Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NR3C1

Cell type

Cell type Class
Blood
Cell type
NALM-6
Primary Tissue
Blood
Tissue Diagnosis
Leukemia

Attributes by original data submitter

Sample

source_name
Nalm6 CASP1 cells
cell line
Nalm6
chip antibody
anti-glucocorticoid receptor antibodies (sc-1003)
genotype
CASP overexpressing

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked with formaldehyde (1% final concentration) for 10 minutes at room temperature and then incubated with glycine (0.125 M final concentration) for 5 minutes to stop the cross-linking reaction. Cells were pelleted and washed with 1X PBS containing protease inhibitors (Roche Protease Inhibitor Cocktail Tablets, 11836153001) and stored at –80C prior to further experimentation. Crosslinked cell pellets were resuspended in cold lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl and 0.5% NP-40 solution) containing protease inhibitors (Roche Protease Inhibitor Cocktail Tablets, 11836153001), and pelleted to isolate nuclei. The pellet was resuspended in cold RIPA lysis buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS solution). Sonication was performed using a Bioruptor sonication system (Diagenode). Sonicated chromatin was added to Dynabeads (Invitrogen) coated with anti-glucocorticoid receptor antibodies (sc-1003) and incubated overnight at 4C. The solution was washed with a LiCl wash solution (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40 and 1% sodium deoxycholate) at 4oC, and a final wash using 1X TE buffer. Dynabeads were resuspended in an elution buffer (1% SDS and 0.1 M NaHCO3) and placed at 65C to reverse crosslinks. DNA purified and a standard library preparation was performed prior to sequencing on an Illumina HiSeq 2000 sequencer.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
14985556
Reads aligned (%)
90.4
Duplicates removed (%)
4.8
Number of peaks
4204 (qval < 1E-05)

hg38

Number of total reads
14985556
Reads aligned (%)
92.2
Duplicates removed (%)
3.6
Number of peaks
4175 (qval < 1E-05)

Base call quality data from DBCLS SRA