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

Raymond Dingledine, Douglas A. Coulter, Brita Fritsch, Jan A. Gorter, Nadia Lelutiu, James McNamara, J. Victor Nadler, Asla Pitkänen, Michael A Rogawski, Pate Skene, Robert S. Sloviter, Yu Wang, Wytse J. Wadman, Claude Wasterlain, Avtar Roopra

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Article number170061
JournalScientific data
Volume4
DOIs
StatePublished - May 9 2017

Fingerprint

Epilepsy
epilepsy
Descriptors
Rats
Cell
Model
Animal Model
Pooling
Concordance
Hierarchical Clustering
Profiling
Gene Expression
Profile
Rat
Disorder
RNA
Gene expression
Animals
Laser
Gene

ASJC Scopus subject areas

  • Education
  • Library and Information Sciences
  • Computer Science Applications
  • Information Systems
  • Statistics, Probability and Uncertainty
  • Statistics and Probability

Cite this

Dingledine, R., Coulter, D. A., Fritsch, B., Gorter, J. A., Lelutiu, N., McNamara, J., ... Roopra, A. (2017). Data Descriptor: Transcriptional profile of hippocampal dentate granule cells in four rat epilepsy models. Scientific data, 4, [170061]. https://doi.org/10.1038/sdata.2017.61

Data Descriptor : Transcriptional profile of hippocampal dentate granule cells in four rat epilepsy models. / 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.

In: Scientific data, Vol. 4, 170061, 09.05.2017.

Research output: Contribution to journalArticle

Dingledine, R, Coulter, DA, Fritsch, B, Gorter, JA, Lelutiu, N, McNamara, J, Nadler, JV, Pitkänen, A, Rogawski, MA, Skene, P, Sloviter, RS, Wang, Y, Wadman, WJ, Wasterlain, C & Roopra, A 2017, 'Data Descriptor: Transcriptional profile of hippocampal dentate granule cells in four rat epilepsy models', Scientific data, vol. 4, 170061. https://doi.org/10.1038/sdata.2017.61
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. / Data Descriptor : Transcriptional profile of hippocampal dentate granule cells in four rat epilepsy models. In: Scientific data. 2017 ; Vol. 4.
@article{cea91fadfcba4786b7be6069fa2e20af,
title = "Data Descriptor: Transcriptional profile of hippocampal dentate granule cells in four rat epilepsy models",
abstract = "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.",
author = "Raymond Dingledine and Coulter, {Douglas A.} and Brita Fritsch and Gorter, {Jan A.} and Nadia Lelutiu and James McNamara and Nadler, {J. Victor} and Asla Pitk{\"a}nen and Rogawski, {Michael A} and Pate Skene and Sloviter, {Robert S.} and Yu Wang and Wadman, {Wytse J.} and Claude Wasterlain and Avtar Roopra",
year = "2017",
month = "5",
day = "9",
doi = "10.1038/sdata.2017.61",
language = "English (US)",
volume = "4",
journal = "Scientific data",
issn = "2052-4463",
publisher = "Nature Publishing Group",

}

TY - JOUR

T1 - Data Descriptor

T2 - Transcriptional profile of hippocampal dentate granule cells in four rat epilepsy models

AU - Dingledine, Raymond

AU - Coulter, Douglas A.

AU - Fritsch, Brita

AU - Gorter, Jan A.

AU - Lelutiu, Nadia

AU - McNamara, James

AU - Nadler, J. Victor

AU - Pitkänen, Asla

AU - Rogawski, Michael A

AU - Skene, Pate

AU - Sloviter, Robert S.

AU - Wang, Yu

AU - Wadman, Wytse J.

AU - Wasterlain, Claude

AU - Roopra, Avtar

PY - 2017/5/9

Y1 - 2017/5/9

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85019156244&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85019156244&partnerID=8YFLogxK

U2 - 10.1038/sdata.2017.61

DO - 10.1038/sdata.2017.61

M3 - Article

C2 - 28485718

AN - SCOPUS:85019156244

VL - 4

JO - Scientific data

JF - Scientific data

SN - 2052-4463

M1 - 170061

ER -