|
| Status |
Public on Mar 12, 2014 |
| Title |
beta-catenin ChIP |
| Sample type |
SRA |
| |
|
| Source name |
SW480
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SW480
cell type: Colon cancer
passage: 10 to 15
antibody: Anti-beta catenin(H102)
antibody vendor: Santa Cruz/sc-7199
|
| Treatment protocol |
None
|
| Growth protocol |
SW480 cells were grown in DMEM supplemented with 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After cross-linking, cells were scraped and sonicated utilizing Diagenode Bioruptor at High setting and cycling 30 seconds ON, 30 seconds OFF. Beta-catenin-DNA complexes were isolated with lab generated anti-beta-catenin antibody .
ChIP DNA fragment ends were repaired and phosphorylated using Klenow, T4 DNA Polymerase and T4 Polynucleotide Kinase. Next, an ‘A’ base was added to the 3’ end of the blunted fragments, followed by ligation of Illumina adapters via T-A mediated ligation. The ligated products were size selected by gel purification and then PCR amplified using Illumina primers. The library size and concentration were determined using an Agilent Bioanalyzer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ChIP-seq data with an immunoprecipitated sample using an antibody against beta-catenin
|
| Data processing |
Alignment with bowtie/0.12.8 using hg19 as reference genome and default parameters
Peak calling with macs/1.4.2 using mfold:10,30, pvalue cutoff: 1.00e-05, bandwidth: 300 to generate peak calling model
samtools/0.1.18 and bedtools/2.15.0 used to interconvert between file formats
Genome_build: hg19 reference assembly
Supplementary_files_format_and_content: bed and wiggle files
|
| |
|
| Submission date |
Jan 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Kazuhide Watanabe |
| E-mail(s) |
kazuhide.watanabe@riken.jp
|
| Phone |
+81-045-503-9222
|
| Organization name |
Riken
|
| Department |
Center for Integrative Medical Sciences
|
| Street address |
1-7-22 Suehiro-cho Tsurumi-ku
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE53927 |
Identification of beta-catenin binding regions in SW480 cells |
|
| Relations |
| BioSample |
SAMN02571058 |
| SRA |
SRX423971 |
