Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
LMNA

Cell type

Cell type Class
Epidermis
Cell type
Dermal fibroblast
NA
NA

Attributes by original data submitter

Sample

source_name
primary dermal fibroblasts
chip antibody
Santa Cruz sc-7292
passages
5-7
genotype
normal
cell type
Fibroblasts

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells (107 per ChIP) were cross-linked in suspension for 10 min in PBS containing 1% formaldehyde before quenching with 1.25 mM glycine. Cells were lysed for 30 min at 4oC on a rotator in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 1 mM PMSF, 1x protease inhibitor cocktail) adjusted to 1% SDS, and sonicated for 3 times 15 min in a Bioruptor (Diagenode) with 30 sec ON/OFF at high power to generate chromatin fragments of ~200-400 base pairs (bp). After sedimentation, chromatin (supernatant from 107 cell-equivalents) was diluted 10 times in RIPA buffer without SDS, and incubated on a rotator overnight at 4oC with 50 µg anti-lamin A/C antibody (Santa Cruz sc-7292) pre-coupled to magnetic Dynabeads Protein G (Invitrogen). An irrelevant mouse IgG was used as control. ChIP material was collected and washed 3 times in 1 ml of ice-cold RIPA buffer without protease inhibitors. The crosslink was reversed and DNA eluted for 6 h on a shaker at 37oC in elution buffer (50 mM NaCl, 20 mM Tris-HCl, pH 7.5, 5 mM EDTA, 1% SDS) containing 0.5 µg/ml RNase A and 2 µg/ml Proteinase K). DNA was purified as described, processed for library preparation. The sequencing library was prepared according to the Illumina protocol for the HSeq2500 at the Norwegian Sequencing Center.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
50398589
Reads aligned (%)
84.4
Duplicates removed (%)
13.3
Number of peaks
1407 (qval < 1E-05)

hg38

Number of total reads
50398589
Reads aligned (%)
87.2
Duplicates removed (%)
11.4
Number of peaks
1623 (qval < 1E-05)

Base call quality data from DBCLS SRA