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Sample GSM542255 Query DataSets for GSM542255
Status Public on Aug 15, 2010
Title BiSulfite "H"
Sample type SRA
Source name Yeast grown in liquid culture
Organism Saccharomyces cerevisiae
Characteristics strain: BY4741
growth stage: Mid-log
Growth protocol Cells were grown at 30 C in a shaking water bath (New Brunswick Scientific) in the following medium: 1.5% yeast extract, 1% peptone, 2% dextrose, 0.2% SC amino acid mix (Sunrise Science). Cells were then harvested by freezing in liquid nitrogen, spun 5 minutes , 3700 x g in a Sorvall Legend RT to pellet the cells, and resuspended in 2 ml RNAlater (Ambion).
Extracted molecule polyA RNA
Extraction protocol Library construction: BiSulfite (see He et al. (2008) Science)
RNA was extracted with the RNeasy kit (Qiagen) and treated with Turbo DNase (Ambion). Polyadenylated RNA was selected with the MicroPoly(A)Purist kit (Ambion).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
Data processing We used Arachne to map the reads to the genome. Reads in single end libraries were mapped uniquely, allowing up to 4 mismatches. Reads in paired-end libraries were first mapped non-uniquely allowing up to 4 mismatches, and then we searched for unique pairing of the non unique read mappings. A unique pairing is defined as a single pair of mappings on the same chromosome, up to 500 bp apart, with reads on opposite strands.
Submission date May 07, 2010
Last update date May 15, 2019
Contact name Joshua Z Levin
Organization name Broad Institute of MIT & Harvard
Street address 320 Charles Street
City Cambridge
State/province MA
ZIP/Postal code 02141
Country USA
Platform ID GPL9377
Series (1)
GSE21739 Comprehensive comparative analysis of strand-specific RNA sequencing methods
SRA SRX022783
BioSample SAMN00016766

Supplementary file Size Download File type/resource
GSM542255_BiSulfite_He.F.bedGraph.gz 6.8 Mb (ftp)(http) BEDGRAPH
GSM542255_BiSulfite_He.R.bedGraph.gz 6.7 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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