|
| Status |
Public on Sep 01, 2016 |
| Title |
CTCF ChIP |
| Sample type |
SRA |
| |
|
| Source name |
SKOV2
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: SKOV3
chip antibody: Anti-CTCF antibody - ChIP Grade,ab70303
|
| Growth protocol |
SKOV3 cells were cultured in DMEM/H (Hyclone) containing 10% fetal bovine serum (Gibco) and 1% penicillin/streptomycin (Beyotime Biotechnology) and incubated at 37℃ in a humidified atmosphere with 5% CO2.Then harvest typically 2–3 × 106 cells per sample.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and CTCF-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~350 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 with the defaut configurations
Couverage track are generated using Deeptools'function BamCompare
Genome_build: hg19
Supplementary_files_format_and_content: BigWig file is gerated using Deeptools
|
| |
|
| Submission date |
Aug 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Bo Zhu |
| E-mail(s) |
b.davis.zhu@gmail.com
|
| Organization name |
Third Military Medical University
|
| Department |
Institute of Cancer, Xinqiao Hospital
|
| Street address |
Institute of Cancer, Xinqiao Hospital, Third Military Medical University
|
| City |
Shanghai |
| ZIP/Postal code |
400037 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE85453 |
CTCF promotes epithelial ovarian cancer metastasis by broadly controlling the expression of metastasis-associated genes |
|
| Relations |
| BioSample |
SAMN05559689 |
| SRA |
SRX2012084 |
