Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K9ac

Cell type

Cell type Class
Blood
Cell type
Acute myeloid leukemia
NA
NA

Attributes by original data submitter

Sample

source_name
AML cells
genotype
Gfi1 36S/36S
antibody
H3K9Ac (ab4441; Abcam)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 1% formaldehyde. Cell lysis was performed using the following buffers: total cell lysis - 5mM PIPES pH 8, 85mM KCl, 0.5% NP-40, 1X protease inhibitor cocktail, 1mM PMSF, and nuclear lysis – 50mM Tris, 10mM EDTA, 1% SDS, 1X protease inhibitor cocktail, 1mM PMSF. After sonication (Covaris E220 sonicator), immunoprecipitation was performed using Protein A/G Dynabeads (Life Technologies) Sequencing libraries were prepared from immunoprecipitated chromatin using the TruSeq DNA kit from Illumina according to the manufacturer’s instructions and sequenced using the TruSeq PE Clusterkit v3-cBot-HS

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
105582912
Reads aligned (%)
39.9
Duplicates removed (%)
59.3
Number of peaks
13050 (qval < 1E-05)

hg19

Number of total reads
105582912
Reads aligned (%)
39.6
Duplicates removed (%)
59.7
Number of peaks
13368 (qval < 1E-05)

Base call quality data from DBCLS SRA