|
| Status |
Public on Jul 10, 2010 |
| Title |
RAP1_ko2 RAP1-Chip-seq |
| Sample type |
SRA |
| |
|
| Source name |
embryonic fibroblast
|
| Organism |
Mus musculus |
| Characteristics |
antibody: RAP1
|
| Growth protocol |
SV40-large T immortalized mouse embryonic fibroblast were grown on DMEM supplemented with fetal calf serum and with puromycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and RAP1-DNA complexes were isolated with antibody. Illumina's "ChIP Sequencing Sample Prep Guide" (part # 11257047 Rev. A) was followed for library preparation. Briefly, DNA was a) end-repaired by T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase; b) treated with Klenow exo (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base; c) ligated to Illumina's adapters by T4 DNA ligase; d) PCR amplified with Illumina primers for 18 cycles. Library was electrophoresed on agarose gel and a fraction of 200+/-25 bp was extracted. The purified DNA was subsequently applied to an Illumina flow cell for cluster generation. Clusters were sequenced on the Genome Analyzer IIx following manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
mixed background
Chromatin IP against RAP1
|
| Data processing |
Alignment: Sequence reads were mapped to the mm9 mouse assembly genome (NCBI m37, April 2007) using the Illumina Genome Analyzer Pipeline 1.4.0 [default ELAND_SEED_LENGTH 32, which allows for no more than 2 mismatches within the seed].
Peaks: Peak detection was performed with the CisGenome algorithm (http://www.biostat.jhsph.edu/~hji/cisgenome/), Processed files include peaks for (WT_1+WT_2) vs (RAP1_ko1+RAP1_ko2)
|
| |
|
| Submission date |
Mar 12, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Paula Martinez |
| E-mail(s) |
pmartinez@cnio.es
|
| Organization name |
CNIO
|
| Street address |
Melchor Fernandez Almagro 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE20867 |
Genome-wide maps of RAP1 binding sites. |
|
| Relations |
| SRA |
SRX018508 |
| BioSample |
SAMN00010686 |
