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Cell-type specific transcriptomics of the the dlPFC in females with MDD [single-nucleus RNA-seq]

ABSTRACT: We performed high-throughput snRNA-seq using the 10X Genomics Chromium platform on archived post-mortem dorsolateral prefrontal cortex (BA9) tissue in female MDD subjects who died by suicide and in female control subjects to identify cell-type specific differentially expressed genes. We further re-processed in parallel a previously generated snRNA-seq dataset in males with or without MDD to generate comparable differential expression results and compare the cell-type specific MDD-associated differences between the sexes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE213982 | GEO | 2023/04/24

REPOSITORIES: GEO

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Single-nucleus RNA-seq in the post-mortem brain in major depressive disorder

Project description: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.

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Project description:We examined the genetic profile of postmortem brain (hippocampal) samples; 15 brains from patients diagnosed with MDD were matched to brains from healthy subjects based on gender, race and age. Gene expression profiles in the dentate gyrus and CA1 subregions of the hippocampus were assessed by cDNA hybridization to 48K human HEEBO whole genome microarrays (Microarray, Inc). Two-group comparison: MDD (13 male, 8 female) vs. Control (11 male, 7 female). Dentate Gyrus (DG): 15 pairs of samples (1 array per pair); CA1: 15 pairs of samples (1 array per pair). Biological replicates. We can not provide a list of normalized values for each individual hybridization (per chip), but rather have a list of average expression values for all hybridizations used in the experiment (n=15). See supplementary files below. CODES: AAm, African American; C, Caucasian; CO, carbon monoxide; CVD, cardiovascular disease; ETOH, ethanol; F, female; Hx, history of alcohol abuse but not currently active; M, male; MDD, Major Depressive disorder, ND, no psychotropic medication detected; NOS, not otherwise specified, OD, drug overdose; PE, prior episode of major depression with psychotic features; PMI, postmortem interval (hours); SIGSW, self-inflicted gunshot wound; [1], Psychotrophic prescriptions within last month; [2], MDD in remission; [3], prescriptions for six days prior to death; *, samples present only in array sets for the dentate gyrus; **, samples present only in array sets for CA1.

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Cell-type specific transcriptomics of the the dlPFC in females with MDD [single-nucleus RNA-seq]

Project description:Cell-type specific transcriptomics of the the dlPFC in females with MDD [single-nucleus RNA-seq]

| PRJNA883411 | ENA

Microarray profiling of PFC, HPC and STR from subjects with schizophrenia, bipolar, MDD or control

2014-01-11 | GSE53987 | GEO

Human postmortem hippocampus: Major depressive disorder (MDD) vs. Control

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Homo sapiens

Project description:Major depression MDD suicide brain study

| PRJNA349028 | ENA

Genome Wide DNA Methylation in the Neuronal Fraction of the Prefrontal Cortex from Depressed, Suicide, and Normal Control Subjects

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