GSM5510507: CTCF pull down for PDX sample 1179; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
TFs and others
Antigen
CTCF
Cell type
Cell type Class
Others
Cell type
Xenograft
NA
NA
Attributes by original data submitter
Sample
source_name
Patient Derived Xenograft
desease state
CTCF Deletion
antibody
CTCF
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_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.