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Sample GSM2224594 Query DataSets for GSM2224594
Status Public on Feb 15, 2017
Title SW480_DNaseI
Sample type SRA
Source name Colorectal cancer cell line
Organism Homo sapiens
Characteristics cell line: SW480
cell type: Colorectal cancer cell line
genetic modification: none
library strategy: DNase I-seq
Treatment protocol COLO320 isogenic lines (G/G, A/A) were generated by CRISPR-CAS9 site specific mutation. COLO320 (G/A) was mocked with the empty vector.
Growth protocol DMEM medium supplemented with 10% fetal bovine, 100 U/ml penicillin and 100 µg/ml streptomycin.
Extracted molecule genomic DNA
Extraction protocol Libraries were purified using QIA quick column (DNase I-seq, ATAC-seq, Targeted RNA-/DNA-seq, and 4C-seq), QIA minElute column (ChIP-seq) or SPRI beads (ATAC-seq).
Libraries were prepared according to Illumina's instructions.
Library strategy DNase-Hypersensitivity
Library source genomic
Library selection DNAse
Instrument model Illumina HiSeq 2000
Description 0.12 Unit of DNase I (Roche) at 37 °C for 15 min; library size: 200 bp; single-end sequencing.
Data processing Illumina Casava software 1.8.2 used for basecalling of Hiseq2000 and NextSeq 500 data.
Library strategy (H3K27ac ChIP-seq): mapping: bwa-aln (0.7.10-r789), peak calling: macs2 (version q=0.01 --broad option
Library strategy (ChIP-seq/Dnase I-seq/Target RNA or DNA-seq): mapping: bwa-aln (0.7.10-r789), peak calling: macs2 (version q=0.01; Allele-specific read counts: IGV (version 2.3)
Library strategy (ATAC-seq): mapping: bwa-mem (0.7.10-r789), peak calling: macs2 (version q=0.01; Allele-specific read counts: IGV (version 2.3)
Library strategy (4C-seq): mapping: bwa-aln (0.7.10-r789), data analysis: R package 'r3Cseq' (version 3.3)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using "bam2bw" script (, bedGraph files were generated using R package "r3Cseq".
Submission date Jul 01, 2016
Last update date Nov 11, 2022
Contact name Ning Qing Liu
Organization name Erasmus University Medical Center Rotterdam
Department Hematology
Street address Wytemaweg 80
City Rotterdam
ZIP/Postal code 3015 CN
Country Netherlands
Platform ID GPL11154
Series (1)
GSE83968 The non-coding variant rs1800734 enhances DCLK3 expression through long-range interaction and promotes colorectal cancer progression
BioSample SAMN05346316
SRA SRX1892845

Supplementary file Size Download File type/resource 169.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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