Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K9ac

Cell type

Cell type Class
Blood
Cell type
ACH-2
NA
NA

Attributes by original data submitter

Sample

source_name
ACH2
cell line
ACH2
cell type
HIV-1 latency T cell line
antibody
anti-H3K9ac
antibody manufacturer
Abcam
antibody catalog number
ab4441

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were resuspended with digestion buffer (50mM Tris-HCL, pH7.6, 1mM CaCl2, 0.2% triton X-100) and 5mM butyrate, 0.5mM PMSF, x proteinase inhibitor. The chromatins were digested with Mnase and enzyme was inactivated by adding the stop buffer (10mM Tris, pH7.6, 5mM EDTA). Pre- cleared Dynabeads Protein A (100.02D, Life Technologies, Carlsbad, CA) were bound with antibodies specific to the histone H3, tri methylated at K4 (rabbit polyclonal, ab8580, Abcam, Cambridge, UK) and acetylated at K9 (rabbit polyclonal, ab4441, Abcam, Cambridge, UK). Digested chromatins were incubated with bead-bound antibody for overnight in RIPA buffer (10 mM Tris, pH7.4, 1mM EDTA, 0.1% SDS, 0.1% Na-Deoxycholate, and 1% Triton X- 100). Bead complex was captured by magnetic stand and washed sequentially twice with RIPA buffer, RIPA + 0.3 M NaCl, and LiCl buffer (0.25 M LiCl, 0.5% NP40, 0.5% Na- Deoxycholate) and once with 1X TE + 0.2% Triton X-100, and 1X TE. Proteinase K digestion and phenol/chloroform extraction was performed to isolate the DNA. Sequencing libraries were manually generated for high-throughput sequencing. Either end of DNA strands was filled using the Epicentre DNA END-Repair kit (Epicentre Biotechnologies, Madison, WI). Adenine was added at 3’ ends by Taq DNA polymerase (New England Biolabs, Beverly, MA) under dATP conditions. Illumina’s adaptor oligomers was ligated at both ends using Quick Ligation kit (Qiagen, Germantown, MD). After purified twice, DNA libraries are amplified using Solexa primers (Illumina, San Diego, CA) and Phusion PCR master mix (Thermo Scientific, Hudson, NH).

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
12459171
Reads aligned (%)
76.1
Duplicates removed (%)
31.9
Number of peaks
23141 (qval < 1E-05)

hg19

Number of total reads
12459171
Reads aligned (%)
75.9
Duplicates removed (%)
32.0
Number of peaks
23116 (qval < 1E-05)

Base call quality data from DBCLS SRA