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| Status |
Public on Apr 02, 2015 |
| Title |
INPUT6 pcf11-2 37C |
| Sample type |
SRA |
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| Source name |
cell culture
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype/variation: pcf11-2 mutant
growth temperature: grown at 37C
chip antibody: CMA601 antibody
chip antibody reference: PMID 25252976
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| Growth protocol |
Strains were grown in YPD (1% yeast extract, 2% Bacto-peptone, 2% glucose)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from 1% formaldehyde fixed, sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP DNA was end-repaired, A-tailed and adaptor ligated before amplification and size selection. Prepared libraries after quality control were multiplexed and single-end sequenced over one "rapid" run on HiSeq sequencer.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
INPUT6 pcf11-2 37C
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| Data processing |
ChIP-seq reads were aligned to the saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer3, April 2011) using Stampy.
Genome coverage was calculated, read count information was binned into 20bp intervals, read count normalized and eventuallu log2 of IP/input ratios were calculated. Such procesed signals were used for all further analysis discribed in the paper.
bedgraph files were generated from the ChIP and input genome coverage files binned into 10 bp bins. Log2 valuses of the ratio of ChIP and input in corresponding bins were calculated.
Genome_build: sacCer3, April 2011
Supplementary_files_format_and_content: tab-delimited text files (bedGraph format) include log2(IP/input) values for each Sample
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| Submission date |
Apr 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Michal R. Gdula |
| E-mail(s) |
[email protected]
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| Organization name |
Oxford University
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| Street address |
South Parks Road
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| City |
Oxford |
| ZIP/Postal code |
OX1 3RF |
| Country |
United Kingdom |
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| Platform ID |
GPL13821 |
| Series (1) |
| GSE67483 |
Pol II chromatin immunoprecipitation in S. cerevisiae |
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| Relations |
| BioSample |
SAMN03455211 |
| SRA |
SRX974683 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not provided for this record |
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