|
Status |
Public on Dec 13, 2016 |
Title |
CTCF_1_ChIP_COLO829 |
Sample type |
SRA |
|
|
Source name |
COLO829 cells
|
Organism |
Homo sapiens |
Characteristics |
chip antibody: CTCF (Millipore 07-729)
|
Growth protocol |
COLO829 cells were cultured in RPMI medium supplemented with 10% fetal bovine serum, glutamax and penicillin/streptomycin.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Early passage cells were cross-linked in 1% formaldehyde and nuclei were extracted. Nuclei were lysed and DNA was sonicated for 6 hours in a Diagenode Pico Bioruptor (30 seconds on/ 30 seconds off). Chromatin was divided across two samples and incubated with polyclonal rabbit anti-CTCF antibody (Millipore 07-729) and rabbit immunoglobulin G (IgG; Sigma I5006) respectively. DNA was then purified, size selected and sequenced. Library construction was performed as per Illumina protocol Rev A 11257047
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|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
Base-calling: Illumina Real Time Analysis, scoring metric v1.5 Raw reads were prefiltered to remove all reads that have 3 or more bases with a quality score of less than Q13 All provided cleaned data have had adaptors clipped except the small RNA-seq data which still contains 5' adaptor: 5'-TGGAATTCTCGTATGCCGTCTTCTGCTTG Alignments were all made against hg19 using bwa (0.7.5a-r405) with default parameters Peaks were called using the Homer Suite with ‘factor’ as the style option and IgG as the background control Genome_build: hg19 Supplementary_files_format_and_content: Bed files contain coordinates for CTCF peak calls
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|
|
Submission date |
May 26, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Rebecca C Poulos |
E-mail(s) |
rebecca.poulos@unsw.edu.au
|
Organization name |
UNSW Australia
|
Street address |
Level 2 ACP UNSW Australia
|
City |
Sydney |
State/province |
NSW |
ZIP/Postal code |
2052 |
Country |
Australia |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE81945 |
Functional mutations form at CTCF-cohesin binding sites in melanoma due to uneven nucleotide excision repair across the motif |
|
Relations |
BioSample |
SAMN05179548 |
SRA |
SRX1801654 |