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Sample GSM2178295 Query DataSets for GSM2178295
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
 
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
 
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

Supplementary file Size Download File type/resource
GSM2178295_CTCF_1_ChIP_COLO829_peaks.bed.gz 382.7 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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