|
| Status |
Public on Aug 24, 2015 |
| Title |
CSL ChIPSeq_HomeMade Ab |
| Sample type |
SRA |
| |
|
| Source name |
primary dermal fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
body site: abdomen skin
passage: 4-6
antibodies: CSL (Eurogentech, Seraign, Belgium - Affinity purified rabbit polyclonal -Epitopes: aa 209-224, aa 426-440 )
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin from 10 milions fixed cells was fragmented to a size range of 100–300 bases with a Diagenode Bioruptor. Solubilized chromatin was immunoprecipitated with two different antibody against CSL. Antibody–chromatin complexes were pulled-down using protein A-sepharose, washed and then eluted. After cross-link reversal and proteinase K treatment, immunoprecipitated DNA was extracted with phenol-chloroform, ethanol precipitated, and treated with RNase.
ChIPed DNA was quantified by fluorometry on the Qubit system (Invitrogen). A total of 10 ng DNA were used for library preparation using NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina, as recommended by the manufacturer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
5ug Ab / 1*10^6 cells
|
| Data processing |
ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Aligner with default parameters
peaks were called using MACS software version 1.4 with default parameter
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated by MACS as output of the analysis
|
| |
|
| Submission date |
Jul 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Paola Ostano |
| Organization name |
Fondazione Edo ed Elvo Tempia
|
| Street address |
via Malta 3
|
| City |
Biella |
| ZIP/Postal code |
13900 |
| Country |
Italy |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE59942 |
Physical and functional CSL-p53 interactions underlie control of cancer stromal cell evolution [ChIP-seq] |
| GSE65474 |
Physical and functional CSL-p53 interactions underlie control of cancer stromal cell evolution |
|
| Relations |
| BioSample |
SAMN02947373 |
| SRA |
SRX666593 |
