Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Blood
Cell type
GM12878
Tissue
blood
Lineage
mesoderm
Description
B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

Attributes by original data submitter

Sample

source_name
GM12878
biomaterial_provider
GM12878
cell type
B-lymphocyte
chip antibody
H3K4me3 (Millipore, catalog# 07-473, lot# 2289139)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked for 5 min with 1% formaldehyde at room temperature prior to quencing with 125mM glycin. Cross-linked cells were sonicated using Covaris S2 sonicator for 14 min with 5% duty, Intensity 3 and Bursts 200. The sonicated lysate was centrifuged at a speed of 14000×g for 10 min under 4°C. The cleared chromatin (10000 cells per 100 µl) in the supernatant was transferred to a new low-bind Eppendorf tube for subsequent microfluidic ChIP. The ChIPed and input DNA was constructed into libraries by using the ThruPLEX FD Kit (Rubicon Genomics, Ann Arbor, MI, USA). During the amplification step, 11cycles was needed to get enough library from input DNA without over-amplification. 12~13 cycles is needed for ChIPed DNA extracted from 10000 cells. 14~15 cycles is normally required for ChIPed DNA from 1000 or less cells.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
15258992
Reads aligned (%)
82.8
Duplicates removed (%)
81.7
Number of peaks
103 (qval < 1E-05)

hg19

Number of total reads
15258992
Reads aligned (%)
82.2
Duplicates removed (%)
83.2
Number of peaks
114 (qval < 1E-05)

Base call quality data from DBCLS SRA