Gabriel Mateus,,Bernardo Harrington
!Sample_contact_email = bernardo-harringtong@cardiff.ac.uk
!Sample_contact_laboratory = Webber Lab
!Sample_contact_institute = UK Dementia Research Institute at Cardiff University
!Sample_contact_address = 52 Maindy Road
!Sample_contact_city = Cardiff
!Sample_contact_zip/postal_code = CF24 4HQ
!Sample_contact_country = United Kingdom
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN50676164
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX30148742
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE310554
!Sample_data_row_count = 0
^SAMPLE = GSM9303437
!Sample_title = Parenchymal fraction, Control, donor 23
!Sample_geo_accession = GSM9303437
!Sample_status = Public on Nov 28 2025
!Sample_submission_date = Nov 19 2025
!Sample_last_update_date = Nov 28 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Prefrontal cortex
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Prefrontal cortex
!Sample_characteristics_ch1 = batch: 3
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = 1g of cortical tissue per sample was isolated, meninges removed, and fine dissection performed at -80⁰C and tissue stored at -80⁰C prior to the experiment. On the experimental day tissue was homogenised using a hand-held motorised homogeniser followed by a 7ml Dounce. The vascular fraction was enriched using differential centrifugation and purified using multi-layer dextran centrifugations. Large vessels were removed using 100um filter and small contaminants using a 40um filter. Finally vessels were digested at 4⁰C using 5mg/ml collagenase II to break down the basement membrane and ground on a 20um filter to obtain a vascular nuclei suspension. Nuclei were purified using FACS prior to 10x loading.
!Sample_extract_protocol_ch1 = Library preparation was performed according to the manufacturer's instructions (Chromium Next GEM Single Cell 3' v3.1 kit, Chromium Next GEM Chip G, 10X Genomics) with the Dual Index Plate TT Set A. Libraries were sequenced on one or multiple lanes of an S4 flow cell of the Illumina NovaSeq 6000 system (300 cycles, R1 with 28bp or 150bp, R2 with 150bp or 151bp, dual sample index reads I1 and I2 with 10bp cycles).
!Sample_description = Library name: P_23
!Sample_data_processing = The raw sequencing data was processed using CellRanger (version 7.1.0, 10X Genomics), which performed initial alignment, filtering, barcode counting, and UMI counting. An updated reference genome (Ensembl version 109 and Gencode version 43 annotations for GRCh38) was generated for use with CellRanger. The resulting gene-barcode matrices were then further processed using the scFlow pipeline implemented in Nextflow
!Sample_data_processing = Assembly: GRCh38
!Sample_data_processing = Supplementary files format and content: processed_seurat_obj.qs is an R Seurat object, details of format here: https://github.com/qsbase/qs. The object contains the processed post-QC data with celltype annotations and relevant sample metadata.
!Sample_data_processing = Supplementary files format and content: raw_counts_matrix.tsv.gz is a gzip tsv file with the raw count data
!Sample_data_processing = Supplementary files format and content: cell_metadata.tsv is a tsv file with the cell metadata
!Sample_platform_id = GPL24676
!Sample_contact_name = Gabriel Mateus,,Bernardo Harrington
!Sample_contact_email = bernardo-harringtong@cardiff.ac.uk
!Sample_contact_laboratory = Webber Lab
!Sample_contact_institute = UK Dementia Research Institute at Cardiff University
!Sample_contact_address = 52 Maindy Road
!Sample_contact_city = Cardiff
!Sample_contact_zip/postal_code = CF24 4HQ
!Sample_contact_country = United Kingdom
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN50676165
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX30148741
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE310554
!Sample_data_row_count = 0
^SAMPLE = GSM9303438
!Sample_title = Vascular fraction, Control, donor 23
!Sample_geo_accession = GSM9303438
!Sample_status = Public on Nov 28 2025
!Sample_submission_date = Nov 19 2025
!Sample_last_update_date = Nov 28 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Prefrontal cortex
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Prefrontal cortex
!Sample_characteristics_ch1 = batch: 3
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = 1g of cortical tissue per sample was isolated, meninges removed, and fine dissection performed at -80⁰C and tissue stored at -80⁰C prior to the experiment. On the experimental day tissue was homogenised using a hand-held motorised homogeniser followed by a 7ml Dounce. The vascular fraction was enriched using differential centrifugation and purified using multi-layer dextran centrifugations. Large vessels were removed using 100um filter and small contaminants using a 40um filter. Finally vessels were digested at 4⁰C using 5mg/ml collagenase II to break down the basement membrane and ground on a 20um filter to obtain a vascular nuclei suspension. Nuclei were purified using FACS prior to 10x loading.
!Sample_extract_protocol_ch1 = Library preparation was performed according to the manufacturer's instructions (Chromium Next GEM Single Cell 3' v3.1 kit, Chromium Next GEM Chip G, 10X Genomics) with the Dual Index Plate TT Set A. Libraries were sequenced on one or multiple lanes of an S4 flow cell of the Illumina NovaSeq 6000 system (300 cycles, R1 with 28bp or 150bp, R2 with 150bp or 151bp, dual sample index reads I1 and I2 with 10bp cycles).
!Sample_description = Library name: V_23
!Sample_data_processing = The raw sequencing data was processed using CellRanger (version 7.1.0, 10X Genomics), which performed initial alignment, filtering, barcode counting, and UMI counting. An updated reference genome (Ensembl version 109 and Gencode version 43 annotations for GRCh38) was generated for use with CellRanger. The resulting gene-barcode matrices were then further processed using the scFlow pipeline implemented in Nextflow
!Sample_data_processing = Assembly: GRCh38
!Sample_data_processing = Supplementary files format and content: processed_seurat_obj.qs is an R Seurat object, details of format here: https://github.com/qsbase/qs. The object contains the processed post-QC data with celltype annotations and relevant sample metadata.
!Sample_data_processing = Supplementary files format and content: raw_counts_matrix.tsv.gz is a gzip tsv file with the raw count data
!Sample_data_processing = Supplementary files format and content: cell_metadata.tsv is a tsv file with the cell metadata
!Sample_platform_id = GPL24676
!Sample_contact_name = Gabriel Mateus,,Bernardo Harrington
!Sample_contact_email = bernardo-harringtong@cardiff.ac.uk
!Sample_contact_laboratory = Webber Lab
!Sample_contact_institute = UK Dementia Research Institute at Cardiff University
!Sample_contact_address = 52 Maindy Road
!Sample_contact_city = Cardiff
!Sample_contact_zip/postal_code = CF24 4HQ
!Sample_contact_country = United Kingdom
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN50676166
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX30148733
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE310554
!Sample_data_row_count = 0
^SAMPLE = GSM9303439
!Sample_title = Parenchymal fraction, AD, donor 24
!Sample_geo_accession = GSM9303439
!Sample_status = Public on Nov 28 2025
!Sample_submission_date = Nov 19 2025
!Sample_last_update_date = Nov 28 2025
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Prefrontal cortex
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Prefrontal cortex
!Sample_characteristics_ch1 = batch: 3
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = 1g of cortical tissue per sample was isolated, meninges removed, and fine dissection performed at -80⁰C and tissue stored at -80⁰C prior to the experiment. On the experimental day tissue was homogenised using a hand-held motorised homogeniser followed by a 7ml Dounce. The vascular fraction was enriched using differential centrifugation and purified using multi-layer dextran centrifugations. Large vessels were removed using 100um filter and small contaminants using a 40um filter. Finally vessels were digested at 4⁰C using 5mg/ml collagenase II to break down the basement membrane and ground on a 20um filter to obtain a vascular nuclei suspension. Nuclei were purified using FACS prior to 10x loading.
!Sample_extract_protocol_ch1 = Library preparation was performed according to the manufacturer's instructions (Chromium Next GEM Single Cell 3' v3.1 kit, Chromium Next GEM Chip G, 10X Genomics) with the Dual Index Plate TT Set A. Libraries were sequenced on one or multiple lanes of an S4 flow cell of the Illumina NovaSeq 6000 system (300 cycles, R1 with 28bp or 150bp, R2 with 150bp or 151bp, dual sample index reads I1 and I2 with 10bp cycles).
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!Sample_data_processing = Assembly: GRCh38
!Sample_data_processing = Supplementary files format and content: processed_seurat_obj.qs is an R Seurat object, details of format here: https://github.com/qsbase/qs. The object contains the processed post-QC data with celltype annotations and relevant sample metadata.
!Sample_data_processing = Supplementary files format and content: raw_counts_matrix.tsv.gz is a gzip tsv file with the raw count data
!Sample_data_processing = Supplementary files format and content: cell_metadata.tsv is a tsv file with the cell metadata
!Sample_platform_id = GPL24676
!Sample_contact_name = Gabriel Mateus,,Bernardo Harrington
!Sample_contact_email = bernardo-harringtong@cardiff.ac.uk
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!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX30148734
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!Sample_series_id = GSE310554
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!Sample_geo_accession = GSM9303440
!Sample_status = Public on Nov 28 2025
!Sample_submission_date = Nov 19 2025
!Sample_last_update_date = Nov 28 2025
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!Sample_data_processing = Supplementary files format and content: raw_counts_matrix.tsv.gz is a gzip tsv file with the raw count data
!Sample_data_processing = Supplementary files format and content: cell_metadata.tsv is a tsv file with the cell metadata
!Sample_platform_id = GPL24676
!Sample_contact_name = Gabriel Mateus,,Bernardo Harrington
!Sample_contact_email = bernardo-harringtong@cardiff.ac.uk
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!Sample_status = Public on Nov 28 2025
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!Sample_data_processing = Supplementary files format and content: raw_counts_matrix.tsv.gz is a gzip tsv file with the raw count data
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!Sample_platform_id = GPL24676
!Sample_contact_name = Gabriel Mateus,,Bernardo Harrington
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!Sample_data_processing = Assembly: GRCh38
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!Sample_data_processing = Supplementary files format and content: raw_counts_matrix.tsv.gz is a gzip tsv file with the raw count data
!Sample_data_processing = Supplementary files format and content: cell_metadata.tsv is a tsv file with the cell metadata
!Sample_platform_id = GPL24676
!Sample_contact_name = Gabriel Mateus,,Bernardo Harrington
!Sample_contact_email = bernardo-harringtong@cardiff.ac.uk
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!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX30148773
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!Sample_geo_accession = GSM9303448
!Sample_status = Public on Nov 28 2025
!Sample_submission_date = Nov 19 2025
!Sample_last_update_date = Nov 28 2025
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!Sample_data_processing = Supplementary files format and content: raw_counts_matrix.tsv.gz is a gzip tsv file with the raw count data
!Sample_data_processing = Supplementary files format and content: cell_metadata.tsv is a tsv file with the cell metadata
!Sample_platform_id = GPL24676
!Sample_contact_name = Gabriel Mateus,,Bernardo Harrington
!Sample_contact_email = bernardo-harringtong@cardiff.ac.uk
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!Sample_data_processing = Supplementary files format and content: raw_counts_matrix.tsv.gz is a gzip tsv file with the raw count data
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!Sample_contact_name = Gabriel Mateus,,Bernardo Harrington
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!Sample_data_processing = Assembly: GRCh38
!Sample_data_processing = Supplementary files format and content: processed_seurat_obj.qs is an R Seurat object, details of format here: https://github.com/qsbase/qs. The object contains the processed post-QC data with celltype annotations and relevant sample metadata.
!Sample_data_processing = Supplementary files format and content: raw_counts_matrix.tsv.gz is a gzip tsv file with the raw count data
!Sample_data_processing = Supplementary files format and content: cell_metadata.tsv is a tsv file with the cell metadata
!Sample_platform_id = GPL24676
!Sample_contact_name = Gabriel Mateus,,Bernardo Harrington
!Sample_contact_email = bernardo-harringtong@cardiff.ac.uk
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!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX30148760
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!Sample_geo_accession = GSM9303456
!Sample_status = Public on Nov 28 2025
!Sample_submission_date = Nov 19 2025
!Sample_last_update_date = Nov 28 2025
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!Sample_data_processing = Assembly: GRCh38
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!Sample_data_processing = Supplementary files format and content: raw_counts_matrix.tsv.gz is a gzip tsv file with the raw count data
!Sample_data_processing = Supplementary files format and content: cell_metadata.tsv is a tsv file with the cell metadata
!Sample_platform_id = GPL24676
!Sample_contact_name = Gabriel Mateus,,Bernardo Harrington
!Sample_contact_email = bernardo-harringtong@cardiff.ac.uk
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!Sample_data_processing = Supplementary files format and content: raw_counts_matrix.tsv.gz is a gzip tsv file with the raw count data
!Sample_data_processing = Supplementary files format and content: cell_metadata.tsv is a tsv file with the cell metadata
!Sample_platform_id = GPL24676
!Sample_contact_name = Gabriel Mateus,,Bernardo Harrington
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!Sample_data_processing = Assembly: GRCh38
!Sample_data_processing = Supplementary files format and content: processed_seurat_obj.qs is an R Seurat object, details of format here: https://github.com/qsbase/qs. The object contains the processed post-QC data with celltype annotations and relevant sample metadata.
!Sample_data_processing = Supplementary files format and content: raw_counts_matrix.tsv.gz is a gzip tsv file with the raw count data
!Sample_data_processing = Supplementary files format and content: cell_metadata.tsv is a tsv file with the cell metadata
!Sample_platform_id = GPL24676
!Sample_contact_name = Gabriel Mateus,,Bernardo Harrington
!Sample_contact_email = bernardo-harringtong@cardiff.ac.uk
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!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX30148769
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!Sample_status = Public on Nov 28 2025
!Sample_submission_date = Nov 19 2025
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!Sample_data_processing = Supplementary files format and content: raw_counts_matrix.tsv.gz is a gzip tsv file with the raw count data
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!Sample_platform_id = GPL24676
!Sample_contact_name = Gabriel Mateus,,Bernardo Harrington
!Sample_contact_email = bernardo-harringtong@cardiff.ac.uk
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!Sample_data_processing = Supplementary files format and content: raw_counts_matrix.tsv.gz is a gzip tsv file with the raw count data
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!Sample_contact_name = Gabriel Mateus,,Bernardo Harrington
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!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: Prefrontal cortex
!Sample_characteristics_ch1 = batch: 3
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = 1g of cortical tissue per sample was isolated, meninges removed, and fine dissection performed at -80⁰C and tissue stored at -80⁰C prior to the experiment. On the experimental day tissue was homogenised using a hand-held motorised homogeniser followed by a 7ml Dounce. The vascular fraction was enriched using differential centrifugation and purified using multi-layer dextran centrifugations. Large vessels were removed using 100um filter and small contaminants using a 40um filter. Finally vessels were digested at 4⁰C using 5mg/ml collagenase II to break down the basement membrane and ground on a 20um filter to obtain a vascular nuclei suspension. Nuclei were purified using FACS prior to 10x loading.
!Sample_extract_protocol_ch1 = Library preparation was performed according to the manufacturer's instructions (Chromium Next GEM Single Cell 3' v3.1 kit, Chromium Next GEM Chip G, 10X Genomics) with the Dual Index Plate TT Set A. Libraries were sequenced on one or multiple lanes of an S4 flow cell of the Illumina NovaSeq 6000 system (300 cycles, R1 with 28bp or 150bp, R2 with 150bp or 151bp, dual sample index reads I1 and I2 with 10bp cycles).
!Sample_description = Library name: V_40
!Sample_data_processing = The raw sequencing data was processed using CellRanger (version 7.1.0, 10X Genomics), which performed initial alignment, filtering, barcode counting, and UMI counting. An updated reference genome (Ensembl version 109 and Gencode version 43 annotations for GRCh38) was generated for use with CellRanger. The resulting gene-barcode matrices were then further processed using the scFlow pipeline implemented in Nextflow
!Sample_data_processing = Assembly: GRCh38
!Sample_data_processing = Supplementary files format and content: processed_seurat_obj.qs is an R Seurat object, details of format here: https://github.com/qsbase/qs. The object contains the processed post-QC data with celltype annotations and relevant sample metadata.
!Sample_data_processing = Supplementary files format and content: raw_counts_matrix.tsv.gz is a gzip tsv file with the raw count data
!Sample_data_processing = Supplementary files format and content: cell_metadata.tsv is a tsv file with the cell metadata
!Sample_platform_id = GPL24676
!Sample_contact_name = Gabriel Mateus,,Bernardo Harrington
!Sample_contact_email = bernardo-harringtong@cardiff.ac.uk
!Sample_contact_laboratory = Webber Lab
!Sample_contact_institute = UK Dementia Research Institute at Cardiff University
!Sample_contact_address = 52 Maindy Road
!Sample_contact_city = Cardiff
!Sample_contact_zip/postal_code = CF24 4HQ
!Sample_contact_country = United Kingdom
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN50676200
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX30148735
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE310554
!Sample_data_row_count = 0
