Transcriptional profile of hippocampal dentate granule cells in four rat epilepsy models

Global expression profiling of neurologic or psychiatric disorders has been confounded by variability among laboratories, animal models, tissues sampled, and experimental platforms, with the result being that few genes demonstrate consistent expression changes. We attempted to minimize these confoun...

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Bibliographic Details
Published in:	Scientific data Vol. 4; no. 1; p. 170061
Main Authors:	Dingledine, Raymond, Coulter, Douglas A., Fritsch, Brita, Gorter, Jan A., Lelutiu, Nadia, McNamara, James, Nadler, J. Victor, Pitkänen, Asla, Rogawski, Michael A., Skene, Pate, Sloviter, Robert S., Wang, Yu, Wadman, Wytse J., Wasterlain, Claude, Roopra, Avtar
Format:	Journal Article
Language:	English
Published:	London Nature Publishing Group UK 09-05-2017 Nature Publishing Group
Subjects:	631/337/2019 692/617/375/178 Animals Data Descriptor Disease Models, Animal Epilepsy - genetics Hippocampus Humanities and Social Sciences multidisciplinary Rats Science Species Specificity Status Epilepticus - genetics Transcriptome
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Summary:	Global expression profiling of neurologic or psychiatric disorders has been confounded by variability among laboratories, animal models, tissues sampled, and experimental platforms, with the result being that few genes demonstrate consistent expression changes. We attempted to minimize these confounds by pooling dentate granule cell transcriptional profiles from 164 rats in seven laboratories, using three status epilepticus (SE) epilepsy models (pilocarpine, kainate, self-sustained SE), plus amygdala kindling. In each epilepsy model, RNA was harvested from laser-captured dentate granule cells from six rats at four time points early in the process of developing epilepsy, and data were collected from two independent laboratories in each rodent model except SSSE. Hierarchical clustering of differentially-expressed transcripts in the three SE models revealed complete separation between controls and SE rats isolated 1 day after SE. However, concordance of gene expression changes in the SE models was only 26–38% between laboratories, and 4.5% among models, validating the consortium approach. Transcripts with unusually highly variable control expression across laboratories provide a ‘red herring’ list for low-powered studies. Design Type(s) transcription profiling by array design • intervention design • disease state design • parallel group design Measurement Type(s) transcription profiling assay Technology Type(s) microarray platform Factor Type(s) treatment portion of study execution • sampling time measurement datum Sample Characteristic(s) Rattus norvegicus • dentate granule cell Machine-accessible metadata file describing the reported data (ISA-Tab format)
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 ObjectType-Undefined-3 R.D. designed and coordinated the project, contributed tissue, analyzed the data and wrote the manuscript. D.C. contributed tissue and revised the manuscript. B.F. contributed tissue. J.G. contributed tissue and revised the manuscript. N.L. performed LCM and wrote the manuscript. J.M. contributed tissue and revised the manuscript. J.V.N. contributed tissue and revised the manuscript. A.P. contributed tissue and revised the manuscript. M.R. contributed tissue and revised the manuscript. P.S. performed LCM and revised the manuscript. R.S.S. performed histology and revised the manuscript. Y.W. performed LCM. W.W. contributed tissue and revised the manuscript. C.W. contributed tissue and revised the manuscript. A.R. analyzed data and wrote the manuscript.
ISSN:	2052-4463 2052-4463
DOI:	10.1038/sdata.2017.61