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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
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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.
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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.
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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 |
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Submission date |
Mar 09, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Matthew D Simon |
E-mail(s) |
matthew.simon@yale.edu
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Phone |
2037373274
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Organization name |
Yale University Chemical Biology Instiute
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Department |
Molecular Biophysics & Biochemistry
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Lab |
Simon Lab
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Street address |
600 West Campus Dr. MIC312
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City |
West Haven |
State/province |
CT |
ZIP/Postal code |
06516 |
Country |
USA |
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Platforms (3) |
GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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Samples (28)
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Relations |
BioProject |
PRJNA378606 |
SRA |
SRP101621 |