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E-GEOD-84767 - Genetics of the hippocampal transcriptome in mouse: a systematic survey and online neurogenomics resource

Status
Released on 26 July 2016, last updated on 30 July 2016
Organism
Mus musculus
Samples (201)
Array (1)
Protocols (7)
Description
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. 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.
Experiment type
transcription profiling by array 
Contacts
Robert W. Williams <geo@ncbi.nlm.nih.gov>, August B Smit, Dan Goldowitz, David C Airey, Fred H Gage, Gerd Kempermann, Glenn D Rosen, Jeremy Peirce, Leonard C Schalkwyk, Lu Lu, Richard S Nowakowski, Robert W Williams, Rupert W Overall, Shirlean Goodwin, Stephen Whatley, Thomas R Sutter
Citation
Genetics of the hippocampal transcriptome in mouse: a systematic survey and online neurogenomics resource. Overall RW, Kempermann G, Peirce J, Lu L, Goldowitz D, Gage FH, Goodwin S, Smit AB, Airey DC, Rosen GD, Schalkwyk LC, Sutter TR, Nowakowski RS, Whatley S, Williams RW. , PMID:20582282
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