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| Status |
Public on Nov 30, 2018 |
| Title |
EnD-Seq and AppEnD: Sequencing 3' ends to identify non-templated tails and degradation intermediates |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Existing methods for detecting RNA intermediates resulting from exonuclease degradation are low-throughput and laborious. In addition, mapping the 3’ ends of RNA molecules to the genome after high-throughput sequencing is challenging, particularly if the 3’ ends contain posttranscriptional modifications. To address these problems, we developed EnD-Seq, a high-throughput sequencing protocol that preserves the 3’ end of RNA molecules, and AppEnD, a computational method for analyzing high-throughput sequencing data. Together these allow determination of the 3’ ends of RNA molecules, including nontemplated additions. Applying EnD-Seq and AppEnD to histone mRNAs revealed that a significant fraction of cytoplasmic histone mRNAs end in one or two uridines, which have replaced the 1-2 nts at the 3’ end of mature histone mRNA maintaining the length of the histone transcripts.
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| Overall design |
Libraries were prepared essentially as described in Welch, Slevin et al. (RNA. 2015 Jul; 21(7): 1375–1389.)
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| Contributor(s) |
Marzluff WF, Holmquist CE |
| Citation(s) |
30397106 |
| Submission date |
Oct 18, 2018 |
| Last update date |
Jan 25, 2019 |
| Contact name |
Christopher Holmquist |
| Organization name |
UNC Chapel Hill
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| Lab |
Marzluff
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| Street address |
208 Fordham Hall
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
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| Platforms (1) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA497386 |
| SRA |
SRP166082 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE121461_RAW.tar |
64.8 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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