|
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 |