Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Ctcf

Cell type

Cell type Class
Epidermis
Cell type
Ear dermal cells
NA
NA

Attributes by original data submitter

Sample

source_name
skin
strain
CD1/C3H
tissue
skin
cell type
ear dermal cells
age
post natal day 50
genotype
Wt/Wt
chip antibody
CTCF (Thermal Fisher,PA5-17143)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
~5-6 million dermal cells were fixed in 1% formaldehyde for 10 min at 37ºC. Crosslinked cells were lysed in lysis buffer (0.3% SDS, 50 mM Tris-HCl, pH=8.0, 20 mM EDTA, and freshly added protease inhibitors) on ice for 10 min, with vortexing every 2 min. Lysed samples were immediately subjected to 36 cycles of sonication at power 10 with a sonicator (Qsonica, Q700) to generate small chromatin fragments. 5 μg of the H3K27ac (ActiveMotif, 39133), and H3K27me3 (Millipore, 07-449), and CTCF (Thermal Fisher, PA5-17143), antibodies were used for immunoprecipitation. ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
53220983
Reads aligned (%)
96.8
Duplicates removed (%)
32.7
Number of peaks
62846 (qval < 1E-05)

mm9

Number of total reads
53220983
Reads aligned (%)
96.5
Duplicates removed (%)
32.6
Number of peaks
62836 (qval < 1E-05)

Base call quality data from DBCLS SRA