Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

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

Attributes by original data submitter

Sample

source_name
WT Tfh
genotype/variation
WT
tissue
Spleen
cell type
SMARTA CD4 T cells
cell subtype
Tfh
molecule subtype
Tn5 transposase treated nuclei DNA

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
The nuclear pellet was resuspended into transposition reaction mixture containing Tn5 transposase from Illumina Nextera DNA Sample Prep Kit and incubated at 37 °C for 30 min. Then the transposase-associated DNA was purified using Qiagen MinElute Purification kit. The DNA was amplified for twelve cycles using KAPA Real-Time Library amplification kit (KAPAbiosystems) with Nextera indexing primers as per Buenrostro et al, 2015. The total amplified DNA was purified using AmPureXP beads.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
32339392
Reads aligned (%)
62.1
Duplicates removed (%)
38.7
Number of peaks
15435 (qval < 1E-05)

mm9

Number of total reads
32339392
Reads aligned (%)
62.1
Duplicates removed (%)
38.7
Number of peaks
15402 (qval < 1E-05)

Base call quality data from DBCLS SRA