GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1016781 Query DataSets for GSM1016781
Status Public on May 10, 2013
Title Hst2 ChIP-seq
Sample type SRA
Source name Genomic DNA
Organism Saccharomyces cerevisiae
Characteristics sample type: Myc tagged Hst2
chip antibody: Anti-myc (9E10)
chip antibody manufacturer: Hybridoma core facility at UVA
strain: ML1
Growth protocol Yeast strains were grown in YPD medium containing 2% glucose as the carbon source. All yeast growth was performed at 30°C.
Extracted molecule genomic DNA
Extraction protocol Log-phase cultures were cross-linked with 1% formaldehyde for 20 min at 30°C.Cells were pelleted by centrifugation and washed 2 times with cold Tris-buffered saline. The cells, in 0.6 ml of FA-140 lysis buffer were lysed with glass beads and a Mini-BeadBeater (Biospec Products). The cell lysate was drawn off the beads, sonicated for 60 cycles (30 s “on” at high level and 30 s “off” per cycle) in a Bioruptor (Diagenode) and spun for 10 min at 16,000x g in a microcentrifuge. Equivalent amounts of lysate (2.5 mg protein) were incubated overnight at 4°C with 5 µg of anti-Myc antibody (9E10) and 20 µl of protein G magnetic beads (Millipore). The immunoprecipitated chromatin was then recovered and the DNA purified using a Magna ChIPTM G Chromatin Immunoprecipitation Kit (Millipore).
The ChIP-sequencing libraries were made using an Illumina ChIP-Seq DNA Sample Prep Kit (cat. # IP-102-1001), starting with 0.5 µg of DNA isolated from the immunoprecipitation step.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
Data processing Basecalls performed using CASAVA version 1.7.0
ChIP-seq reads were aligned to the sacCer2 genome assembly using BWA version 0.5.7.
Data were filtered on basis of quality score and repeats were allowed only on rDNA locus on chrXII
peaks were called using BayesPeak version 1.2.3.
Genome_build: sacCer2
Supplementary_files_format_and_content: BedGraph files were generated where Scores represent tag counts
Submission date Oct 09, 2012
Last update date May 15, 2019
Contact name Kunal Poorey
Phone 434-982-3237
Fax 434-924-5069
Organization name University of Virginia Health System
Department Biomedical Sciences: Biochemistry, Molecular Biology & Genetics
Lab Auble Lab
Street address 1340 Jefferson Park Avenue
City Charlottesville
State/province VA
ZIP/Postal code 22908
Country USA
Platform ID GPL9377
Series (1)
GSE41415 Genome-wide Analysis of Functional Sirtuin Chromatin Targets in Yeast
SRA SRX193142
BioSample SAMN01760469

Supplementary file Size Download File type/resource
GSM1016781_Hst2_new_yeast_rDNA_repeat.bedGraph.gz 3.8 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap