|
| Status |
Public on Dec 16, 2014 |
| Title |
A high resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies |
| Organisms |
Danio rerio; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
To monitor the relative regulatory contributions of RNA production, processing and degradation, we sampled RNA from mouse DCs every 15 minutes, for the first 3 hours of their response to LPS (13 samples in total), following a short (10 minute) metabolic labeling pulse with 4sU preceding the sampled time point. We isolated RNA from each of these samples in two ways. First, to comprehensively measure total RNA regardless of its transcription time, we isolated RNA depleted of rRNA. Second, to measure only newly made RNA, we isolated 4sU-labeled RNA, which could only have been transcribed during the 10 minute labeling pulse and is thus enriched for short-lived transcripts, including mRNA precursors and processing intermediates. We deeply sequenced each isolated RNA population to provide the necessary depth to study exons, introns, and splicing junctions across the transcriptome. We showed our approach general utility by also applying it to lincRNAs and early zebrafish development data
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| |
|
| Overall design |
Time-course mRNA profiles of mouse DCs that were stimulated with LPS, and labeled with a short (10 minute) 4sU pulse (0-3 hours, 15 min. intervals, 13 time points).
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| |
|
| Contributor(s) |
Rabani M, Regev A, Pauli A, Schier AF |
| Citation(s) |
25497548 |
| Submission date |
Apr 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Michal Rabani |
| E-mail(s) |
michal.rabani@mail.huji.ac.il
|
| Phone |
026585705
|
| Organization name |
Hebrew University of Jerusalem
|
| Street address |
Hebrew University, Edmond J. Safra Campus, Silberman building
|
| City |
Jerusalem |
| ZIP/Postal code |
9190401 |
| Country |
Israel |
| |
|
| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
|
| Samples (27)
|
|
| Relations |
| BioProject |
PRJNA245102 |
| SRA |
SRP041343 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE56977_RAW.tar |
180.0 Kb |
(http)(custom) |
TAR (of TXT) |
| GSE56977_expression.4sU.M.txt.gz |
460.0 Kb |
(ftp)(http) |
TXT |
| GSE56977_expression.4sU.P.txt.gz |
418.7 Kb |
(ftp)(http) |
TXT |
| GSE56977_expression.total.M.txt.gz |
482.1 Kb |
(ftp)(http) |
TXT |
| GSE56977_expression.total.P.txt.gz |
406.8 Kb |
(ftp)(http) |
TXT |
| GSE56977_expression_gene.4sU.M.txt.gz |
336.6 Kb |
(ftp)(http) |
TXT |
| GSE56977_expression_gene.4sU.P.txt.gz |
335.6 Kb |
(ftp)(http) |
TXT |
| GSE56977_expression_gene.total.M.txt.gz |
352.5 Kb |
(ftp)(http) |
TXT |
| GSE56977_expression_gene.total.P.txt.gz |
333.8 Kb |
(ftp)(http) |
TXT |
| GSE56977_rates.dg.txt.gz |
81.8 Kb |
(ftp)(http) |
TXT |
| GSE56977_rates.px.txt.gz |
72.1 Kb |
(ftp)(http) |
TXT |
| GSE56977_rates.tx.txt.gz |
239.6 Kb |
(ftp)(http) |
TXT |
| GSE56977_rates_gene.dg.txt.gz |
67.0 Kb |
(ftp)(http) |
TXT |
| GSE56977_rates_gene.px.txt.gz |
48.4 Kb |
(ftp)(http) |
TXT |
| GSE56977_rates_gene.tx.txt.gz |
180.7 Kb |
(ftp)(http) |
TXT |
| GSE56977_read_counts.4sU.txt.gz |
11.7 Mb |
(ftp)(http) |
TXT |
| GSE56977_read_counts.total.txt.gz |
11.4 Mb |
(ftp)(http) |
TXT |
| GSE56977_readme.txt |
1.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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