GSM7226970: K3P CTCF D3 rep2; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
TFs and others
Antigen
CTCF
Cell type
Cell type Class
Epidermis
Cell type
Foreskin
MeSH Description
The double-layered skin fold that covers the GLANS PENIS, the head of the penis.
Attributes by original data submitter
Sample
source_name
Foreskin
tissue
Foreskin
cell type
cultured keratinocyte
treatment
1,25D3
chip antibody
CTCF, Diagenode C15410210, lot A2359-00234D
geo_loc_name
missing
collection_date
missing
Sequenced DNA Library
library_name
GSM7226970
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Dissected CLH or CLT tissues were homogenized and cross-linked with 1% paraformaldehyde for 8 min (H3K27ac) or for 15 min (MED1), sonicated using a ultrasonicator (Covaris) to obtain DNA fragments with an average length of 300±50 bp. Sheared chromatin was thereafter immunoprecipitated with Protein A-coated magnetic beads (Diagenode) preincubated with 4.5 microgram/IP MED1 antibody (Bethyl A300-793A) or 3 ug/IP H3K27ac antibody (ab4729, Abcam). Chromatin input samples were used as reference. Complexes were then washed and eluted from the beads with washing buffer and crosslinks were reversed by incubation at 65°C for 4 hours. Immunoprecipitated DNA along with genomic DNA (Inputs) were purified using the IPure v2 kit (Diagenode). IP efficiency was confirmed by qPCR using primers provided in the kits. Experiments were carried out in duplicates. ChIP-Seq libraries were generated using the Accel-NGS 2S Plus DNA library kits (Swift Sciences) and amplified by PCR for 11-13 cycles. High molecular weight smear was removed in the library by right side size selection using SPRI beads (Beckman Coulter). The libraries were quantified by Agilent 2100 Bioanalyzer with the high sensitivity DNA assay and sequenced on an Illumina HiSeq 4000 (UCSF Center of advanced technology) in a single strand 50 bp run.