Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

Cell type Class
Blood
Cell type
B cells
NA
NA

Attributes by original data submitter

Sample

source_name
B220
cell type
B cell
transduction
sh-kmt2d
stain
tumor
antibody
H3K4me1/2 (abcam 32356)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was sheared to 200-400bp, incubated with H3K4me1/2 antibody (abcam 32356) overnight at 4C on a rocker, antibody chromatin complex was captured by ProteinA agarose beads, washed with low salt, high salt, LiCl, and TE buffer, eluted and then de-crosslinked at 65C with 0.3M NaCl final for at least 6 hr. Final chormatin was purified using Qiagen PCR purification columns. RNA was purified using the RNAeasy Plus Kit (QIAGEN) that included a genomic DNA elimination step. DNA was purified using PCR purification columns (QIAGEN). RNA-seq libraries were generated using Illumina’s TruSeq RNA sample Prep Kit v2. ChIP-seq libraries were prepared using 10ng of DNA and Illumina’s TruSeq ChIP sample prep. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT dsDNA HS Assay (Life Technologies).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
61262387
Reads aligned (%)
97.1
Duplicates removed (%)
17.0
Number of peaks
43569 (qval < 1E-05)

mm9

Number of total reads
61262387
Reads aligned (%)
96.8
Duplicates removed (%)
16.9
Number of peaks
43565 (qval < 1E-05)

Base call quality data from DBCLS SRA