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Sample GSM5510507 Query DataSets for GSM5510507
Status Public on Apr 29, 2023
Title CTCF pull down for PDX sample 1179
Sample type SRA
 
Source name Patient Derived Xenograft
Organism Homo sapiens
Characteristics desease state: CTCF Deletion
antibody: CTCF
Growth protocol Viably frozen diagnostic patient samples or patient-derived xenograft (PDX) cells were thawed
Extracted molecule genomic DNA
Extraction protocol ChIP-seq was performed according to the SimpleChIP® Enzymatic Chromatin IP kit #9003 (Cell Signaling Technologies, Danvers, MA) procedure. The chromatin was sheared using the Biorupter Pico (Diagenode, Liege, Belgium; 7 cycles of 30’ on, 30’ off). After sonication, samples were divided and ~4x10e6 cells were used for each ChIP experiment. Antibodies were added to concentrations as recommended by the manufacturer and incubated overnight at 4°C under continuous rotation. Antibodies used are anti-CTCF (3418S) (Cell Signaling Technologies), anti-SMC3 (ab9263) (Abcam, Cambridge, UK) and normal rabbit IgG #2729 (Cell Signaling Technologies). DNA was pelleted with ChIP-grade Protein G Magnetic Beads #9006 (Cell Signaling Technologies) and washed according to the manufacturer’s protocol. After reverse cross-linking, DNA was purified with spin columns from the SimpleChIP kit or the Qiaquick PCR Purification Kit (Qiagen, Hilden, Germany). DNA concentrations were measured using the Qubit HS DNA sensitivity kit (ThermoFischer, Waltham, MA).
Libraries were prepared using the NEXTflex™ Rapid DNA Sequencing Kit (Bio Scientific). Samples were PCR amplified, checked for size and the absence of adaptor dimers on 2% agarose gel. Barcoded libraries were sequenced for 75 bp at a single end using the Illumina NextSeq500 sequencer.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Reads were aligned to CRCh37, using BWA with default settings.
Peakcalling was done with MACS2, version 2.1.1.20160309, with the setting for narrowPeak calling. A q-value of 0.01 was applied while other settings were kept at default
Genome_build: CRCh37
Supplementary_files_format_and_content: narrowPeak peak text files
 
Submission date Aug 10, 2021
Last update date Apr 29, 2023
Contact name Rico Hagelaar
E-mail(s) [email protected]
Organization name Princess Maxima Center
Street address Heidelberglaan 25
City Utrecht
ZIP/Postal code 3584CS
Country Netherlands
 
Platform ID GPL18573
Series (2)
GSE181759 Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia [CTCF_ChIPseq]
GSE182317 Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia
Relations
BioSample SAMN20693636
SRA SRX11704512

Supplementary file Size Download File type/resource
GSM5510507_1179CTCF_peaks.narrowPeak.gz 591.9 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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