Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMC1A

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
SMC1A ChIP-Seq
biomaterial_provider
CC
cell line
GM12878
cell type
LCL from B-Lymphocyte
chip antibody
SMC1A (Bethyl, A300-055A)

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

hg19

Number of total reads
31025084
Reads aligned (%)
81.8
Duplicates removed (%)
6.4
Number of peaks
45631 (qval < 1E-05)

hg38

Number of total reads
31025084
Reads aligned (%)
82.3
Duplicates removed (%)
6.1
Number of peaks
44075 (qval < 1E-05)

Base call quality data from DBCLS SRA