|
| Status |
Public on May 26, 2021 |
| Title |
DLD1_bCatenin_CHIPseq |
| Sample type |
SRA |
| |
|
| Source name |
Colon carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DLD1 colorectal cancer cell line
crispr knockout: control
chip antibody: anti-beta-catenin (Cell Signalling, #9581)
|
| Growth protocol |
Cells were cultured as adherent monolayers in Dulbecco’s Modified Eagle’s Medium (DMEM) (Sigma-Aldrich #D5796) supplemented with 10% (v/v) fetal bovine serum (Bovogen #SFBS-AU), 2mM L-glutamine (Life technologies #25030081), 100 units/mL penicillin and 0.1% (w/v) streptomycin (Life technologies #15140122) (complete DMEM, C-DMEM). Cells were grown at 37°C in a 5% CO2 humidified incubator, and passaged every 2-3 days (30-80% confluency).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on a NexSeq 500 (100 bp, single end reads).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls performed using BWA algorithm with default settings
ChIP-seq reads were aligned to the human genome (hg38) using the BWA algorithm.
The tags are extended in silico at their 3 ́- ends to a length of 200bp. To identify the density of fragments along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined.
Peaks were callled using Model-based Analysis of ChIP-Seq (MACS) to identify significant enrichments in the ChIP/IP data file when compared to the Input data file.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files contains the density of fragments in every 32-nt bin of the genome.
|
| |
|
| Submission date |
Aug 12, 2020 |
| Last update date |
May 26, 2021 |
| Contact name |
Ron Firestein |
| E-mail(s) |
[email protected]
|
| Organization name |
Hudson Institute of Medical Research
|
| Department |
CCR
|
| Lab |
Functional Genomics
|
| Street address |
21 Wright street
|
| City |
Clayton |
| State/province |
VIC |
| ZIP/Postal code |
3168 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE156081 |
Genome-scale CRISPR-Cas9 screen of Wnt/β-catenin signalling identifies therapeutic targets for Colorectal Cancer (ChIP-seq) |
| GSE156083 |
Genome-scale CRISPR-Cas9 screen of Wnt/β-catenin signalling identifies therapeutic targets for Colorectal Cancer |
|
| Relations |
| BioSample |
SAMN15801159 |
| SRA |
SRX8929135 |
