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Series GSE142524 Query DataSets for GSE142524
Status Public on Jan 13, 2020
Title Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq
Organisms Saccharomyces cerevisiae; Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Accurate mapping of transcription start sites (TSSs) is key for understanding transcriptional regulation. However, current protocols for genome-wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5’-ends from as little as 50 ng total RNA. Including depletion of uncapped RNA and SPRI bead cleanups, a STRIPE-seq library can be constructed in approximately four hours. We demonstrate application of STRIPE-seq to TSS profiling in yeast and human cells and show that it can also be effectively used for measuring transcript levels and for differential gene expression analysis. In conjunction with our ready-to-use computational analysis workflows, STRIPE-seq is a straightforward, efficient means by which to probe the landscape of transcriptional initiation.
Overall design STRIPE-seq and RNA-seq in two organisms.
Contributor(s) Policastro RA, Zentner GE
Citation(s) 32660958
NIH grant(s)
Grant ID Grant title Affiliation Name
R35 GM128631 Regulation of transcription by the Mediator complex INDIANA UNIVERSITY GABRIEL ZENTNER
Submission date Dec 23, 2019
Last update date Jul 23, 2020
Contact name Gabriel E Zentner
Phone 812-856-7377
Organization name Indiana University
Department Biology
Street address 915 E 3rd St
City Bloomington
State/province IN
ZIP/Postal code 47405
Country USA
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19756 Illumina NextSeq 500 (Saccharomyces cerevisiae)
Samples (24)
GSM4231283 RNAseq_S288C_10ug_untreated_1
GSM4231284 RNAseq_S288C_10ug_untreated_2
GSM4231285 RNAseq_S288C_10ug_untreated_3
BioProject PRJNA597322
SRA SRP238585

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Supplementary file Size Download File type/resource
GSE142524_RAW.tar 1.9 Gb (http)(custom) TAR (of BED, BEDGRAPH, BIGWIG)
GSE142524_stripe-seq-library-construction-2ivgce6.pdf 206.4 Kb (ftp)(http) PDF
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Raw data are available in SRA
Processed data provided as supplementary file

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