Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NR3C1

Cell type

Cell type Class
Unclassified
Cell type
Unclassified
NA
NA

Attributes by original data submitter

Sample

source_name
Human patient-derived xenograft cells
host organism
Mus musculus
chip antibody
GR
antibody manufacturer
Cell Signaling
catalog number
3660S

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ALL xenograft cells were inoculated by tail-vein injection into NOD/SCID mice, and engraftment was monitored weekly as previously described25. When >70% %huCD45+ engraftment in the peripheral blood was apparent, which occurred 8-10 weeks post-transplantation, mice were treated with either dexamethasone (15 mg/kg) or vehicle control by intra-peritoneal (IP) injection, and culled at 8 hours following the treatment. 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. ChIP DNA was fragmented to 100-500bp by sonication or micrococcal nuclease digestion. DNA-end was repaired to overhang a 3'-dA, then adapters were ligated to the end DNA fragments. DNA fragments with proper size (usually 100-300bp, including adaptor sequence) were selected after PCR amplification.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
22095594
Reads aligned (%)
77.8
Duplicates removed (%)
11.2
Number of peaks
9453 (qval < 1E-05)

hg38

Number of total reads
22095594
Reads aligned (%)
79.2
Duplicates removed (%)
10.2
Number of peaks
9381 (qval < 1E-05)

Base call quality data from DBCLS SRA