|
| Status |
Public on Jul 08, 2016 |
| Title |
Input wt2 |
| Sample type |
SRA |
| |
|
| Source name |
Input wt
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype/variation: wild type
chip antibody: none
|
| Treatment protocol |
formaldehyde was added to the cells at a final concentration of 1% for 15 min then quenching was performed by adding 125mM Glycine
|
| Growth protocol |
exponentially growing yeast in YES medium
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
cells were harvested and lysed with a FastPrep cell disrupter (FP120, Bio101 Thermo Savant). DNA was sheared to a range of 250-400bp with a Bioruptor Standard (Diagenode). For Ser5PolII ChiP-seq we used αPolIIser5 monoclonal antibody (Abcam/ab5131) combined with Dynabeads Protein A (Life Technologies). After reversing the crosslinks DNA was purified using phenol-chloroform and precipitated with LiCl and isopropanol
Illumina TruSeq RNA Sample Prep Kit, 48 SetA Ref: 15013135 Lot: 6103158. Although this is Chip-DNA, the “TruSeq RNA Sample Prep Kit” has been used for Library Preparation
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
genomic DNA
|
| Data processing |
Solexa Illumina ChIP-Seq data for Saccharomyces pombe Pol2Ser5 in wild-type samples and Pol2Ser5 in ABP1d mutant samples, together with their respective Inputs were aligned against the reference genome using Bowtie 0.12.5 allowing for 2 mismatches in the read seed. In order to estimate enrichment in repeated regions (i.e. transposons, rRNA units) in an unbiased manner, all possible sites for multiple hits were considered.
Afterwards, strand shift bias and duplicated reads were estimated and removed with the htSeqTools package using the default options.
Significantly enriched regions in ChIP-Seq data were detected with the enrichedRegions function, considering only regions within the IP sample with a coverage above 2.5 times the first quartile, and using a Benjamini Hochberg pvalue threshold of 0.05.
Afterwards the enrichedPeaks function was used to detect significantly enriched peaks (putative binding sites), setting the minimum coverage difference between IP and Input at 200, and merging adjacent peaks if they were closer than 300bp apart.
Genome_build: Spombe Sanger 09052011
Supplementary_files_format_and_content: BED file includes chromosome, start and end columns of the identified peaks in the Sanger 09052011 SPombe genome. Additional column indicates peak coverage for the IP sample.
|
| |
|
| Submission date |
May 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Oscar Reina Garcia |
| E-mail(s) |
oscar.reina@irbbarcelona.org
|
| Organization name |
IRB Barcelona
|
| Department |
Biostatistics and Bioinformatics
|
| Street address |
C/Baldiri Reixac 10
|
| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08028 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13988 |
| Series (2) |
| GSE81323 |
The CENP-B fission yeast homolog, ABP1, is involved in the repression of cryptic transcription from the Tf2 and rRNA genes repeat [ChIP-Seq_BGI] |
| GSE81326 |
The CENP-B fission yeast homolog, ABP1, is involved in the repression of cryptic transcription from the Tf2 and rRNA genes repeat |
|
| Relations |
| BioSample |
SAMN04979171 |
| SRA |
SRX1756586 |
