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Sample GSM5481079 Query DataSets for GSM5481079
Status Public on Mar 09, 2022
Title SW480_PCAT2_KI
Sample type SRA
 
Source name SW480 colon cancer cells
Organism Homo sapiens
Characteristics cell type: SW480 colon cancer cells knocked-in with PCAT2 gene
Extracted molecule genomic DNA
Extraction protocol Cells were treated with Proteinase K and 1% SDS overight at 55C and genomic DNA was isolated using PCI method.
Sequencing libraries were generated using Illumina TruSeq V3 protocol and subject to 51 bp single-end sequencing on Illumina HiSeq2000.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Data processing Library strategy: DNase-seq
Base-calling with Illumina run time analysis software 1.12.4.2
Alignment to hg38 using Casava Eland extended
DNase hypersensitive sites were identified as hotspots using DNase2Hotspots.
Genome_build: hg38
Supplementary_files_format_and_content: BedGraph
 
Submission date Jul 27, 2021
Last update date Mar 09, 2022
Contact name Songjoon Baek
Organization name NCI / NIH
Department CCR
Lab LRBGE
Street address 41 Library Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL11154
Series (2)
GSE180957 Oncogenic lncRNAs alter epigenetic memory at a fragile chromosomal site in human cancer cells [WGS]
GSE180959 Oncogenic lncRNAs alter epigenetic memory at a fragile chromosomal site in human cancer cells
Relations
BioSample SAMN20437057
SRA SRX11570549

Supplementary file Size Download File type/resource
GSM5481079_sw480_pcat2_insert_only.bed.gz 29.2 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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