Curated Sample Data


Genome
mm9
Antigen Class
DNase-seq
Antigen
DNase-Seq
Cell type Class
Blood
Cell type
HPC-7

Cell type information


NA
NA

Attributes by Original Data Submitter


Alias
E-MTAB-3954:DNase1_HPC7_rep3
Broker name
ArrayExpress
Description
Protocols: HPC-7 cells (Pinto do O et al., 1998) were grown in Stem Cell Factor. Hi-C and CHi-C was performed as described previously (Schoenfelder et al., 2015). Sequencing libraries were prepared according to the manufactures instructions.
ENA checklist
ERC000011
INSDC center alias
University of Cambridge
INSDC center name
University of Cambridge
INSDC first public
2016-02-29T17:01:41Z
INSDC last update
2018-03-09T09:21:08Z
INSDC status
public
SRA accession
ERS939095
Sample Name
ERS939095
Title
DNase1_HPC7_rep3
cell line
HPC-7
cell type
haematopoietic stem/progenitor cell
organism
Mus musculus
sequencing type
Hi-C sequencing

Metadata from Sequence Read Archive

Library Description


library_name
DNase1_HPC7_rep3
library_strategy
DNase-Hypersensitivity
library_source
GENOMIC
library_selection
DNase
library_construction_protocol
HPC-7 cells (Pinto do O et al., 1998) were grown in Stem Cell Factor. Hi-C and CHi-C was performed as described previously (Schoenfelder et al., 2015). Sequencing libraries were prepared according to the manufactures instructions.

Platform Information


instrument_model
Illumina HiSeq 1000

External Database Query

Logs in read processing pipeline


Number of total reads
129512449
Reads aligned (%)
87.9
Duplicates removed (%)
28.5
Number of peaks
38916 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA