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Sample GSM2430216 Query DataSets for GSM2430216
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) mjbuck@buffalo.edu
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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