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Sample GSM843762 Query DataSets for GSM843762
Status Public on Jan 06, 2012
Title footprints for the 3 timepoint of the ndt80 release timecourse
Sample type SRA
Source name S. cerevisiae sporulation media
Organism Saccharomyces cerevisiae
Characteristics strain: SK1
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.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
Description Ribosome-protected mRNA
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].
Submission date Dec 06, 2011
Last update date May 15, 2019
Contact name Gloria Brar
Organization name UCSF
Street address 1700 4th Street, BH404
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
Platform ID GPL9377
Series (1)
GSE34082 High-resolution view of the yeast meiotic program revealed by ribosome profiling
SRA SRX110564
BioSample SAMN00761944

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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