Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
LMNA

Cell type

Cell type Class
Adipocyte
Cell type
Pre-adipocytes
NA
NA

Attributes by original data submitter

Sample

source_name
Pre-adipocytes from liposuction material, cultured, 3 days after adipogenic stimulation (Day 3).
passages
Cells in passage 5-7
initial cell type
pre-adipocytes
cell differentiation status
Non-proliferating, differentiated for 3 days
chip antibody
anti-Lamin A/C Santa Cruz sc7292

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq: Cells (10e7 cells/ChIP) were harvested and fixed with 1% formaldehyde for 10 min before quenching with 125 mM glycine. Cells were lysed for 30 min at 4C 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% deoxycholate, 1 mM PMSF, protease inhibitor cocktail) adjusted to 1% SDS, and sonicated 3 times 15 min in a Bioruptor® (Diagenode). After sedimentation at 10,000 g for 10 min, the supernatant was collected and diluted 10x in RIPA buffer without SDS to constitute input chromatin. Chromatin was incubated overnight at 4oC on a rotator with antibodies coupled to magnetic Dynabeads Protein G. ChIP samples were washed 3 times in ice-cold RIPA buffer. Crosslinks were reversed and DNA eluted for 6 h at 37C in 50 mM NaCl, 20 mM Tris-HCl pH 7.5, 5 mM EDTA, 1% SDS, 0.5 µg/ml RNase A, and 2 µg/ml Proteinase K added twice. DNA was purified and dissolved in H2O. Sequencing library was prepared according to the Illumina protocol, and sequenced on an Illumina HiSeq2500 at the Norwegian Sequencing Center.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
22551567
Reads aligned (%)
80.9
Duplicates removed (%)
16.5
Number of peaks
945 (qval < 1E-05)

hg38

Number of total reads
22551567
Reads aligned (%)
83.4
Duplicates removed (%)
14.8
Number of peaks
850 (qval < 1E-05)

Base call quality data from DBCLS SRA