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| Status |
Public on Jan 06, 2012 |
| Title |
footprints for the 12 timepoint of the ndt80 release timecourse (the first lane of this) |
| Sample type |
SRA |
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| Source name |
S. cerevisiae sporulation media
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: SK1
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| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNA fragments were size selected via gel purification, dephosphorylated, polyA tailed, and reverse transcribed. The resulting cDNA was circulizarized and PCR amplified [Ingolia et al.,n, Science, (Mar 12, 2009)]. More at Brar et al, PMID 22194413.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
Ribosome-protected mRNA
s_t12-fp_090706_l7
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| Data processing |
Alignments were performed using the first 25 nt of each read. mRNA wiggle files are generated using location assignment that is distributed along the length of the read ('coverage' mapping), while footprint wiggle files are generated using a single location assignment to a position 13 nt from the 5' end of the read ('start' mapping; corresponding to the ribosome P-site position). csv files describe annotated uORF and AUG units and include RPKM quantitation of genome-wide expression of annotated genes using the included SK1 gff file [Yassour et al., Genome Biol 11, R87 (2010)]. All the processed data files are available on Series records [processed_wig_files.tar.gz].
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| Submission date |
Dec 06, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Gloria Brar |
| E-mail(s) |
gloria.brar@ucsf.edu
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| Organization name |
UCSF
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| Street address |
1700 4th Street, BH404
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platform ID |
GPL9377 |
| Series (1) |
| GSE34082 |
High-resolution view of the yeast meiotic program revealed by ribosome profiling |
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| Relations |
| SRA |
SRX110573 |
| BioSample |
SAMN00761953 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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