Sample information curated by ChIP-Atlas

Antigen

Antigen Class
DNase-seq
Antigen
DNase-Seq

Cell type

Cell type Class
Blood
Cell type
CD4+ T cells
NA
NA

Attributes by original data submitter

Sample

source_name
Memory splenic CD4+ T-cells
cell type
Memory splenic CD4+ T-cells
pma treatment
0 min
dnasei origin
Worthington

Sequenced DNA Library

library_strategy
DNase-Hypersensitivity
library_source
GENOMIC
library_selection
DNase
library_construction_protocol
NP-40 permeabilised 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 analysed 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 favourable samples by agarose gel extraction and further validated by qPCR analysis before library preparation. Libraries were prepared from approximately 10ng DNA from DNaseI samples. Libraries for sequencing on the Solid platform were prepared according to the manufacturer's instructions. Samples were sequenced using 50bp reads. All other libraries were prepared using the Tru-Seq library preparation kit according to the manufacturer's instructions (Illumina). These samples were sequenced on the Illumina HiSeq platforms using 50bp single end reads

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
257065491
Reads aligned (%)
87.2
Duplicates removed (%)
79.1
Number of peaks
8875 (qval < 1E-05)

mm9

Number of total reads
257065491
Reads aligned (%)
87.0
Duplicates removed (%)
79.2
Number of peaks
8943 (qval < 1E-05)

Base call quality data from DBCLS SRA