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Sample GSM999653 Query DataSets for GSM999653
Status Public on Jul 30, 2014
Title Mock
Sample type SRA
Source name mid-log phase ASF1-18myc cells, mock
Organism Saccharomyces cerevisiae
Characteristics strain: ASF1-18myc
genetic background: S288c
growth phase: mid-log (OD 600=0.7)
chip antibody: normal rabbit IgG
Treatment protocol Cells were fixed with formaldehyde (final conc. 1%) for six hours and quenched with glycine (final conc. 0.125M) for 10 minutes.
Growth protocol The ASF1-18myc strain was grown to A600 = 0.7 in YEP + 2% glucose medium at 30 degrees Celsius.
Extracted molecule genomic DNA
Extraction protocol The ChIP protocol is essentially as described in Liu et al., 2005 (PMID 16122352). Immunoprecipitated chromatin was reverse cross-linked at 65 degrees for 10 hours. After one hour of RNase A treatment, DNA was extracted with phenol-chloroform-isoamyl alcohol (PCI) twice and precipitated using ethanol. Anti-Myc tag antibody, clone A46 (Upstate (Millipore), catalog number: 05-724, lot: JBC1868960) and Protein A and G Sepharose 4 Fast Flow (GE Healthcare) beads were used. IP and Mock DNA samples were processed according to the Illumina standard protocol for ChIP-seq.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
Data processing Reads with phred score < 20 on 80% of the bases were filtered out with FASTX toolkit V0.0.13.
Reads were aligned to the yeast genome using Bowtie 0.12.8 allowing unique alignments with 3 mismatches and taking the best stratum.
Reads were extended to ChIP fragment size (160 bp).
Read coverage at each position in the genome is scaled to 1 million and normalized to the total number of reads in the library.
Genome_build: sacCer3
Supplementary_files_format_and_content: Coverage at each base is bundled as .bedGraph files.
Submission date Sep 09, 2012
Last update date May 15, 2019
Contact name Pooran Singh Dewari
Organization name Centre for Cellular and Molecular Biology
Department Transcription Lab
Lab W313
Street address Uppal Road
City Hyderabad
State/province Andhra Pradesh
ZIP/Postal code 500007
Country India
Platform ID GPL9377
Series (1)
GSE40717 Genome-wide targets of conserved histone chaperone Asf1 in budding yeast
SRA SRX185636
BioSample SAMN01163652

Supplementary file Size Download File type/resource
GSM999653_Mock_ChIPseq.bedgraph.gz 11.4 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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