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Series GSE84767 Query DataSets for GSE84767
Status Public on Jul 26, 2016
Title Genetics of the hippocampal transcriptome in mouse: a systematic survey and online neurogenomics resource
Organism Mus musculus
Experiment type Expression profiling by array
Summary The Hippocampus Consortium data set provides estimates of mRNA expression in the adult hippocampus of 99 genetically diverse strains of mice including 67 BXD recombinant inbred strains, 13 CXB recombinant inbred strains, a diverse set of common inbred strains, and two reciprocal F1 hybrids.
The hippocampus is an important and intriguing part of the forebrain that is crucial in memory formation and retrieval, and that is often affected in epilepsy, Alzheimer's disease, and schizophrenia. Unlike most other parts of the brain, the hippocampus contains a remarkable population of stems cells that continue to generate neurons and glial cells even in adult mammals (Kempermann, 2005). This genetic analysis of transcript expression in the hippocampus (dentate gyrus, CA1-CA3) is a joint effort of 14 investigators that is supported by numerous agencies described in the acknowledgments section.
 
Overall design Pooled RNA samples (usually one pool of male hippocampii and one pool of female hippocampii) were prepared using standard protocols. Samples were processed using a total of 206 Affymetrix GeneChip Mouse Expression 430 2.0 short oligomer arrays (MOE430 2.0 or M430v2; see GEO platform ID GPL1261), of which 201 passed quality control and error checking. This particular data set was processed using the PDNN protocol. To simplify comparisons among transforms, PDNN values of each array were adjusted to an average of 8 units and a standard deviation of 2 units.
Web link http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=112
 
Contributor(s) Williams RW, Airey DC, Goldowitz D, Overall RW, Kempermann G, Peirce J, Lu L, Gage FH, Goodwin S, Smit AB, Rosen GD, Schalkwyk LC, Sutter TR, Nowakowski RS, Whatley S
Citation(s) 20582282, 30564271
Submission date Jul 25, 2016
Last update date Feb 11, 2019
Contact name Robert W. Williams
Organization name University of Tennessee
Department Department of Genetics, Genomics and Informatics
Street address 71 Manassas St.
City Memphis
State/province TN
ZIP/Postal code 38163
Country USA
 
Platforms (1)
GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
Samples (201)
GSM2249886 B6D2F1 Female H2 26-Sep-05
GSM2249887 B6D2F1 Male H3 9-Jun-05
GSM2249888 B6D2F1 Male H4 26-Sep-05
Relations
BioProject PRJNA331104

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
GSE84767_GN110_Hippo_Individual_Samples_M430v2_RMA_ZScore_MetaData.txt.gz 17.9 Mb (ftp)(http) TXT
GSE84767_GN111_Hippo_Individual_Samples_M430v2_Mas5_ZScore_MetaData.txt.gz 18.9 Mb (ftp)(http) TXT
GSE84767_GN112_Hippo_Individual_Samples_M430v2_PDNN_ZScore_MetaData.txt.gz 16.7 Mb (ftp)(http) TXT
GSE84767_RAW.tar 1.2 Gb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table
Processed data is available on Series record

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