|
| Status |
Public on Mar 13, 2023 |
| Title |
DLD-1 Clone 18 |
| Sample type |
SRA |
| |
|
| Source name |
DLD-1 Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: neo-DLD + CENP-A C-H3 - p6-derived clones - Clone 18
|
| Treatment protocol |
n/a (clones and parental cells were obtained from the authors of Ly et al., Nat. Genet. 2019)
|
| Growth protocol |
DLD-1 cells were grown in RPMI supplemented with 10% FBS and 1X Pen-Strep in 100 mm dish (Corning Corning™ 100 mm TC-Treated Culture Dishes)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction was performed according to Buenrostro et. al. 2015
Library prepared according to Buenrostro et. al. 2015
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The raw reads were trimmed using fastp to remove low-quality bases from reads (quality < 20) and adapter sequences. The trimmed reads were aligned using Bowtie2 [PMID: 22388286 ] to UCSC genome assembly (hg38)
Filter aligned atac reads: 1) Reads aligning to mitochrondrial DNA were removed using the removeChrom.py script at https://github.com/harvardinformatics/ATAC-seq/blob/master/atacseq/removeChrom.py. 2) Reads with low mapping quality score (MAPQ < 15) were removed using samtools (version 1.13) view with the - q parameter set to 15.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig for visualization
|
| |
|
| Submission date |
Nov 06, 2021 |
| Last update date |
Mar 13, 2023 |
| Contact name |
Albert S Agustinus |
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Street address |
408 East 69th Street, Room 419-G
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE186589 |
Epigenetic dysregulation from chromosomal transit in micronuclei |
| GSE188346 |
Epigenetic dysregulation from chromosomal transit in micronuclei [DLD-1 ATAC-seq] |
|
| Relations |
| BioSample |
SAMN22959144 |
| SRA |
SRX13025643 |
