|
| Status |
Public on Nov 27, 2020 |
| Title |
Double_Ifh1_Sfp1_Control |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: YJB338
genotype: W303 background; Mat alpha tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 SFP1-FRB::KANMX IFH1-FRB::HIS
antibody: Anti-RNA polymerase II CTD repeat YSPTSPS (Abcam ab5131)
|
| Treatment protocol |
No rapamycin
|
| Growth protocol |
Cells were grown at 30 degrees in YPD to mid-log phase before treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNAPII and Hmo1 ChIP-seq was performed as described previously (Ribaud et al., 2012) (PMID: 21952045) with the following modification. A defined amount (5% of total chromatin) of previously cross-linked chromatin from S.pombe was added to S.cerevisiae chromatin prior to immunoprecipitation step)
ChIP-seq libraries were prepared by using TruSeq ChIP library preparation kit (Illumina)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
For ChIP-Seq raw reads were aligned to the sacCer3 genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800"
For ChIP-Seq, data were filtered to retain only the mapped reads with at most 5 hits in the reference.
For ChIP-seq the reads were shifted by 100 bp and extended by 50 bp
For ChIP-Seq, reads mapped uniquely to the sacCer3 genome were first normalized to total number of mapped reads in sacCer3 and then to total number of uniquely mapped reads in 972-h pombe in the same sample as described in (Hu et al. 2015)
For ChEC-seq experiments the mapped reads were extended by 1 bp only to indicate cut sites and then, the signal for each protein tested was normalized to the signal of free MNase using a Bayesian approach
Genome_build: sacCer3, 972-h pombe
Supplementary_files_format_and_content: BigWig files were obtained using GALAXY
|
| |
|
| Submission date |
Jul 27, 2020 |
| Last update date |
Nov 28, 2020 |
| Contact name |
Sevil Zencir |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Geneva
|
| Department |
Department of Molecular and Cellular Biology
|
| Lab |
Francoise Stutz
|
| Street address |
30, quai Ernest-Ansermet
|
| City |
Geneva |
| ZIP/Postal code |
CH-1211 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17342 |
| Series (1) |
| GSE155235 |
Mechanisms Coordinating Ribosomal Protein Gene Transcription in Response to Stress |
|
| Relations |
| BioSample |
SAMN15655061 |
| SRA |
SRX8833558 |
