Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KMT2D

Cell type

Cell type Class
Blood
Cell type
B cells
NA
NA

Attributes by original data submitter

Sample

source_name
germinal center B cells from tonsil tissues
tissue
tonsil
cell type
germinal center B cell
gc cell pool
CB5
chip antibody
anti-MLL2 (Sigma, catalog# HPA035977, lot# A69497)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed on two independent pools of GC cells, each comprising 3-5 donors. Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris). Nuclei were sonicated using the S220 Ultrasonicator (Covaris) in order to obtain chromatin fragments of 200-500bp. ChIP-seq libraries were constructed starting from 4ug of ChIP or Input DNA as reported in Blecher-Gonen et al., 2013, Nature protocol. Libraries were quantified using the KAPA SYBR FAST Universal qPCR Kit (KAPA Biosystems), normalized to 10nM, pooled and sequenced in an Illumina HiSeq 2500 instrument as single-end 101 bp reads, obtaining on average 25x10^6 reads/sample.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
34613003
Reads aligned (%)
79.9
Duplicates removed (%)
18.0
Number of peaks
2442 (qval < 1E-05)

hg38

Number of total reads
34613003
Reads aligned (%)
82.0
Duplicates removed (%)
16.7
Number of peaks
2686 (qval < 1E-05)

Base call quality data from DBCLS SRA