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| Status |
Public on Mar 24, 2016 |
| Title |
Targeted paired-end sequencing of nascent RNA from S. cerevisiae |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
Targeted paired-end sequencing of cDNA from unfragmented nascent RNA from exponentially growing S. cerevisiae cells was employed to obtain Pol II transcription elongation and splicing information from single transcripts.
Nascent RNA was prepared from the yeast chromatin fraction (Carrillo Oesterreich, Preibisch, Neugebauer, Mol Cell 2010) or enriched from total RNA with polyadenylated RNA depletion. The nascent 3’ end was labeled with a 3’ DNA adaptor through ligation.
A PCR with a forward primer in the first exon of select intron-containing genes amplifies nascent transcripts of specific genes and ensures sequencing adaptor attachment for paired-end sequencing.
With this approach co-transcriptional splicing progression with distance from the intron end could be analyzed for 87 genes. Note that the unmapped and mapped data also include genes that did not pass the read coverage requirements in SMIT analysis.
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| Overall design |
Nascent RNA profiles for mainly intron-containing genes were generated with paired-end sequencing with Illumina HiSeq technology.
|
| Web link |
http://www.sciencedirect.com/science/article/pii/S0092867416301957
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| |
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| Contributor(s) |
Herzel L, Carrillo Oesterreich F, Straube K, Neugebauer KM |
| Citation(s) |
27020755 |
| |
| Submission date |
Jul 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Lydia Herzel |
| E-mail(s) |
[email protected]
|
| Organization name |
Freie Universität
|
| Department |
Biology, Chemistry and Pharmacy
|
| Lab |
Herzel
|
| Street address |
Takustr. 6
|
| City |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
| |
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| Platforms (2) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
| GPL17342 |
Illumina HiSeq 2500 (Saccharomyces cerevisiae) |
|
| Samples (34)
|
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| This SubSeries is part of SuperSeries: |
| GSE70908 |
Splicing of nascent RNA coincides with intron exit from RNA polymerase II |
|
| Relations |
| BioProject |
PRJNA289902 |
| SRA |
SRP061165 |
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