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| Status |
Public on Jul 02, 2018 |
| Title |
Single-molecule nascent RNA sequencing reveals regulatory domain architecture ant promoters and enhancers |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Other
Expression profiling by high throughput sequencing
|
| Summary |
CoPRO adapts PRO-cap for paired end sequencing, and includes a total of three different libraries that were enriched for either capped nascent RNAs only, uncapped nascent RNAs only, or both. With paired end sequencing, each read tells us where an RNA polymerase molecule initiated, and then where its active site is located. Comparison of the libraries for different capping states allows us identify the precise location of pausing, and of where nascent RNAs become capped across the tens of thousands of initiation sites that we detect. The paired nature of the data enabled identification of sites of transcription initiation with unprecedented precision: we could use the pattern of pausing and elongation as a sensitive way of calling real initiation sites, and filter out termination by comparing capped and uncapped treatments. Because CoPRO maps nascent RNA, it is not affected by the post-transcriptional stability of the initiation and pausing events detected. Thus, it puts non-coding transcription (such as eRNAs and upstream divergent RNAs) on an equal footing with longer lived RNAs like mRNA and lncRNAs. With our comprehensive maps of transcription initiation, we are able to compare the architecture of initiation sites with other features of the genome. For this purpose, we chose human K562 cells for direct comparison with dozens of publically available genome-wide datasets.
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| Overall design |
CoPRO libraries for Capped nascent transcripts only, Uncapped nascent transcripts only, or both Capped and Uncapped nascent transcripts were prepared from K562 cells, each in biological duplicate. CoPRO libraries for Capped nascent transcripts were prepared from MEF cells with and without 60 minutes of heat shock at 42 Celsius.
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| |
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| Contributor(s) |
Tome JM, Tippens ND, Lis JT |
| Citation(s) |
30349116 |
| |
| Submission date |
Jul 01, 2018 |
| Last update date |
Mar 26, 2019 |
| Contact name |
Jacob Michael Tome |
| E-mail(s) |
jacobmtome@gmail.com
|
| Organization name |
Cornell University
|
| Department |
Molecular Biology and Genetics
|
| Lab |
John Lis
|
| Street address |
416 Biotechnology Building
|
| City |
Ithaca |
| State/province |
New York |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (14)
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| Relations |
| BioProject |
PRJNA478717 |
| SRA |
SRP151707 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE116472_CoPRO_AllMerge_Cap_3p_mn.bw |
38.2 Mb |
(ftp)(http) |
BW |
| GSE116472_CoPRO_AllMerge_Cap_3p_pl.bw |
38.8 Mb |
(ftp)(http) |
BW |
| GSE116472_CoPRO_AllMerge_Cap_5p_mn.bw |
34.1 Mb |
(ftp)(http) |
BW |
| GSE116472_CoPRO_AllMerge_Cap_5p_pl.bw |
34.7 Mb |
(ftp)(http) |
BW |
| GSE116472_CoPRO_AllMerge_CappedAndUncapped_3p_mn.bw |
55.7 Mb |
(ftp)(http) |
BW |
| GSE116472_CoPRO_AllMerge_CappedAndUncapped_3p_pl.bw |
57.2 Mb |
(ftp)(http) |
BW |
| GSE116472_CoPRO_AllMerge_CappedAndUncapped_5p_mn.bw |
55.0 Mb |
(ftp)(http) |
BW |
| GSE116472_CoPRO_AllMerge_CappedAndUncapped_5p_pl.bw |
56.5 Mb |
(ftp)(http) |
BW |
| GSE116472_CoPRO_AllMerge_Pooled.Rdata.gz |
686.7 Mb |
(ftp)(http) |
RDATA |
| GSE116472_CoPRO_AllMerge_Rep1.Rdata.gz |
205.0 Mb |
(ftp)(http) |
RDATA |
| GSE116472_CoPRO_AllMerge_Rep2.Rdata.gz |
488.6 Mb |
(ftp)(http) |
RDATA |
| GSE116472_CoPRO_AllMerge_Uncapped_3p_mn.bw |
128.9 Mb |
(ftp)(http) |
BW |
| GSE116472_CoPRO_AllMerge_Uncapped_3p_pl.bw |
132.0 Mb |
(ftp)(http) |
BW |
| GSE116472_CoPRO_AllMerge_Uncapped_5p_mn.bw |
125.3 Mb |
(ftp)(http) |
BW |
| GSE116472_CoPRO_AllMerge_Uncapped_5p_pl.bw |
128.7 Mb |
(ftp)(http) |
BW |
| GSE116472_CoPRO_HScap_3p_mn.bw |
21.8 Mb |
(ftp)(http) |
BW |
| GSE116472_CoPRO_HScap_3p_pl.bw |
21.9 Mb |
(ftp)(http) |
BW |
| GSE116472_CoPRO_HScap_5p_mn.bw |
22.1 Mb |
(ftp)(http) |
BW |
| GSE116472_CoPRO_HScap_5p_pl.bw |
22.0 Mb |
(ftp)(http) |
BW |
| GSE116472_CoPRO_NHScap_3p_mn.bw |
18.4 Mb |
(ftp)(http) |
BW |
| GSE116472_CoPRO_NHScap_3p_pl.bw |
18.5 Mb |
(ftp)(http) |
BW |
| GSE116472_CoPRO_NHScap_5p_mn.bw |
18.2 Mb |
(ftp)(http) |
BW |
| GSE116472_CoPRO_NHScap_5p_pl.bw |
18.1 Mb |
(ftp)(http) |
BW |
| GSE116472_MEF_Rep1_Pooled.Rdata.gz |
125.6 Mb |
(ftp)(http) |
RDATA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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