Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

Cell type

Cell type Class
Blood
Cell type
TEX
NA
NA

Attributes by original data submitter

Sample

source_name
TEX_MTCH2_KD_C646
cell line
TEX
cell type
Acute Myeloid leukemia cell line
genotype/variation
MTCH2 knockdown
treatment
C646 (5 µM) for 3 days
chip antibody
H3K27ac (Abcam#ab4729, Lot# GR3231937-1)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27ac antibody. Samples were prepared as outlined by Takara Bio USA Inc's ThruPLEX DNA-seq Kit user guide. Briefly, samples were normalized to 10ng of DNA input and topped up to 10ul with nuclease-free water. Samples were then mixed with 3ul of template preparation master mix and incubated at 22°C for 25 minutes, then 55°C for 20 minutes in a Veriti 96-well thermocycler (Thermo Fisher). Following template preparation, samples were mixed with 2ul of library synthesis master mix and incubated at 22°C for 40 minutes on the same cycler. Samples were prepared for library amplification as outlined in the user guide and indexed individually. From here, PCR cycles were optimized by adding 0.75ul of 10x SYBR green I nucleic acid gel stain (Thermo Fisher) to each sample. Once mixed, 10ul from each sample was removed and run on a CFX96 Touch Real-Time PCR cycler (Bio-Rad). Samples were normalized to 1/3 of their amplification curve and amplified on a Veriti 96-well thermocycler. Samples were topped up to 50ul with nuclease-free water prior to bead cleanup with AMPure XP beads (Beckman Coulter). Final library sizing and QC was evaluated on Agilent's high sensitivity DNA kit run on the 2100 Bioanalyzer (Agilent Technologies).

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
57955729
Reads aligned (%)
97.5
Duplicates removed (%)
14.7
Number of peaks
23493 (qval < 1E-05)

hg19

Number of total reads
57955729
Reads aligned (%)
96.9
Duplicates removed (%)
15.0
Number of peaks
22993 (qval < 1E-05)

Base call quality data from DBCLS SRA