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Series GSE144136 Query DataSets for GSE144136
Status Public on Feb 25, 2020
Title Single-nucleus RNA-seq in the post-mortem brain in major depressive disorder
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary We performed high-throughput snRNA-seq using the 10X Genomics Chromium platform on archived post-mortem dorsolateral prefrontal cortex (BA9) tissue in MDD subjects who died by suicide and in control subjects to identify cell-type specific differentially expressed genes.
Overall design 10X Genomics Chromium snRNA-seq was performed on nuclei extracted from BA9 of the post-mortem brain tissue of 17 control subjects and 17 MDD cases who died by suicide. All subjects were male. Cell-types were identified by unsupervised clustering and diffrential gene expression was performed between cases and controls for each cell-type cluster. The library preparation was performed with the Chromium Singel Cell 3’ Reagent Kits v2. Paired-end sequencing was performed on the HiSeq Illumina 4000. FastQ files were produced with Cellranger v2.1.0 mkfastq. Alignments and gene counts were generated with Cellranger v2.1.0 count.
Contributor(s) Turecki G
Citation(s) 32341540, 33602921
Submission date Jan 23, 2020
Last update date Mar 10, 2021
Contact name Gustavo Turecki
Organization name McGill University
Department Psychiatry
Lab McGill Group for Suicide Studies
Street address 6875 Boulevard LaSalle
City Montreal
State/province Quebec
ZIP/Postal code H4H 1R3
Country Canada
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (34)
GSM4281974 1: Post-mortem dosolateral prefrontal cortex
GSM4281975 2: Post-mortem dosolateral prefrontal cortex
GSM4281976 3: Post-mortem dosolateral prefrontal cortex
BioProject PRJNA602867
SRA SRP244344

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE144136_Astros_3_filtered_cells.csv.gz 6.0 Kb (ftp)(http) CSV
GSE144136_CellNames.csv.gz 671.3 Kb (ftp)(http) CSV
GSE144136_Ex_10_L2_4_filtered_cells.csv.gz 132.2 Kb (ftp)(http) CSV
GSE144136_Ex_1_L5_6_filtered_cells.csv.gz 6.2 Kb (ftp)(http) CSV
GSE144136_Ex_3_L4_5_filtered_cells.csv.gz 46.4 Kb (ftp)(http) CSV
GSE144136_Ex_4_L_6_filtered_cells.csv.gz 5.0 Kb (ftp)(http) CSV
GSE144136_Ex_5_L5_filtered_cells.csv.gz 22.8 Kb (ftp)(http) CSV
GSE144136_Ex_6_L4_6_filtered_cells.csv.gz 20.7 Kb (ftp)(http) CSV
GSE144136_Ex_7_L4_6_filtered_cells.csv.gz 30.3 Kb (ftp)(http) CSV
GSE144136_Ex_8_L5_6_filtered_cells.csv.gz 15.3 Kb (ftp)(http) CSV
GSE144136_Ex_9_L5_6_filtered_cells.csv.gz 2.0 Kb (ftp)(http) CSV
GSE144136_GRCh38-1.2.0_premrna.tar.gz 10.0 Gb (ftp)(http) TAR
GSE144136_GeneBarcodeMatrix_Annotated.mtx.gz 413.4 Mb (ftp)(http) MTX
GSE144136_GeneNames.csv.gz 185.3 Kb (ftp)(http) CSV
GSE144136_Inhib_1_filtered_cells.csv.gz 16.5 Kb (ftp)(http) CSV
GSE144136_Inhib_2_VIP_filtered_cells.csv.gz 26.5 Kb (ftp)(http) CSV
GSE144136_Inhib_3_SST_filtered_cells.csv.gz 6.5 Kb (ftp)(http) CSV
GSE144136_Inhib_5_filtered_cells.csv.gz 27.1 Kb (ftp)(http) CSV
GSE144136_Inhib_6_SST_filtered_cells.csv.gz 19.3 Kb (ftp)(http) CSV
GSE144136_Inhib_7_PVALB_filtered_cells.csv.gz 4.9 Kb (ftp)(http) CSV
GSE144136_Inhib_8_PVALB_filtered_cells.csv.gz 6.1 Kb (ftp)(http) CSV
GSE144136_Micro_Macro_filtered_cells.csv.gz 8.5 Kb (ftp)(http) CSV
GSE144136_OPCs_1_filtered_cells.csv.gz 15.3 Kb (ftp)(http) CSV
GSE144136_OPCs_2_filtered_cells.csv.gz 4.6 Kb (ftp)(http) CSV
GSE144136_Oligos_1_filtered_cells.csv.gz 2.4 Kb (ftp)(http) CSV
GSE144136_Oligos_3_filtered_cells.csv.gz 31.9 Kb (ftp)(http) CSV
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