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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 09, 2023 |
| Title |
SIR_mutpromoter_Rpb3FLAG ChIP rep1 |
| Sample type |
SRA |
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| Source name |
Saccharomyces cerevisiae
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
tissue: Saccharomyces cerevisiae
cell line: JRy15352
genotype: ADE2, lys2, TRP1, hmlalpha2delta*Rap1bs-mutation::CRE, ura3delta::pGPD:loxP:yEmRFP;tCYC1:hygMX:loxP:yEGFP:tADH1; 3xV5_Rap1-N-terminal ; RPB3-3xFLAG-KanMX; hmrdelta::HygMX; matdelta::k.l.LEU2
treatment: anti-FLAG® M2 antibody (MilliporeSigma, product F1804) and DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed by mechanical disruption in a bead beater. Chromatin was fragmented by sonication. IPs were performed using 5mL mouse monoclonal anti-FLAG® M2 antibody (MilliporeSigma, product no F1804) and 50uL DynaBeads Protein G magnetic beads (ThermoFisher Scientific catalog number 10003D). DNA was purified using Qiagen spin column kit
NEB Ultra II library prep kit
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
FASTQ generation using Illumina Casava v2.2.
Raw reads were mapped to SacCer3 genome modified to include the mutant promoter site where applicable, and mat∆hmr∆ or hml∆mat∆, using Bowtie2 with following options: --local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant
PCR duplicates were removed using, sequentially, SAMtools -fixmate -sort -markdup
bedgraph files were generated that included reads between 0-500bp (average fragment size from sonication) and normalized to the genome-wide median (median excluded subtelomeres, chromosome III, and rDNA)
Assembly: SacCer3 (modified)
Supplementary files format and content: bedgraph (normalized to genome-wide median)
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| Submission date |
Mar 20, 2023 |
| Last update date |
May 09, 2023 |
| Contact name |
Eliana Rose Bondra |
| Organization name |
University of California, Berkeley
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| Department |
Molecular and Cell Biology
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| Lab |
Rine
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| Street address |
440 Barker Hall
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| City |
Berkeley |
| State/province |
California |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platform ID |
GPL27812 |
| Series (2) |
| GSE227760 |
Context dependent function of transcriptional regulator Rap1 in gene silencing and activation [ChIP-seq III] |
| GSE227763 |
Context dependent function of transcriptional regulator Rap1 in gene silencing and activation |
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| Relations |
| BioSample |
SAMN33832043 |
| SRA |
SRX19733279 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7107690_15352_IP_median_normalized.bedgraph.gz |
70.6 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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