|
| Status |
Public on Jul 08, 2016 |
| Title |
ABP1 wt1 |
| Sample type |
SRA |
| |
|
| Source name |
ABP1 wt
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype/variation: wild type
chip antibody: HA tag antibody [12CA5] (abcam16918)
|
| 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). Monoclonal anti-HA tag antibody [12CA5] (abcam16918) was used to retrieve HA-tagged Abp1 combined with Dynabeads Protein A (Life Technologies). After reversing the crosslinks DNA was purified using phenol-chloroform and precipitated with LiCl and isopropanol
Libraries were prepared using Illumina’s ChIP-Seq Sample Prep Kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
HA-tagged Abp1
|
| Data processing |
Solexa Illumina ChIP-Seq data for Saccharomyces pombe ABP1 and Input control in wild-type samples 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.
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 |
GPL15167 |
| Series (2) |
| GSE81324 |
The CENP-B fission yeast homolog, ABP1, is involved in the repression of cryptic transcription from the Tf2 and rRNA genes repeat [ChIP-Seq_CNAG] |
| 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 |
SAMN04979176 |
| SRA |
SRX1756591 |
