GSM3505013: 011 sample ID 11; Mus musculus; ATAC-seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
ATAC-Seq
Antigen
ATAC-Seq
Cell type
Cell type Class
Blood
Cell type
Treg
NA
NA
Attributes by original data submitter
Sample
source_name
Ptpn2+/-_Treg 72h
experiment
Invivo
strain background
BALB/c
background
FoxP3eGFP SKG
genotype
Ptpn2+/-
cell-type
Treg 72h
Sequenced DNA Library
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Live cells were lysed to extract nuclei in Omni-ATAC lysis buffer (10mM Tric-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween20 and 0.01% Digitonin). Nuclei were re-suspended in 50 microL Transposition mix (25 microL 2xTD buffer, 2.5 microL transposase [Nextera, Illumina], 16.5 microL PBS, 0.5 microL, 1% Digitonin, 0.5 microL, 10% Tween20 and 5 microL H2O) and the transposase reaction was conducted for 30 min at 37 °C. Right after tagmentation, fragments were purified by DNA precipitation and capture on columns (Zymo Research), elured and stored for further processing Library amplification and barcoding were performed using Nextera DNA sample preparation kit and index kit (Illumina). Tagmented fragments were pre-amplified for 5 cycles followed by a second round of amplification based on the cell number (10 cycles for 0.5x105 cells, 9 cycles for 1.0x105 cells and 8 cycles for 1.5x105 cells). Amplified libraries were purified using 1:1.8 ratio of Ampure XP Beads. Library fragments ranging in size, between 100 to 600bp, were size selected, using Ampure XP beads (ratios 1:0.5 and 1:1.8; Beckman Coulter). Libraries were quantified by Picogreen assay (Invitrogen) and size distribution was assessed using fragment analyzer (Advance Analytics). Single-end sequencing was performed on a HiSeq 2500 (Illumina) generating in total more than 250 millions 50 bp short sequencing reads (HiSeq SBS and SR Cluster v4 kits, Illumina catalog# FC-401-4002 and GD-401-4001, respectively). Raw data from the sequencer was demultiplexed and FASTQ files were generated using bcl2fastq conversion software (Illumina).