|
| Status |
Public on Jul 30, 2021 |
| Title |
MED5-3HA_kin28as-med16D_NAPP1_R2 |
| Sample type |
SRA |
| |
|
| Source name |
GZY392
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
chip tag: MED5-3xHA
background: BY4705
treatment: 15 mins of 6uM NaPP1 in DMSO
|
| Treatment protocol |
6μM of 1-Naphthyl PP1 (NA-PP1; Tocris Bioscience) or DMSO for 15 min at 30°C prior to crosslinking
|
| Growth protocol |
ATP analog sensitive kin28as strains were pre-cultured in yeast nitrogen base (YNB) medium lacking uracil before inoculation in yeast extract-peptone-dextrose (YPD) medium
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq done as in Jeronimo et al. 2016 [PMID:27773677]
Library preparation done as described in Jeronimo et al. 2019 [PMID:31365865]
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Alignment by Bowtie 2
Unmapped and low quality reads were removed using Samtools with parameters “-F 2048 -f 2”
Duplicated reads were removed using Samtools with parameters “fixmate -m”
BAM files were converted to BED files using robtools (version 1.0 available at https://github.com/francoisrobertlab/robtools)
Coverage for each base pair was computed using genomeCoverageBed from BEDTools (version 2.27.1) and normalized to 1 million reads.
Genome_build: UCSC sacCer3
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Apr 13, 2021 |
| Last update date |
Jul 30, 2021 |
| Contact name |
Gabriel E Zentner |
| E-mail(s) |
gzentner@indiana.edu
|
| Phone |
812-856-7377
|
| Organization name |
Indiana University
|
| Department |
Biology
|
| Street address |
915 E 3rd St
|
| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47405 |
| Country |
USA |
| |
|
| Platform ID |
GPL21656 |
| Series (2) |
| GSE169748 |
Connection of core and and tail Mediator modules restrains transcription from TFIID-dependent promoters |
| GSE171981 |
Connection of core and tail Mediator modules restrains transcription from TFIID-dependent promoters [ChIP-Seq] |
|
| Relations |
| BioSample |
SAMN18723117 |
| SRA |
SRX10592372 |
