Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Nr3c1

Cell type

Cell type Class
Embryonic fibroblast
Cell type
MEF
Tissue
Embryonic Fibroblast
Lineage
primaryCells
Description
Mouse Embryonic Fibroblast

Attributes by original data submitter

Sample

source_name
Cultured WT embryonic fibroblasts
genotype
wild type
cell type
embryonic fibroblast
antibody
in-house GR antibody

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation (ChIP) was performed as described previously described (PMID: 23508109), with the following modifications: cross-linking was performed by adding methanol-free 16% formaldehyde directly to the culture media to a final concentration of 1% and incubating for 5 minutes at room temperature with gentle rocking; samples were subsequently sonicated with a Diagenode Bioruptor at high power in 30-second bursts separated by 30-second incubations in ice water for a total of 23 cycles. A minimum of 1 ng DNA from ChIP samples were used to prepare libraries using the Nugen Ovation Ultralow System V2 1-16 Part No. 0344 according to the manufacturer’s instructions. Samples were run on an Illumina HiSeq using 1X50 bp end reads

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
18039885
Reads aligned (%)
97.9
Duplicates removed (%)
21.9
Number of peaks
4403 (qval < 1E-05)

mm9

Number of total reads
18039885
Reads aligned (%)
97.6
Duplicates removed (%)
22.0
Number of peaks
4399 (qval < 1E-05)

Base call quality data from DBCLS SRA