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Whole transcriptome analysis of postmortem human hippocampus dentate gyrus granlule cells

ABSTRACT: We investigated the transcriptome of dentate gyrus (DG) granule cells in postmortem hippocampus from 79 subjects with mental illness (schizophrenia, bipolar disorder, major depression) or non-psychiatric controls.

ORGANISM(S): Homo sapiens

PROVIDER: GSE42546 | GEO | 2014/04/09

SECONDARY ACCESSION(S): PRJNA182544

REPOSITORIES: GEO

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Whole transcriptome analysis of postmortem human hippocampus dentate gyrus granlule cells

Project description:We investigated the transcriptome of dentate gyrus (DG) granule cells in postmortem hippocampus from 79 subjects with mental illness (schizophrenia, bipolar disorder, major depression) or non-psychiatric controls. Material for RNA-seq analysis was harvested from tissue slides using laser capture microdissection (LCM) and aRNA amplification. Equimolar amounts of triplicate aRNA samples for each of the 79 subjects were then pooled for the preparation of sequencing libraries. Sequencing libraries were prepared using Applied Biosystem's Total RNA Sequencing Kit, following the directions for Whole Transcriptome Libraries, and analyzed with an Applied Biosystems SOLiD 4 high-throughput sequencer. We compared the performance of different normalization methods (length normalization vs. noise reductin scaling), and assembled evidence for dysruption of signaling by the micro RNA miR-182 in subjects with major depression and schizophrenia.

2014-04-09 | E-GEOD-42546 | biostudies-arrayexpress

Effect of methanol fixation on single cell RNA sequencing of the murine dentate gyrus.

Project description:We evaluated the effect of methanol (MeOH) fixation on adult murine dentate gyrus (DG) single cell suspensions.

2023-09-22 | GSE232052 | GEO

Effect of methanol fixation on single cell RNA sequencing of the murine dentate gyrus (droplet-based scRNAseq).

Project description:We evaluated the effect of methanol (MeOH) fixation on adult murine dentate gyrus (DG) single cell suspensions processed with droplet-based scRNA-seq.

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

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.

2010-10-17 | E-GEOD-24095 | biostudies-arrayexpress

Molecular profiles of cognitive aging

Project description:Gene expression was measured from the dentate gyrus and entorhinal cortex harvested from human postmortem samples. We harvested the dentate gyrus DG from healthy human brains ranging from 33 to 88 years of age. Additionally, from each brain we harvested the entorhinal cortex (EC) as a within-brain control. Using Affymetrix microarray chips we generated gene-expression profiles of each individual tissue samples. DG expression levels were first normalized against the EC, and the normalized DG transcripts were then correlated against age.

2013-04-19 | E-GEOD-46193 | biostudies-arrayexpress

The developing mouse dentate gyrus

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Transcriptome analysis of long term potentiation in rat dentate gyrus

Project description:In vivo high frequency stimulated of left dentate gyrus was performed on anaesthetised rats followed by RNA-seq to study long-term potentiation. Both left and right dentate gyrus was collected, sequenced and compared against each other for naive rats and for rats 30 min, 2 hours, and 5 hours post-HFS.

2015-10-20 | E-MTAB-3375 | biostudies-arrayexpress

Single-Cell Analysis of Aging Mouse Dentate Gyrus

Project description:The dentate gyrus of the hippocampus is a brain region involved in learning, memory formation, and spatial coding. We performed single-cell RNA-sequencing of the dentate gyrus of young and old mice to identify the age-induced changes.

2023-07-19 | GSE205936 | GEO

The developing mouse dentate gyrus

Project description:The gene expression patterns in the dentate gyrus of wild-type mice during postnatal development were examined using Affymetrix GeneChip arrays.

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