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| Status |
Public on Apr 24, 2023 |
| Title |
F10 |
| Sample type |
SRA |
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| Source name |
Brain BA9 dlPFC
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Brain BA9 dlPFC
Sex: Female
group: Control
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Chromium Single Cell 3’ Reagent Kits v2 and v3.1
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Batch: 6F, Chemistry: v3
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| Data processing |
10X Genomics Cellranger v3.1.0 mkfastq
10X Genomics Cellranger v5.0.1 count
Cell filtering as described in publication
Clustering and cell type annotation: Unsupervised clustering of nuclei was performed with the Seurat algorithm, after using highly variable genes for PCA and correcting for batch effects with the Harmony R package. Clusters were annotated to cell types based on the enrichment of expression of known marker genes.
Differential expression analysis between cases and controls was performed separately for males and females within each broad cell type and cluster, using the summed counts of every gene per subject and with the muscat and edgeR R packages.
Assembly: refdata-gex-GRCh38-2020-A, https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build
Supplementary files format and content: count matrix for filtered genes and barcodes for all samples combined. This includes, in Matrix Market format, female samples whose raw data is provided here and male samples from the previous study. The matrix row names (genes) and column names (barcodes and cell-type annotations) are also given in CSV format.
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| Submission date |
Sep 22, 2022 |
| Last update date |
Apr 24, 2023 |
| Contact name |
Gustavo Turecki |
| E-mail(s) |
gustavo.turecki@mcgill.ca
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| Organization name |
McGill University
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| Department |
Psychiatry
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| Lab |
McGill Group for Suicide Studies
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| Street address |
6875 Boulevard LaSalle
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| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H4H 1R3 |
| Country |
Canada |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE213982 |
Cell-type specific transcriptomics of the the dlPFC in females with MDD [single-nucleus RNA-seq] |
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| Relations |
| BioSample |
SAMN30965505 |
| SRA |
SRX17676970 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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