Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Blood
Cell type
Tfh
NA
NA

Attributes by original data submitter

Sample

source_name
STAT4 KO_Splenic Tfh cells
strain background
C57BL/6
genotype/variation
STAT4 Knockout
transferred with
naïve Stg TCR transgenic CD4 T cells
infected with
LCMV Armstrong
timepoint
Day 8 post LCMV infection
cell type
Splenic Tfh cells (CD4+PSGL1loLy6cloCXCr5hiPD-1hi)

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Sorted cells were lysed in buffer (10mM Tris-HCl, 10mM NaCl 3mM MgCL2 and 0.1% IGEPAL) for 15 minutes at 4C, then centrifuged and re-suspended with transposase reaction mix (2x tagmented DNA buffer, transposase [Ilumina Nextera]), and nuclease-free water) and incubated for 30 min at 37 degrees. Cells were then added to MinElute column (Qiagen) and PCR amplified in KAPA HiFi 2x mix (Kapa Biosystems) with barcoding primers(Buenrostro et al., 2013) at 98C for 45 sec (45s) + 5 x at (98C for 15s + 63C for 30s + 72C for 30s) + 72C for 1 min. PCR products were cleaned with MinElute columns and size exclusion was performed with magJet NGS Cleanup and Size Selection kit (Thermo Fisher). Q-PCR library amplification test and PCR library amplification was performed as previously described(Buenrostro et al., 2015).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
45931731
Reads aligned (%)
98.3
Duplicates removed (%)
64.5
Number of peaks
14914 (qval < 1E-05)

mm9

Number of total reads
45931731
Reads aligned (%)
98.2
Duplicates removed (%)
64.6
Number of peaks
14872 (qval < 1E-05)

Base call quality data from DBCLS SRA