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Sample GSM1054743 Query DataSets for GSM1054743
Status Public on Jul 24, 2013
Title ECM5_4hrs_DMSO_RapExpt_ChIP
Sample type SRA
 
Source name S. cerevisiae Ecm5-13Myc strain
Organism Saccharomyces cerevisiae
Characteristics yeast strain: Ecm5-13Myc
treatment: DMSO
hours treatment: 4
antibody: anti-Myc (9E10 monoclonal)
Treatment protocol An aliquot of each yeast culture was taken for the 0 hour (T0) ChIP/Input samples. Each culture was then divided into two separate cultures: one of these was treated with rapamycin dissolved in DMSO (final rapamycin concentration 50 nM), while the other cultures was treated with DMSO as a control. Samples were taken 0.5 and 4 hours after treatment 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 21 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 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 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)
GSE43001 The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress (rapamycin or DMSO)
GSE43002 The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress
Relations
SRA SRX211422
BioSample SAMN01831695

Supplementary file Size Download File type/resource
GSM1054743_ECM5_dmso_4hr_CHIP_CAGATC_L008_R1_001.bowtie.bam.wig.gz 2.1 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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