Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NR3C1

Cell type

Cell type Class
Blood
Cell type
RS4-11
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Acute Lymphocytic

Attributes by original data submitter

Sample

source_name
RS4;11_no stimulation
cell line
RS4;11
cell type
acute lymphoblastic leukemia cell line
treated with
none (no stimulation control)
chip antibody
GR (Novus, NB300-731; Cell Signaling, D8H2; Abcam ab3579)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Histone modification ChIP and DHS were performed on MNase-digested and DNase-digested native chromatin, respectively. Transcription factor ChIP was performed on sonicated nuclei isolated from cells treated with EGS and formaldehyde cross-linking agents. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 7-9 cycles and library fragments of ~270 bp for histone modification libraries, ~75 bp for DHS libraries, and ~320 bp for transcription factor libraries (insert plus adaptor and PCR primer sequences) were size selected using PippinPrep (Sage Science) 2% agarose gels. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
31082737
Reads aligned (%)
55.5
Duplicates removed (%)
30.5
Number of peaks
885 (qval < 1E-05)

hg38

Number of total reads
31082737
Reads aligned (%)
57.2
Duplicates removed (%)
29.1
Number of peaks
755 (qval < 1E-05)

Base call quality data from DBCLS SRA