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Series GSE132660 Query DataSets for GSE132660
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
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.
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.
Web link
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
Organization name New England Biolabs
Street address County Road
City Ipswich
State/province MA
ZIP/Postal code 01938
Country USA
Platforms (4)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (30)
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
BioProject PRJNA548673
SRA SRP201308

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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
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