Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RUNX1

Cell type

Cell type Class
Adipocyte
Cell type
LPS141
NA
NA

Attributes by original data submitter

Sample

source_name
LPS141
cell type
liposarcoma cells
chip antibody
pan-RUNX (Abcam, #ab92336)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed by following a standard protocol. Briefly, cells were fixed with 1% formaldehyde for 10 min at room temperature, followed with 3 washes by cold PBS. Nuclei were extracted and re-suspended in SDS lysis buffer for 10 min on ice before sonication by Bioruptor (Diagenode). Optimal condition of sonication yielded genomic fragments around 200 to 500 bp. After sonication, cell debris was removed by centrifugation (13,000 rpm, 10 min). Supernatant was then pre-cleared and incubated with magnetic beads (Invitrogen Dynabeads) conjugated with specific antibodies (Supplementary Table 5). After overnight incubation, magnetic beads were washed stepwise with cold low salt wash buffer, high salt wash buffer, LiCl wash buffer and TE buffer. Bound DNA was eluted, reverse-crosslinked, and purified by QIAquick PCR purification kit (Qiagen). Standard Illumina library preparation protocol

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
45047412
Reads aligned (%)
72.8
Duplicates removed (%)
25.4
Number of peaks
1918 (qval < 1E-05)

hg38

Number of total reads
45047412
Reads aligned (%)
74.7
Duplicates removed (%)
24.1
Number of peaks
1930 (qval < 1E-05)

Base call quality data from DBCLS SRA