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Sample GSM1054403 Query DataSets for GSM1054403
Status Public on Jul 24, 2013
Title snt2D_0.5hrs_rep2
Sample type SRA
 
Source name S. cerevisiae snt2 deletion strain
Organism Saccharomyces cerevisiae
Characteristics yeast strain: BY4741 snt2D
hours h2o2: 0.5
biol. replicate #: 2
Treatment protocol One half of each yeast culture was taken for the 0 hour (T0) sample. H2O2 was added to remaining cultures at a final concentration of 0.4 mM. Samples were taken 0.5 hours after H2O2 addition for the 0.5 hour (T0.5) sample.
Growth protocol Saturated overnight cultures of strains (Snt2-Myc, Ecm5-Myc, or BY4741) were diluted in YPD and grown to mid-log phase (OD600=0.3).
Extracted molecule total RNA
Extraction protocol Total RNA was obtained through hot acid phenol extraction (Collart, M. A., and S. Oliviero. 200; Current Prot. Mol. Bio.)
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit (cat # RS-122-2001). After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing RNA-seq reads were aligned to the SacCer2 genome assembly using TopHat v1.4 with 25 bp segment length
Aligned BAM files were converted to Wig files using IGVtools
Genome_build: sacCer2
 
Submission date Dec 18, 2012
Last update date May 15, 2019
Contact name David Allis
Organization name The Rockefeller University
Department Laboratory of Chromatin Biology and Epigenetics
Lab Allis Laboratory
Street address 1230 York Ave Box 78
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL13821
Series (2)
GSE42983 The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress (RNA-seq)
GSE43002 The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress
Relations
SRA SRX211392
BioSample SAMN01831665

Supplementary file Size Download File type/resource
GSM1054403_snt2T0p5rep2_acceptedhits.bam.wig.gz 2.0 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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