|
| Status |
Public on Dec 29, 2021 |
| Title |
Rpb3 ChIP-seq (no SM) Repl. 3 [AGH64_9] |
| Sample type |
SRA |
| |
|
| Source name |
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 ino80∆::kanMX4
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: YR092
genetic information: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 ino80{delta}::kanMX4
treatment: Formaldehyde-fixed and sonicated
|
| Treatment protocol |
Cells were fixed with formaldhyde and sonicated with bioruptor. The detail was described previously in Qiu et al., Genome Research 26:211-225 (2006) and Rawal et al., Genes and Development 32:695-710 (2018)
|
| Growth protocol |
All strains were grown to mid-log phase (OD600 about 0.6 to 0.8) at 30 degC in synthetic complete medium lacking isoleucine and valine (SC-Ilv), sulfometuron (SM) was added at 1µg/ml for 25 min to induce Gcn4, or without adding SM (no SM).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sonicated chromatin extracts were immunoprecipitated with anti-Gcn4 (home-made), anti-TBP (from Joseph Reese's lab), anti-myc (Sigma, Cat# 11667203001) and anti-Rpb3 (NeoClone, Cat# W0012). Immunoprecipitated chromatin were treated with proteinase K and DNA were extracted with chloroform and precipitated with iso-propanol.
Libraries were prepared using DNA Library Prep Kit for llumina (Cat# E7370) from New England Biolabs.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Biological replicate 3
AGH64_9
|
| Data processing |
Paired-end sequences of immunoprecipited DNA were aligned to the yeast genome (SacCer3) using Bowtie2 with parameters -X 1000 --very-sensitive, to map sequences up to 1 kb with maximum accuracy.
Occupancies profiles of Gcn4, TBP, myc-tagged chromatin remoderlers and Rpb3 were created using custom R programs.
The processed data were converted to the bigwig files supplied here: different DNA length exclusion limits were used in the processing (listed with Processed Data Files)
Genome_build: SacCer3
Supplementary_files_format_and_content: bigWig (Lengths used in .bw files; Range: 50 - 300 bp)
|
| |
|
| Submission date |
Dec 24, 2021 |
| Last update date |
Dec 29, 2021 |
| Contact name |
Alan G Hinnebusch |
| E-mail(s) |
[email protected]
|
| Phone |
3014964480
|
| Organization name |
NIH, NICHD
|
| Street address |
6 Center Drive, 6/230
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL23014 |
| Series (1) |
| GSE192592 |
Distinct functions of three chromatin remodelers in activator binding and preinitiation complex assembly |
|
| Relations |
| BioSample |
SAMN24388706 |
| SRA |
SRX13504920 |
