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Series GSE95854 Query DataSets for GSE95854
Status Public on Jan 12, 2018
Title TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary RNA sequencing (RNA-seq) offers a snapshot of cellular RNA populations, but not temporal information about the sequenced RNA. Here we report TimeLapse-seq, which uses oxidative-nucleophilic-aromatic substitution to convert 4-thiouridine into cytidine analogs, yielding apparent U-to-C mutations that mark new transcripts upon sequencing. TimeLapse-seq is a single-molecule approach that is adaptable to many applications and reveals RNA dynamics and induced differential expression concealed in traditional RNA-seq.
 
Overall design RNA isolated from cells +/- s4U feed was subjected to oxidative-nucleophilic-aromatic-substitution chemistry and sequenced. All sequencing was performed in duplicate per condition assessed.
 
Contributor(s) Schofield JA, Duffy EE, Kiefer L, Sullivan MC, Simon MD
Citation(s) 29355846
NIH grant(s)
Grant ID Grant title Affiliation Name
DP2 HD083992 Integrating RNAs into signaling pathways by engineering covalent RNA modification YALE UNIVERSITY Matthew David Simon
Submission date Mar 09, 2017
Last update date May 15, 2019
Contact name Matthew D Simon
E-mail(s) matthew.simon@yale.edu
Phone 2037373274
Organization name Yale University Chemical Biology Instiute
Department Molecular Biophysics & Biochemistry
Lab Simon Lab
Street address 600 West Campus Dr. MIC312
City West Haven
State/province CT
ZIP/Postal code 06516
Country USA
 
Platforms (3)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (28)
GSM2843695 JS170730
GSM2843696 JS170731
GSM2843697 JS170732
Relations
BioProject PRJNA378606
SRA SRP101621

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Supplementary file Size Download File type/resource
GSE95854_HS_MEF_1707.bedGraph.tar.gz 88.4 Mb (ftp)(http) TAR
GSE95854_K562_4h_TL.bedGraph.tar.gz 133.9 Mb (ftp)(http) TAR
GSE95854_MEF1707-MM.bedGraph.tar.gz 41.4 Mb (ftp)(http) TAR
GSE95854_MEF1707-MP.bedGraph.tar.gz 46.1 Mb (ftp)(http) TAR
GSE95854_MEF1707-PM.bedGraph.tar.gz 36.0 Mb (ftp)(http) TAR
GSE95854_MEF1707-PP.bedGraph.tar.gz 77.0 Mb (ftp)(http) TAR
GSE95854_TTtimeLapse.bedGraph.tar.gz 592.7 Mb (ftp)(http) TAR
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Raw data are available in SRA
Processed data are available on Series record

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