Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me2

Cell type

Cell type Class
Embryo
Cell type
Embryonic heart
NA
NA

Attributes by original data submitter

Sample

source_name
E11.5 embryonic hearts
antibody
H3K4me2
strain
C57BL/6
cell type
heart
developmental stage
E11.5
replicate
replicate 2
genotype
Mutant Tnnt2::Cre; Kmt2d(fl/fl)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-Seq Library Prep: Immunoprecipitated complexes were washed and isolated. Crosslinks were reversed overnight (65C, 0.54M NaCl). DNA was then isolated and treated with T4 DNA polymerase, E. coli Pol I large (Klenow) fragment, and T4 polynucleotide kinase to ensure all dsDNA fragments are blunt-ended with 5' phosphates. DNA then repurified and treated with Klenow 3' -> 5' exo minus and dATP to adenylate the 3' end of each fragment. DNA was repurified and ligated to Illumina TruSeq indexed adapters containing a T-overhang using T4 DNA ligase. DNA was repurified and PCR amplified using primers complimentary to the Illumina TruSeq adapter sequence. Amplified fragments between 200 and 500bp were isolated from an agarose gel and purified. This DNA was then clustered on an Illumina flow cell and sequenced on an Illumina HiSeq 2500. Both WT and mutant hearts were thawed on ice and pooled into 3 replicates of 30 hearts each. Samples were crosslinked with 1% formaldehyde, lysed with cell lysis and nuclei lysis buffer, and sonicated to shear chromatin into 200-600 bp fragments. Each replicate was further split into input and 3 samples. Chromatin immunoprecipitation was performed with 3 ug of anti-H3K4me1/2/3 antibody (Abcam) overnight with Protein G Dynabead (Life Technologies). After washing, DNA was eluted, reverse-crosslinked and precipitated with AmPure XP magnetic beads (Beckman Coulter).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
57001211
Reads aligned (%)
97.4
Duplicates removed (%)
25.4
Number of peaks
638 (qval < 1E-05)

mm9

Number of total reads
57001211
Reads aligned (%)
97.0
Duplicates removed (%)
25.3
Number of peaks
727 (qval < 1E-05)

Base call quality data from DBCLS SRA