|
| Status |
Public on May 10, 2013 |
| Title |
Hst4 ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Genomic DNA
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
sample type: Myc tagged Hst4
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 |
| E-mail(s) |
kp9y@virginia.edu
|
| 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 |
|
| Relations |
| SRA |
SRX193144 |
| BioSample |
SAMN01760471 |
