Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

Cell type

Cell type Class
Blood
Cell type
Acute myeloid leukemia
NA
NA

Attributes by original data submitter

Sample

source_name
H3K27ac BB727 T1
cell type
Primary AML
chip antibody
H3K27ac
chip antibody vendor
Abcam, Cambridge, UK

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed using anti-H3K27ac (ab4729, Abcam) and anti-H3K9me3 (ab8898, Abcam). 10^8 cells were used for each precipitation as described by Lee et al. (2006). Cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature before the reaction was quenched with 0.125M glycine. Cell pellets were washed twice with PBS and nuclear lysates sonicated for 6 cycles using a Bioruptor® Pico (Diagenode). 10μg of antibody bound to 100μl of magnetic beads (Dynabeads Protein G, Invitrogen, Carlsbad, CA) was added to each sample and immunoprecipiation performed overnight on a rotator at 4°C and 20 rpm. After 5 washes with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCl), chromatin IP-bound fractions were extracted by incubating for 15 min at 65°C with elution buffer (50mM TrisHCl pH8, 10mM EDTA, 1% SDS). Crosslinking was then reversed by incubation at 65°C for 6 hours. RNaseA (1mg/ml) and proteinase K (20mg/ml) were added to eliminate RNA and protein from the samples. DNA was extracted using phenol:chloroform:isoamyl alcohol and precipitated by adding 2 volumes of ice-cold 100% ethanol, glycogen (20μg/μl), 200mM NaCl and freezing at -80°C for at least 1 hour. Pellets were washed with 70% ethanol and eluted in 50μl 10mM TrisHCl pH8.0. Libraries were prepared for sequencing using a Microplex Library Preparation Kit (Diagenode). 200-800bp fragments were selected using AMPure beads (Beckman Coulter) and quantified by qPCR with a KAPA Library Quantification Kit (Kapa Biosystems).

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
38928532
Reads aligned (%)
95.9
Duplicates removed (%)
19.8
Number of peaks
37021 (qval < 1E-05)

hg19

Number of total reads
38928532
Reads aligned (%)
95.7
Duplicates removed (%)
19.8
Number of peaks
36890 (qval < 1E-05)

Base call quality data from DBCLS SRA