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Series GSE140642 Query DataSets for GSE140642
Status Public on Jun 01, 2020
Title RNA metabolic rates profiling in Fragile X neurons
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Fragile X syndrome (FXS) is caused by inactivation of FMR1 gene and loss of its encoded product the RNA binding protein FMRP, which generally represses translation of its target transcripts in the brain. In mouse models of FXS (i.e., Fmr1 knockout animals; Fmr1 KO), deletion of Cpeb1, which encodes a translational activator, mitigates nearly all pathophysiologies associated with the disorder. We have observed that the wide-spread dys-regulation of RNA abundance in Fmr1 KO brain cortex and its rescue to normal levels in Fmr1/Cpeb1 double KO mice were the driver of the observed dys-regulation and rescue of translation as measured by whole transcriptome ribosome occupany in the brain. We hypothesize that in Fragile X brain there is wide spread dys-regulation at RNA stability level. Here we test this hypothesis by profiling RNA synthesis, processing and degradation rates in Fragile X and wild type neurons, by taking advantage of short 5-EU labeling and computational modeling. We show that, while RNA synthesis and processing rates were barely changed, there is wide-spread evelated RNA degradation rates in the Fragile X neurons, particularly for genes using optimal codons.
 
Overall design RNA metabolic labeling coupled to RNA-seq in Fmr1-KO and wild type mouse neurons
 
Contributor(s) Shu HR, Donnard E, Liu B, Richter JD
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Submission date Nov 19, 2019
Last update date Jun 01, 2020
Contact name Huan Raya Shu
E-mail(s) dr.huan.shu@gmail.com
Organization name University of Massachusetts Medical School
Department Program in Molecular Medicine
Lab Richter Lab
Street address 373 Plantation St
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (10)
GSM4176146 WT.5EU1hr
GSM4176147 WT.5EU20min
GSM4176148 WT.input.rep1
Relations
BioProject PRJNA590361
SRA SRP230603

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
GSE140642_INSPEcTrates.txt.gz 502.1 Kb (ftp)(http) TXT
GSE140642_LimmaDiff_Deg.txt.gz 347.7 Kb (ftp)(http) TXT
GSE140642_LimmaDiff_Pro.txt.gz 323.6 Kb (ftp)(http) TXT
GSE140642_LimmaDiff_Syn.txt.gz 322.9 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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