Antigen

Antigen Class

TFs and others

Antigen

MED1

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

Sample

source_name

MED1 ChIP-Seq

biomaterial_provider

CC

cell line

GM12878

cell type

LCL from B-Lymphocyte

chip antibody

MED1 (Bethyl, A300-793A)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

ChIP-Seq experiments were performed in duplicates as described previously (Fournier et al., 2016). Briefly, 50 million cells were crosslinked for 10 minutes with 1% formaldehyde and quenched with 125mM glycine for 5 min. Then cells were washed with PBS, pelleted, flash frozen and stored at -80°C.  Sonicated DNA fragments were immunoprecipitated with antibodies directed against NIPBL (Bethyl Laboratories, A301-779A), SMC1A (Bethyl Laboratories, A300-055A) and MED1 (Bethyl Laboratories, A300-793A). The TruSeq DNA sample prep kit with indexing adapters was used according to the manufacturer's recommendations (Illumina)

Sequencing Platform

instrument_model

Illumina HiSeq 2000

hg38

Number of total reads

39358044

Reads aligned (%)

91.2

Duplicates removed (%)

2.7

Number of peaks

9072 (qval < 1E-05)

hg19

Number of total reads

39358044

Reads aligned (%)

90.6

Duplicates removed (%)

3.2

Number of peaks

9166 (qval < 1E-05)