|
| Status |
Public on Feb 20, 2023 |
| Title |
control biological replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
cell type: breast
chip antibody: anti-MTF1
treatment: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Epicypher CUT&RUN protocol (version 1.6, August 2020)
Illumina NEBNext Ultra II ChIP-Seq sample kit, according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
FASTQs were adaptor trimmed using Bbtools bbduk (v 38.87) using supplied adaptor reference file adaptors.fa with parameters ktrim=r k=23 mink=11 hdist=1 tpe tbo
FASTQs were aligned to hg38 reference genome using Bowtie2 *v 2.3.4.1) sam files were converted to bam files and biological replicates were merged using samtools v. 1.8
bigwig files were generated for merged bam files using deeptools Bamcoverage
Peak calling performed using Epic2 v. 0.0.50 using default parameters with merged bam files as --treatment using --genome hg38
Assembly: hg38
Supplementary files format and content: bigwig files contain coverage tracks using CPM
Supplementary files format and content: peak calling bed files for both control and cadmium treated samles
Library strategy: CUT&RUN
|
| |
|
| Submission date |
Jan 10, 2023 |
| Last update date |
Feb 20, 2023 |
| Contact name |
Gregory Wright |
| Organization name |
University of Colorado Anschutz Medical Campus
|
| Street address |
12800 East 19th Ave
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE222587 |
CUT&RUN in cadmium resistant breast cancer MDA-MB-231 cells |
|
| Relations |
| BioSample |
SAMN32668227 |
| SRA |
SRX18994995 |
