|
| Status |
Public on Jul 30, 2014 |
| Title |
Asf1_ChIPseq1 |
| Sample type |
SRA |
| |
|
| Source name |
mid-log phase ASF1-18myc cells, ChIP
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: ASF1-18myc
genetic background: S288c
growth phase: mid-log (OD 600=0.7)
chip antibody: anti-Myc tag antibody, clone A46
|
| 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 |
| E-mail(s) |
dewndrop@ccmb.res.in
|
| 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 |
|
| Relations |
| SRA |
SRX185634 |
| BioSample |
SAMN01163650 |
