Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

Cell type

Cell type Class
Blood
Cell type
CH12
Tissue
Blood
Lineage
cellLine
Description
B-cell lymphoma (GM12878 analog)

Attributes by original data submitter

Sample

source_name
CH12 B cell line
genotype
WT
cell type
lymphoma cell line
chip antibody
Abcam. ab4729

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Promoter Capture HiC-Seq: we used the same protocol at Montefiori et al., (Elife, 2018 Jul 10; 7) BS-seq: Genomic DNA was isolated from 3×106 cells using Qiagen DNeasy blood and tissue kit (Cat #: 69506). The bisulfite conversion was performed using the EZ DNA Methylation-Gold™ Kit (Cat #: D5005) from Zymo Research. Whole-genome bisulfite sequencing libraries were prepared from 50 ng converted DNA using Illumina TruSeq® DNA Methylation Kit (Cat #: EGMK91324), which was performed following the manufacturer's protocol. Promoter Capture HiC-seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 100 cycles of sequencing data were acquired on the HiSeq 3000 (Illumina). BS-seq: standard RNA-Seq library preparation was performed following the genomic DNA protocol with 20% PhiX. 50 cycles of sequencing data were acquired on HiSeq 3000 (Illumina)

Sequencing Platform

instrument_model
Illumina HiSeq 3000

mm10

Number of total reads
18052666
Reads aligned (%)
99.2
Duplicates removed (%)
18.4
Number of peaks
21687 (qval < 1E-05)

mm9

Number of total reads
18052666
Reads aligned (%)
99.1
Duplicates removed (%)
18.4
Number of peaks
21699 (qval < 1E-05)

Base call quality data from DBCLS SRA