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Sample GSM5678040 Query DataSets for GSM5678040
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

Supplementary file Size Download File type/resource
GSM5678040_Clone_18.GRCh38.filter.bam.bigWig 391.1 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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