|
| Status |
Public on Nov 01, 2021 |
| Title |
Rap1_IP_H4_shutoff_t2_R2 |
| Sample type |
SRA |
| |
|
| Source name |
cultured cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: UKY403
time point (hrs): 2
antibody: Rap1p antibody (Santa Cruz Biotechnology Rap1 Y-300, sc-20167)
|
| Treatment protocol |
For time-course experiments, cells were initially inoculated in 5ml YPG liquid media and cultured at 30C. Logarithmically growing cells were then transferred and diluted into larger 1-1.5L YPG cultures for growth overnight at 30C while shaking in containers with 4x equivalent free-air volume. The following morning, mid-log phase cells (OD600 ~0.6-1.2) were collected by centrifugation, washed 2x within 5 minutes with ~250-500ml YP dextrose (YPD), and re-suspended in equivalent volume of YPD media for 0, 2, and 4 hours of continued growth at 30C.
|
| Growth protocol |
H4 shutoff (UKY403) and isogenic control (UKY412) strains of S. cerevisiae were obtained from the Grunstein lab. Cells were maintained on agar plates containing YPG media (1% yeast extract, 2% peptone, 2% galactose).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Rap1p ChIPs were performed on whole cell extracts using a Rap1p antibody (Santa Cruz Biotechnology Rap1 Y-300, sc-20167) following established protocols. Two independent biological replicates from separate time-course experiments were performed for each experimental time-point
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Rap1 Ips during histone H4 Shutoff
|
| Data processing |
alignment with Bowtie VN:1.0.0 bowtie sgd_r64/SacCer3 --best -l 32 -n 2
ChIP-seq replicates were merged with samtools merge -@ 8
Rap1 binding sites peaks called with MACS2 --- -g 12157105 --nomodel --extsize 147
|
| |
|
| Submission date |
Dec 15, 2016 |
| Last update date |
Nov 01, 2021 |
| Contact name |
Michael Buck |
| E-mail(s) |
[email protected]
|
| Phone |
7168817569
|
| Organization name |
SUNY at Buffalo
|
| Department |
Biochemistry
|
| Street address |
701 Ellicott St
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14203 |
| Country |
USA |
| |
|
| Platform ID |
GPL9377 |
| Series (2) |
| GSE92467 |
Nucleosomes inhibit intragenic binding of Rap1p and subsequent cryptic transcription [ChIP-seq] |
| GSE92468 |
Nucleosomes inhibit intragenic binding of Rap1p and subsequent cryptic transcription |
|
| Relations |
| BioSample |
SAMN06145965 |
| SRA |
SRX2426672 |
