Sample information curated by ChIP-Atlas

Antigen

Antigen Class
DNase-seq
Antigen
DNase-Seq

Cell type

Cell type Class
Others
Cell type
Mesenchymal stem cells
NA
NA

Attributes by original data submitter

Sample

source_name
BM-hMSC-TERT4 osteAdlast diff 14d
cell line
BM-hMSC-TERT4
differentiation status
adipocyte
timepoint
14d
chip antibody
n/a

Sequenced DNA Library

library_strategy
DNase-Hypersensitivity
library_source
GENOMIC
library_selection
DNase
library_construction_protocol
Nuclei were isolated from cells grown on 150 mm dishes using a 0.04% NP-40 buffer (15 mM Tris-HCl pH=8.0, 15 mM NaCl, 60 mM KCl, 1 mM EDTA pH=8.0, 0.5 mM EGTA pH=8.0, 0.5 mM Spermidine). 10 million freshly isolated nuclei were treated with 40 units/ml DNase I for 3 minutes at 37°C as decribed previously (Siersbaek R, et al.2011. EMBO Journal 30:1459-72). After RNase and Proteinase K treatment, DNA was isolated by phenol-chloroform-extraction and separated by ultra-centrifugation on a sucrose gradient overnight. DNA-fragments between 100 and 500 bp (representing 2-hit cutting events) were isolated, checked for enrichment of open chromatin over background using real- time PCR. DNase-seq and ChIP-seq libraries were constructed from 10 to 20 ng of genomic DNA according to the manufacturer's instructions (Illumina) as described in (Nielsen R, et al. 2014. Methods in Enzymology 537: 261-279).

Sequencing Platform

instrument_model
Illumina HiSeq 1500

hg38

Number of total reads
14122631
Reads aligned (%)
98.6
Duplicates removed (%)
27.5
Number of peaks
24377 (qval < 1E-05)

hg19

Number of total reads
14122631
Reads aligned (%)
97.9
Duplicates removed (%)
28.6
Number of peaks
24290 (qval < 1E-05)

Base call quality data from DBCLS SRA