|
Status |
Public on Mar 13, 2023 |
Title |
DLD-1 Clone 12 |
Sample type |
SRA |
|
|
Source name |
DLD-1 Cells
|
Organism |
Homo sapiens |
Characteristics |
cell type: neo-DLD + CENP-A C-H3 - p6-derived clones - Clone 12
|
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
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|
|
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 |
SAMN22959149 |
SRA |
SRX13025638 |