|
| Status |
Public on Jul 01, 2011 |
| Title |
SCH9 STB3-TAP |
| Sample type |
SRA |
| |
|
| Source name |
SCH9 STB3-TAP nucleus
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: AH624
genotype: TB50alpha SCH9::pRS304 STB3-TAP::HIS3MX6
tissue: nucleus
treatment: 300 nM 1NM-PP1 20 min
|
| Treatment protocol |
20 min treatment with 300 nM 1NM-PP1.
|
| Growth protocol |
Exponential growth in YPD at 30C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared using ChIP-Seq sample preparation kits (Illumina) according to the manufacturer's instructions. DNA fragments ends were repaired using a mix of Klenow DNA polymerase, T4 DNA polymerase and T4 polynucleotide kinase. DNA was then purified and 3' A overhangs were added using a Klenow fragment (3' to 5' exo minus). DNA was purified again and ligated to adapters. 190 ± 10bp fragments were selected using the E-Gel SizeSelect system (Invitrogen) and purified. Fragments with adapters were finally enriched with 18 cycles of PCR and purified. High-throughput sequencing of libraries was performed on a Genome Analyzer IIx machine (Illumina), each in a separate channel.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
2b
Chromatin IP for TAP tag. The bait proteins were tagged with Protein A (TAP tag), which binds to rabbit IgG via their constant fragment.
|
| Data processing |
Sequencing reads were mapped on the SGD1.01 (sacCer2 build) genome assembly using Bowtie 0.12.1 (Langmead et al, 2009) with parameters -n 3 --best --strata --solexa1.3-quals -a -m 20 and viewed with the USCS Genome Browser (Kent et al, 2002). Libraries sequencing and reads alignment to the yeast genome are summarized in table S7. The MACS algorithm v 1.7.3.1 (Zhang et al, 2008) was used to detect Sds3-TAP binding peaks by comparing the mapped read counts obtained from the sch9as SDS3-TAP vs. the untagged sch9as strains with parameters --mfold=2 --pvalue=1e-5.
|
| |
|
| Submission date |
May 06, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Jacques Rougemont |
| E-mail(s) |
jacques.rougemont@epfl.ch
|
| Organization name |
EPFL
|
| Department |
School of Life Sciences
|
| Lab |
Bioinformatics and Biostatistics Core Facility
|
| Street address |
Station 15
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL13272 |
| Series (2) |
| GSE29124 |
Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L (ChIP-Seq data) |
| GSE29125 |
Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L |
|
| Relations |
| SRA |
SRX062027 |
| BioSample |
SAMN00264863 |
