|
| Status |
Public on Mar 09, 2022 |
| Title |
SW_Cntrl_CpA_R2 |
| Sample type |
SRA |
| |
|
| Source name |
SW480 colon cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: SW480 colon cancer cells
chip antibody: CENP-A (Custom)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For CENP-A ChIP, the samples were crosslinked with 1% formaldehyde for 10 minutes at room temperature. After crosslinking, chromatin was extracted overight followed by incubation in CENP-A a/b overnight and a/b bound DNA was captured using Protein A/G tagged magnetic beads (Dynabeads). The DNA was extracted using PCI menthod. Samples were treated with RNase I followed by one more PCI to isolate RNA free DNA. DNA fragments with a size range of 150 to 300 base pairs.
Sequencing libraries were generated using Illumina TruSeq V3 protocol and subject to 51 bp single-end sequencing on Illumina HiSeq2000.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base-calling with Illumina run time analysis software 1.12.4.2
Alignment to mm9 using Casava Eland extended
ChIP-seq binding sites were identified as hotspots after adjustment using the input DNA control.
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) |
| GSE180938 |
Oncogenic lncRNAs alter epigenetic memory at a fragile chromosomal site in human cancer cells [ChIP-seq] |
| GSE180959 |
Oncogenic lncRNAs alter epigenetic memory at a fragile chromosomal site in human cancer cells |
|
| Relations |
| BioSample |
SAMN20437012 |
| SRA |
SRX11570203 |
