Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HMGB2

Cell type

Cell type Class
Lung
Cell type
Lung fibroblasts
NA
NA

Attributes by original data submitter

Sample

source_name
fetal lung fibroblast cells
cell type
fetal lung fibroblast cells
donor
single donor
genotype
WT
treatment
proliferating
chip antibody
alpha-HMGB2, ab67282, Abcam, lot# GR149806

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For each batch of ChIP experiments approx. 25 million cells, cultured to >80% confluence in 15-cm dishes, were crosslinked in 15 mM EGS/PBS (ethylene glycol bis(succinimidyl succinate); Thermo Scientific) for 20 min at room temperature, followed by fixation for 40 min at 4°C in 1% PFA. From this point onwards, cells were processed using the ChIP-IT High Sensitivity kit (Active motif) as per manufacturer’s instructions. Chromatin was sheared to 200-500 bp fragments on a Bioruptor Plus (Diagenode; 2x 9 cycles of 30 sec on and 30 sec off, at the highest power setting), and immuno-precipitation was carried out by adding 4 μg of the appropriate antiserum (HMGB1: 4F10, DSHB, HMGB2: ab67282, Abcam; CTCF: 61311, Active motif) to approx. 30 μg of chromatin and incubating on a rotaror overnight at 4°C in the presence of protease inhibitors. Following addition of protein A/G agarose beads and washing, DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research). DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 20 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg19

Number of total reads
51813595
Reads aligned (%)
116.3
Duplicates removed (%)
36.7
Number of peaks
2590 (qval < 1E-05)

hg38

Number of total reads
51813595
Reads aligned (%)
117.3
Duplicates removed (%)
36.4
Number of peaks
2864 (qval < 1E-05)

Base call quality data from DBCLS SRA