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

• 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
• DOI: 10.1038/sdata.2017.61
• EISSN: 2052-4463

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)