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
cell type
B-lymphocyte
chip antibody
H3K4me3 (07-473, Millipore,Billerica, MA, USA)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The procedure was different for preparing sonicated chromatin from 100 or 600 cells directly. Cells were counted with a hematocytometer and 100/600 cells were transferred to a 1.5 ml LoBind Eppendorf tube containing 10 µl 10% FBS in PBS. Cells were then cross-linked for 5 min at room temperature by adding 0.625 µl 16% formaldehyde to yield a final concentration of 1%. Cross-linking was quenched by adding 1.25 µl 2.5 M glycine for 5 min at room temperature. The cross-linked sample was then diluted using 120 µl Covaris sonication buffer (to give a total volume of 130 µl) and sonicated with a Covaris E220 sonicator for 8 min with 5% duty, 105 peak incident power and 200 cycles per burst in a Covaris microtube (520045, Covaris). The sonicated lysate was centrifuged at 14000×g for 10 min at 4°C. Sonicated chromatin in the supernatant was transferred to a new 1.5 ml LoBind Eppendorf tube for MOWChIP-Seq. 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
19175864
Reads aligned (%)
61.5
Duplicates removed (%)
74.2
Number of peaks
153 (qval < 1E-05)

hg19

Number of total reads
19175864
Reads aligned (%)
60.9
Duplicates removed (%)
75.6
Number of peaks
131 (qval < 1E-05)

Base call quality data from DBCLS SRA