|
| Status |
Public on Apr 05, 2018 |
| Title |
ChIPSeq_Htz1_4KR_caffeine-30-min_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Saccharomyces cerevisiae cells grown in caffeine
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: bar1::HIS htz1::TRP + p[htz1K3,8,10,14R-URA3]
|
| Growth protocol |
Cells were grown to mid-log phase in drug-free medium (SD-Ura) and then caffeine (Sigma) was added to 10 mM. MG-132 (Merck) 150 mM treatment was carried out in medium containing 0.006% SDS to facilitate drug uptake. For histone deacetylase inhibition, 75mM VPA was added to cells for 45 minutes.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cultures were crosslinked with 1% (v/v) formaldehyde, quenched with glycine, and cells were lysed with beads in a FastPrep-24 (MP Biomedicals) cell homogeniser. Sonicated, clarified extracts were immunoprecipitated with anti-Htz1 antibodies before washing and DNA extraction, or were used directly to prepare input DNA.
Illumina TruSeq ChIP Sample Prep Kit were used for ChIP-seq library preparation. RNA library was prepared using the Illumina TruSeq stranded mRNA sample preparation kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ChIP-seq and RNA-seq reads were mapped to the S. cerevisiae genome assembly sacCer1 using Bowtie2 and Tophat2 respectively, allowing up to 2 mismatches per sequence and no ambiguously mapped reads.
Normalisation for ChIP-seq (wild-type (WT) and 4KR samples) was performed based on the assumption that the genomic background is constant over the time course. Background signal was set to 1.2 standard deviations above the mean of the ChIP:input ratios and then subtracted from the ChIP-seq signal.
Genome_build: sacCer1
|
| |
|
| Submission date |
Apr 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Muxin Gu |
| E-mail(s) |
muxingu@gmail.com, mg445@cam.ac.uk
|
| Phone |
01223767800
|
| Organization name |
University of Cambridge
|
| Department |
Haematology
|
| Lab |
George Vassiliou
|
| Street address |
Jeffrey Cheah Biomedical Centre, Puddicombe Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0AW |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE97822 |
H2A.Z acetylation fine-tunes gene expression dynamics by regulating H2A.Z degradation |
|
| Relations |
| BioSample |
SAMN06758146 |
| SRA |
SRX2737490 |
