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Series GSE42546 Query DataSets for GSE42546
Status Public on Apr 09, 2014
Title Whole transcriptome analysis of postmortem human hippocampus dentate gyrus granlule cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary 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.
Overall design 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.
Contributor(s) Kohen R, Dobra A, Tracy JH, Haugen E
Citation(s) 24594777
Submission date Nov 27, 2012
Last update date May 15, 2019
Contact name Ruth Kohen
Organization name University of Washington
Department Psychiatry and Behavioral Sciences
Street address 1959 Pacific Ave NE
City Seattle
State/province WA
ZIP/Postal code 98195-6560
Country USA
Platforms (1)
GPL13393 AB SOLiD 4 System (Homo sapiens)
Samples (79)
GSM1044803 B1
GSM1044804 B2
GSM1044805 B3
SRA SRP017329
BioProject PRJNA182544

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Supplementary file Size Download File type/resource
GSE42546_CleanedRawCounts.txt.gz 692.9 Kb (ftp)(http) TXT
GSE42546_LengthNormalizedScaledCounts.txt.gz 1.3 Mb (ftp)(http) TXT
GSE42546_NoiseReductionScaledCounts.txt.gz 1.2 Mb (ftp)(http) TXT
GSE42546_RawCounts.txt.gz 4.8 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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