|
| Status |
Public on Dec 19, 2013 |
| Title |
Cerevisiae_3Pseq |
| Sample type |
SRA |
| |
|
| Source name |
saccharomyces cerevisiae cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: W303
|
| Treatment protocol |
3P-Seq library was prepared from 75 μg of isolated RNA as described previously (Jan et al., 2011).
|
| Growth protocol |
Yeast were grown in YPD to mid-log phase in accordance with standard protocols.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
3P-Seq library was prepared from 75 μg of isolated RNA as described previously (Jan et al., 2011).
Libraries were constructed exactly as described in Jan et al., 2011 (GSE24924). 3P-Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
3P-Seq:
Data was processed exactly as described in Jan et al., 2011 (GSE24924)
Reads were reverse complemented and aligned to the Saccharomyces cerevisiae genome (sacCer3) using Bowtie. Reads that aligned best to one genomic locus and had one or more mismatches at their 3' end within a terminal adenylate-run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file.
Genome_build: sacCer3
Supplementary_files_format_and_content: Processed data is BED file containing 3P-seq clusters
|
| |
|
| Submission date |
Dec 13, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
David E Weinberg |
| E-mail(s) |
david.weinberg@ucsf.edu
|
| Phone |
4155149723
|
| Organization name |
University of California, San Francisco
|
| Lab |
Weinberg
|
| Street address |
600 16th Street, GH S572F
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL9377 |
| Series (2) |
| GSE53268 |
Translation rates and 3' ends of *S. cerevisiae* genes |
| GSE53310 |
3P-seq analysis of S. cerevisiae |
|
| Relations |
| BioSample |
SAMN02443933 |
| SRA |
SRX391768 |
