|
| Status |
Public on Aug 31, 2016 |
| Title |
POLII_YNG2-WA_1 |
| Sample type |
SRA |
| |
|
| Source name |
POLII_YNG2-WA_1
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: MYC-Epl1 deltaeaf7 strain
growth conditions: untreated cells, normal growth conditions, 30°C, YPD
antibody #lot number: H4K8ac (millipore 07328, #2433445)
|
| Growth protocol |
Exponentially growing cells in YPD
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatins were prepared from sonicated cell lysates and histone-DNA complexes were isolated with specific antibody.
Libraries were prepared according to Illumina's instructions . Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation library fragments of ~200-500 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel and DNA was PCR amplified with Illumina primers for 18 cycles. Amplicons were purified with Qiagen QIA Quick MinElute PCR purification kit and libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
MYC-Epl1
MYC-Epl1 ∆eaf7 strain
|
| Data processing |
Reads were mapped on sacCer3 build using bowtie version 0.12.8.
Duplicated reads were removed using samtools version 0.1.18
Bam files were converted to BigWig using BEDTools version 2.16.2 and the UCSC tool bedGraphToBigWig
Genome_build: sacCer3
Supplementary_files_format_and_content: bw files
|
| |
|
| Submission date |
Feb 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Eric R Paquet |
| Organization name |
EPFL
|
| Department |
Life sciences
|
| Lab |
Naef lab
|
| Street address |
Station 15 CH - 1015
|
| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE77945 |
Role of Yng2 PHD and CHD-containing Eaf3 subunits of NuA4 on genome wide histone H4K8 acetylation, NuA4 localization and Pol II distribution |
|
| Relations |
| SRA |
SRX1585402 |
| BioSample |
SAMN04504312 |
