Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RUNX1

Cell type

Cell type Class
Pluripotent stem cell
Cell type
iPS cells
NA
NA

Attributes by original data submitter

Sample

source_name
human iPSCs
age
day 18
chip antibody
RUNX1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Formaldehyde fixed cell pellets were suspended into 0.5ml of sonication buffer (0.1% SDS, 1% Triton, 1 mM EDTA, 16.7 mM Tris pH 8, 167 mM NaCl) with 1x proteasome inhibitor cocktail (Millipore, #535140). The samples were sonicated with Bioruptor Pico (Diagenode) for 12 cycle with 30s on/off. ChIP was performed at 4°C O/N with 1 mg of chromatin DNA sample, 1.5 mg of antibody to RUNX1 (Abcam, ab23980) or normal Rabbit IgG (Santa Cruz Biotech, sc-2027), 20 mL of magnetic Protein A/G beads (NEB). The beads were washed twice with each following buffer: high salt buffer (0.1% SDS, 1 % Triton, 2 mM EDTA, 20 mM Tris pH 8, 500 mM NaCl); Li buffer (0.25 M LiCl, 1% NP40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris pH 8); Tris (pH 8). The beads were suspended in 13 ml of H2O, 15 ml of TD and 2 ml of TDE1 (Illumina, 15028212) and incubated at 37°C with constant shaking for 1 h. The beads were washed twice with TE (pH 8), resupsended in 20 ml buffer (100 mM Tris pH 8, 1mM EDTA, 0.1% SDS, 250 mM NaCl) with 1 ml of Proteinase K (Invitrogen, AM2546) and incubated at 65°C for 4 h. The DNA in the supernatant was purified with 2x Ampure beads (Beckman). The purified DNA was used for PCR for 12 cycles with a pair of P7 and P5 index primers

Sequencing Platform

instrument_model
Illumina HiSeq 1500

hg19

Number of total reads
19715927
Reads aligned (%)
80.7
Duplicates removed (%)
10.1
Number of peaks
717 (qval < 1E-05)

hg38

Number of total reads
19715927
Reads aligned (%)
83.8
Duplicates removed (%)
8.1
Number of peaks
885 (qval < 1E-05)

Base call quality data from DBCLS SRA