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Series GSE98289 Query DataSets for GSE98289
Status Public on Mar 08, 2018
Title Post-transcriptional remodelling is temporally deregulated during motor neurogenesis in human ALS models
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Mutations causing amyotrophic lateral sclerosis (ALS) strongly implicate regulators of RNA-processing that are ubiquitously expressed throughout development. To understand the molecular impact of ALS-causing mutations on early neuronal development and disease, we performed transcriptomic analysis of differentiated human control and VCP-mutant induced pluripotent stem cells (iPSCs) during motor neurogenesis. We identify intron retention (IR) as the predominant splicing change affecting early stages of wild-type neural differentiation, targeting key genes involved in the splicing machinery. Importantly, IR occurs prematurely in VCP-mutant cultures compared with control counterparts; these events are also observed in independent RNAseq datasets from SOD1- and FUS-mutant motor neurons (MNs). Together with related effects on 3’UTR length variation, these findings implicate alternative RNA-processing in regulating distinct stages of lineage restriction from iPSCs to MNs, and reveal a temporal deregulation of such processing by ALS mutations. Thus, ALS-causing mutations perturb the same post-transcriptional mechanisms that underlie human motor neurogenesis.
 
Overall design Bulk RNA-seq at different timepoints throughout a 35-day differentiation protocol that converted iPSC cells to highly enriched motor neurons.
 
Contributor(s) Luisier R, Tyzack GE, Hall CE, Ule J, Luscombe NM, Patani R
Citation(s) 28564594, 29789581
Submission date Apr 27, 2017
Last update date Jul 25, 2021
Contact name Raphaelle Luisier
E-mail(s) raphaelle.luisier@gmail.com
Phone 0041762432198
Organization name Idiap Research Institute
Lab Genomics and Health Informatics
Street address Rue Marconi 19, PO Box 592
City Martigny
State/province Valais
ZIP/Postal code 1920
Country Switzerland
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (11)
GSM2590537 Sample 4 [MUT 1 d7]
GSM2590538 Sample 5 [MUT 2 d7]
GSM2590539 Sample 6 [MUT 3 d7]
This SubSeries is part of SuperSeries:
GSE98290 Post-transcriptional remodelling is temporally deregulated during motor neurogenesis in human ALS models
Relations
BioProject PRJNA384598
SRA SRP105348

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
GSE98289_RAW.tar 22.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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