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| Status |
Public on Jun 14, 2019 |
| Title |
Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We develop a method Re-Cappable-seq for determining eukaryotic transcription start sites derived from all RNA polymerases at nucleotide resolution. In particular, this method identifies the Pol-I and Pol-III TSSs, which are missing by CAGE.
Applied to human A549 cell line, our method results in the identification of 33,468 and 5,269 high confidence Pol-II and non-Pol-II TSS respectively. Re-Cappable-seq identifies Pol-II TSS with higher specificity than CAGE.
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| Overall design |
We isolated total RNA from human A549 cancer cell line. First we used yDcpS to decap the canonical G-cap structure from Pol-II transcripts leaving a di-phosphorylated 5'end. Then we used VCE to specifically add a biotin cap to these di-phosphorylated 5'ends as well as the tri-phosphorylated 5'ends from the non-Pol-II transcripts. Finally we isolated these biotin capped RNA using streptavidin beads and sequenced using illumina. Here the RNA without streptavidin enrichment served as control. In addition, we also performed CIP treatment before decapping, which was used to distinguish the Pol-II and non-Pol-II transcripts.
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| Web link |
https://genome.cshlp.org/content/32/1/162.long
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| Contributor(s) |
Yan B, Tzertzinis G, Schildkraut I, Ettwiller L |
| Citation(s) |
34815308 |
| Submission date |
Jun 13, 2019 |
| Last update date |
Mar 09, 2022 |
| Contact name |
Bo Yan |
| E-mail(s) |
elitaonerezo@gmail.com
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| Organization name |
New England Biolabs
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| Street address |
County Road
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| City |
Ipswich |
| State/province |
MA |
| ZIP/Postal code |
01938 |
| Country |
USA |
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| Platforms (4)
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| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (30)
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| GSM3885082 |
A549, CIP treatment, Re-Cappable-seq enrich library, replicate 1 |
| GSM3885083 |
A549, CIP treatment, Re-Cappable-seq enrich library, replicate 2 |
| GSM3885084 |
A549, CIP treatment, Re-Cappable-seq control library, replicate 1 |
| GSM3885085 |
A549, CIP treatment, Re-Cappable-seq control library, replicate 2 |
| GSM3885086 |
A549, Re-Cappable-seq enrich library, replicate 1 |
| GSM3885087 |
A549, Re-Cappable-seq enrich library, replicate 2 |
| GSM3885088 |
A549, Re-Cappable-seq control library, replicate 1 |
| GSM3885089 |
A549, Re-Cappable-seq control library, replicate 2 |
| GSM3885090 |
A549, CAGE library, replicate 1 |
| GSM3885091 |
A549, CAGE library, replicate 2 |
| GSM4467058 |
Brain, Re-Cappable-seq enrich library, replicate 1 |
| GSM4467059 |
Brain, Re-Cappable-seq enrich library, replicate 2 |
| GSM4467060 |
A549 rRNA depletion RNA-seq |
| GSM4467061 |
A549 total RNA-seq |
| GSM5652058 |
Jurkat, Re-Cappable-seq enrich library, replicate 1 |
| GSM5652059 |
Jurkat, Re-Cappable-seq enrich library, replicate 2 |
| GSM5652060 |
Jurkat, Re-Cappable-seq control library, replicate 1 |
| GSM5652061 |
Jurkat, Re-Cappable-seq control library, replicate 2 |
| GSM5652062 |
Jurkat, CIP treatment, Re-Cappable-seq enrich library, replicate 1 |
| GSM5652063 |
Jurkat, CIP treatment, Re-Cappable-seq enrich library, replicate 2 |
| GSM5652064 |
Jurkat, CIP treatment, Re-Cappable-seq control library, replicate 1 |
| GSM5652065 |
Jurkat, CIP treatment, Re-Cappable-seq control library, replicate 2 |
| GSM5652066 |
K562, Re-Cappable-seq enrich library, replicate 1 |
| GSM5652067 |
K562, Re-Cappable-seq enrich library, replicate 2 |
| GSM5652068 |
K562, Re-Cappable-seq control library, replicate 1 |
| GSM5652069 |
K562, Re-Cappable-seq control library, replicate 2 |
| GSM5652070 |
K562, CIP treatment, Re-Cappable-seq enrich library, replicate 1 |
| GSM5652071 |
K562, CIP treatment, Re-Cappable-seq enrich library, replicate 2 |
| GSM5652072 |
K562, CIP treatment, Re-Cappable-seq control library, replicate 1 |
| GSM5652073 |
K562, CIP treatment, Re-Cappable-seq control library, replicate 2 |
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| Relations |
| BioProject |
PRJNA548673 |
| SRA |
SRP201308 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE132660_CAGE_TSS.gtf.gz |
24.0 Mb |
(ftp)(http) |
GTF |
| GSE132660_CIP_ReCappable_TSS.gtf.gz |
9.0 Mb |
(ftp)(http) |
GTF |
| GSE132660_J_CIP_En.tsscount.gtf.gz |
1.1 Mb |
(ftp)(http) |
GTF |
| GSE132660_J_Con.tsscount.gtf.gz |
2.1 Mb |
(ftp)(http) |
GTF |
| GSE132660_J_En_rep1.tsscount.gtf.gz |
1.4 Mb |
(ftp)(http) |
GTF |
| GSE132660_J_En_rep2.tsscount.gtf.gz |
1.4 Mb |
(ftp)(http) |
GTF |
| GSE132660_K_CIP_En.tsscount.gtf.gz |
1.2 Mb |
(ftp)(http) |
GTF |
| GSE132660_K_Con.tsscount.gtf.gz |
2.3 Mb |
(ftp)(http) |
GTF |
| GSE132660_K_En_rep1.tsscount.gtf.gz |
1.1 Mb |
(ftp)(http) |
GTF |
| GSE132660_K_En_rep2.tsscount.gtf.gz |
1.1 Mb |
(ftp)(http) |
GTF |
| GSE132660_ReCappable_TSS.gtf.gz |
8.3 Mb |
(ftp)(http) |
GTF |
| GSE132660_ReCappable_control_TSS.gtf.gz |
7.0 Mb |
(ftp)(http) |
GTF |
| GSE132660_SupplementaryData1.txt.gz |
733.1 Kb |
(ftp)(http) |
TXT |
| GSE132660_SupplementaryData2.gtf.gz |
341.2 Kb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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