|
| Status |
Public on Dec 26, 2020 |
| Title |
Spt16-TAP Mock |
| Sample type |
SRA |
| |
|
| Source name |
Log-phase cells in the 1X YEP with 2% dextrose
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
antibody: Protein A Sepharose (GE Healthcare product code: 17-1279-02, lot number: 10204516)
strain: Spt16-TAP
nutrient status: normal
|
| Treatment protocol |
Cells were fixed with 1% formaldehyde for 30 min. and quenched with 0.125M Glycine
|
| Growth protocol |
Spt16-TAP strain was grown up to A600~0.8 in YEP medium at 30°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
IP, Input and mock DNA samples were processed according to 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 aligned to yeast genome using Bowtie 0.12.8 allowing unique alignments with 3 mismatches and taking the best stratum.
Reads are extended to ChIP fragment size (170bp)
Read coverage at each position in the genome is scaled to 1 million and normalized to total number of reads in the library.
Coverage at each base is bundled as .bedGraph files.
Genome_build: sacCer3
Supplementary_files_format_and_content: BEDGRAPH
|
| |
|
| Submission date |
Jun 07, 2016 |
| Last update date |
Dec 27, 2020 |
| Contact name |
Ashutosh Shukla |
| E-mail(s) |
ashubiochem@gmail.com
|
| Organization name |
CSIR-Centre for Cellular and Molecular Biology
|
| Street address |
Habsiguda X Road
|
| City |
Hyderabad |
| State/province |
Telangana |
| ZIP/Postal code |
500007 |
| Country |
India |
| |
|
| Platform ID |
GPL9377 |
| Series (1) |
| GSE83086 |
Genome-wide profiling of histone chaperone FACT in Saccharomyces cerevisiae |
|
| Relations |
| BioSample |
SAMN05213613 |
| SRA |
SRX1829041 |
