GSM2091498: HP DHS; Mus musculus; DNase-Hypersensitivity
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
DNase-seq
Antigen
DNase-Seq
Cell type
Cell type Class
Pluripotent stem cell
Cell type
mESC derived haematopoietic progenitor
NA
NA
Attributes by original data submitter
Sample
source_name
HP
cell type
WT hematopoietic progenitor IVD cells
dnasei origin
Worthington
Sequenced DNA Library
library_strategy
DNase-Hypersensitivity
library_source
GENOMIC
library_selection
DNase
library_construction_protocol
NP-40 permeabilized cells were digested with DNase I for 3 minutes at 22oC as previously described (Bert et al). A range of DNase I concentrations was used to get the optimal digestion, the initial amounts varied depending on the cell type. Following DNA purification, samples were analyzed by qPCR comparing the amount of PCR product generated between regions expected to be DNase I hypersensitive (e.g. TBP promoter) and regions which should not be cleaved (e.g. a gene desert region of chromosome 1). Optimally digested samples gave a ratio of ~0.7. DNA fragments (80-300bp) were isolated from favorable samples by agarose gel extraction and further validated by qPCR analysis before library preparation. Libraries were prepared from approximately 10ng DNA from DNaseI samples, according to manufacturer's instructions (Illumina). Samples were sequenced using 50bp single end reads