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Sample GSM1054129 Query DataSets for GSM1054129
Status Public on Jul 24, 2013
Title SNT2_0.5hrs__H2O2Expt_ChIP
Sample type SRA
 
Source name S. cerevisiae Snt2-13Myc strain
Organism Saccharomyces cerevisiae
Characteristics yeast strain: Snt2-13Myc
hours h2o2: 0.5
antibody: anti-Myc (9E10 monoclonal)
Treatment protocol One third of each yeast culture was taken for the 0 hour (T0) ChIP/Input samples. H2O2 was added to remaining cultures at a final concentration of 0.4 mM. Samples were taken 0.5 and 4 hours after H2O2 addition for ChIP/Inputs
Growth protocol Saturated overnight cultures of strains (Snt2-Myc, Ecm5-Myc, or BY4741) were diluted in YPD and grown to mid-log phase (OD600=0.4)
Extracted molecule genomic DNA
Extraction protocol Samples were crosslinked by adding formaldehyde (final conc 1%) at room temp for 20 minutes, and then quenched with glycine (final conc 125 mM). ChIPs were performed as described (Aparicio et al. 2005 Curr Protoc Mol Biol). Briefly cells were lysed using glass beads, and chromatin was sheared to 150-500 bp. Chromatin was isolated and used for ChIP with the anti-Myc 9E10 antibody (Millipore #05-419) according to standard procedures.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA Sample Preparation Kit (cat # FC-121-2001). After adapter ligation DNA was PCR amplified with Illumina primers for 20 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. 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 ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing ChIP-seq reads were aligned at 51bp to the SacCer2 genome assembly using Bowtie: only unique reads with no more than 2 mismatches were kept
Aligned BAM files were converted to Wig files using IGVtools
Genome_build: sacCer2
 
Submission date Dec 17, 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)
GSE42971 The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress (H2O2)
GSE43002 The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress
Relations
SRA SRX211365
BioSample SAMN01831635

Supplementary file Size Download File type/resource
GSM1054129_SNT2_T0.5_ChIP.bowtie.bam.wig.gz 1.9 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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