Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Embryonic fibroblast
Cell type
NIH/3T3
Primary Tissue
Embryo
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
NIH3T3 cells grown in vitro
cell line
NIH3T3
operation
na

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Cardiac fibroblasts, Tcf21 lineage GFP positive, were isolated from hearts by langendorff perfusion. Sorted cells were spun down and lysed prior to tagmentation according to the Fast-ATAC-seq protocol (Corces et al., 2016). Briefly For Fast-ATAC (ATAC-seq), sorted cells were spun down, FACS buffer was removed, the pellet was then re-suspended in a transposase-containing reaction mixture complete with 0.05% digitonin prior to tagmentation at 370C with 1000 rpm agitation for 30 minutes. Next, transposed DNA was purified with a Qiagen PCR MinElute kit (Qiagen 28004). Fast-ATAC libraries were purified with a 1.8X SPR purification using AMPure XP beads following PCR amplification.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
32762479
Reads aligned (%)
97.2
Duplicates removed (%)
5.6
Number of peaks
60300 (qval < 1E-05)

mm9

Number of total reads
32762479
Reads aligned (%)
97.0
Duplicates removed (%)
5.6
Number of peaks
60035 (qval < 1E-05)

Base call quality data from DBCLS SRA