|
| Status |
Public on Aug 01, 2014 |
| Title |
Scc2-ChIP |
| Sample type |
SRA |
| |
|
| Source name |
Inmunoprecipitated DNA
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: Y2422
genotype/variation: MATa, Scc2-Pk9::TRP1
chip antibody: PK, clone SV5-Pk1
chip antibody vendor: Serotec
chip antibody cat. #: MCA1360
chip antibody batch #: #0407
|
| Treatment protocol |
Cells were cross-linked with 1% Formaldehide for 30 minutes at room temperature. The reaction was stopped with 0.125 M Glycine for 10 minutes.
|
| Growth protocol |
Cells were grown in YP + 2% Glucose to an OD600 of 0,6
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin Immunoprecipitation (ChIP) was performed as described (Lengronne et al. 2004) followed byhigh throughput sequencing on a Genome Analyzer IIx (Illumina).
Sequencing libraries were prepared according to the manufacturer's protocol (11257047 Rev. A). The kit used for these preps was the IP-102-1001.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
DNA inmunoprecipitated with anti-Pk
|
| Data processing |
The data sets were aligned using Eland (version 1.4) to the Saccharomyces cerevisiae genome (version sacCer2)
To identify protein enriched regions, the genomic distance between every pair of forward and reverse strand mapped reads was calculated and the average fragment size was taken to be the median of these distances. Half of this value was used with MACS version 1.3.7.1 in NOMODEL mode to identify regions enriched in the aligned data over a whole genome input DNA sample that was processed and sequenced in parallel
Default settings were used apart from 'model fold=32' and an effective genome size of 1.2x10e8.
Genome-wide wig files were generated normalised to 20 million reads.
Genome_build: Saccharomyces cerevisiae genome (version sacCer2)
Supplementary_files_format_and_content: Genome-wide wig files
|
| |
|
| Submission date |
Apr 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Lidia Lopez-Serra |
| E-mail(s) |
lidia.lopez-serra@cancer.org.uk
|
| Organization name |
Canser Research UK
|
| Department |
Chromosome segregation
|
| Street address |
44 Lincoln's Inn Fields
|
| City |
London |
| ZIP/Postal code |
WC2A 3LY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13272 |
| Series (2) |
| GSE56993 |
The Scc2NIPBL/Scc4MAU2 complex acts in sister chromatid cohesion and transcriptional regulation by maintaining nucleosome-free regions [ChIP-seq] |
| GSE56994 |
The Scc2NIPBL/Scc4MAU2 complex acts in sister chromatid cohesion and transcriptional regulation by maintaining nucleosome-free regions. |
|
| Relations |
| BioSample |
SAMN02732232 |
| SRA |
SRX523902 |
