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Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq

Robert A. Policastro, View ORCID ProfileR. Taylor Raborn, Volker P. Brendel, View ORCID ProfileGabriel E. Zentner
doi: https://doi.org/10.1101/2020.01.16.905182
Robert A. Policastro
1Department of Biology, Indiana University, Bloomington, IN 47405, USA
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R. Taylor Raborn
1Department of Biology, Indiana University, Bloomington, IN 47405, USA
4The Biodesign Institute Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
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  • ORCID record for R. Taylor Raborn
Volker P. Brendel
1Department of Biology, Indiana University, Bloomington, IN 47405, USA
2Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
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Gabriel E. Zentner
1Department of Biology, Indiana University, Bloomington, IN 47405, USA
3Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA
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  • ORCID record for Gabriel E. Zentner
  • For correspondence: gzentner@indiana.edu
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Abstract

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 about five 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 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.

Footnotes

  • https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142524

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 16, 2020.
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Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq
Robert A. Policastro, R. Taylor Raborn, Volker P. Brendel, Gabriel E. Zentner
bioRxiv 2020.01.16.905182; doi: https://doi.org/10.1101/2020.01.16.905182
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Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq
Robert A. Policastro, R. Taylor Raborn, Volker P. Brendel, Gabriel E. Zentner
bioRxiv 2020.01.16.905182; doi: https://doi.org/10.1101/2020.01.16.905182

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