Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PML

Cell type

Cell type Class
Epidermis
Cell type
NHDF
Primary Tissue
Skin
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
NHDF
cell type
Normal Human Dermal Fibroblasts (NHDF)
chip antibody
PML antibody conjugated with horse-radish peroxidase (PG-M3, sc-966 HRP, Santa Cruz)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were scraped off in PBS containing 0.5% BSA and collected into a 50-mL Eppendorf tube. Pellet cells at 2,000 rpm for 8 min, and transfer cells into 1.5 mL tubes. Cells were lysed in sonication buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS, 1 mM PMSF, cocktail) and sonicated using Bioruptor (Diagenode). The supernatant of Lysate was diluted at 1:10 using RIPA buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Na-doxycholate, cocktail), and incubated with Dynabeads M-280 streptavidin (11206D, Thermo Fisher Scientific) for affinity purification. The beads were washed once with low salt buffer (150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0), once with high salt buffer (500 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0), once with LiCl buffer (250 mM LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0), and twice with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Beads were collected into new EP tubes with TE buffer and incubated on a Mixing Block at 65 ℃ overnight at 1,000 rpm to reverse the formaldehyde cross-links. The supernatant was incubated with 200 ng/μL of RNase A at 37 ℃ for 1 h and then 200 ng/μL of proteinase K at 55 ℃ for 2 h. DNA was extracted with phenol and precipitated with ethanol using 30 μg glycogen (10901393001, Roche) as the carrier. DNA pellet was dissolved in TE buffer Libraries were prepared according to Illumina's instructions accompanying the NEBNext® Ultra™ DNA Library Prep Kit. Libraries were sequenced on an Illumina HiSeq™ 2500 platform with 6G base PE150 reads.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
37251443
Reads aligned (%)
90.4
Duplicates removed (%)
48.8
Number of peaks
418 (qval < 1E-05)

hg38

Number of total reads
37251443
Reads aligned (%)
92.5
Duplicates removed (%)
48.1
Number of peaks
1149 (qval < 1E-05)

Base call quality data from DBCLS SRA