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| Status |
Public on Nov 27, 2020 |
| Title |
WT_Vehicle20_RNAPII |
| Sample type |
SRA |
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| Source name |
whole organism
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: YDS2
genotype: W303 background; Mat a leu2-3,112 his3-11,15 ura3-1 ade2-1 trp1-1 can1-100
antibody: Anti-RNA polymerase II CTD repeat YSPTSPS (Abcam ab5131)
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| Treatment protocol |
No rapamycin
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| Growth protocol |
Cells were grown at 30 degrees in YPD to mid-log phase before treatment
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| 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)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| 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
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| Submission date |
Jul 27, 2020 |
| Last update date |
Nov 28, 2020 |
| Contact name |
Sevil Zencir |
| E-mail(s) |
[email protected]
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| Organization name |
University of Geneva
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| Department |
Department of Molecular and Cellular Biology
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| Lab |
Francoise Stutz
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| Street address |
30, quai Ernest-Ansermet
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| City |
Geneva |
| ZIP/Postal code |
CH-1211 |
| Country |
Switzerland |
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| Platform ID |
GPL17342 |
| Series (1) |
| GSE155235 |
Mechanisms Coordinating Ribosomal Protein Gene Transcription in Response to Stress |
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| Relations |
| BioSample |
SAMN15655070 |
| SRA |
SRX8833550 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4697872_WT_Vehicle20.bigwig |
32.9 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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