Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NR3C1

Cell type

Cell type Class
Blood
Cell type
ALL xenograft
NA
NA

Attributes by original data submitter

Sample

source_name
ALL xenograft cells
tissue
ALL xenograft cells
treatment
vehicle
chip antibody
GR

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cell suspensions of spleens were prepared and mononuclear cells enriched to >97% human by density gradient centrifugation. The spleen-harvested cells were used for ChIP-seq assay. Lysates were clarified from sonicated nuclei and crosslinked protein-DNA complexes were isolated with antibody. Library preparation was performed by Novogene (Hong Kong) using a variation of the Illumina's standard protocol. Briefly, the pipeline consists of 3 steps; 1. DNA-end repair, 3'-dA overhang and ligation of methylated sequencing adaptors; 2. PCR amplification and size selection (usually 100-300bp, including adaptor sequence); 3. Qualified library for cluster preparation and sequencing.

Sequencing Platform

instrument_model
HiSeq X Ten

hg19

Number of total reads
72794226
Reads aligned (%)
54.9
Duplicates removed (%)
32.4
Number of peaks
1496 (qval < 1E-05)

hg38

Number of total reads
72794226
Reads aligned (%)
56.9
Duplicates removed (%)
30.6
Number of peaks
1594 (qval < 1E-05)

Base call quality data from DBCLS SRA