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Series GSE227761 Query DataSets for GSE227761
Status Public on May 09, 2023
Title Context dependent function of transcriptional regulator Rap1 in gene silencing and activation [ChIP-seq timecourse]
Organisms Saccharomyces cerevisiae; Saccharomyces paradoxus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary As part of a study on the function of Rap1 at HML and MAT in Saccharomyces cerevisiae, we performed an Anchor Away experiment on Rap1, inducibly depleting it from the nucleus upon addition of Rapamycin, followed by a ChIP-seq time-course. This was done in a strain that had SNPs introduced to HMLalpha to make it distinguishable from MATalpha. Samples were spiked with a constant amount (5% by OD) of a S.paradoxus strain that also expressed 2xV5-Rap1. Reads from the S.paradoxus sample served as the normalization factor. Peaks were then fit to a non-linear regression model to extract the k(off) and apparent residence time in vivo.
Overall design 2xV5-FRB-Rap1 ChIP-seq timecourse (t = 0 (DMSO), 5min, 10min, 15min, 20min, 30min, 45min, 60min) following addition of Rapamycin in S. cerevisiae + Spike-in of 5% cells (by OD) of 2xV5-tagged S.paradoxus strain. Replicates are included for each experiment.
Contributor(s) Bondra E, Rine J
Citation(s) 37214837, 37769255
Submission date Mar 20, 2023
Last update date Oct 18, 2023
Contact name Eliana Rose Bondra
Organization name University of California, Berkeley
Department Molecular and Cell Biology
Lab Rine
Street address 440 Barker Hall
City Berkeley
State/province California
ZIP/Postal code 94720
Country USA
Platforms (1)
GPL33270 Illumina NovaSeq 6000 (Saccharomyces cerevisiae; Saccharomyces paradoxus)
Samples (24)
GSM7107741 t0_DMSO_V5Rap1 ChIP rep 1
GSM7107744 t0_DMSO_V5Rap1 ChIP rep 2
GSM7107747 t0_DMSO_V5Rap1 input rep 1
This SubSeries is part of SuperSeries:
GSE227763 Context dependent function of transcriptional regulator Rap1 in gene silencing and activation
BioProject PRJNA946777

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Supplementary file Size Download File type/resource
GSE227761_RAW.tar 518.1 Mb (http)(custom) TAR (of BEDGRAPH)
GSE227761_normalization.xlsx 9.4 Kb (ftp)(http) XLSX
GSE227761_raw.xlsx 501.5 Kb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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