Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Embryonic fibroblast
Cell type
MEF
Tissue
Embryonic Fibroblast
Lineage
primaryCells
Description
Mouse Embryonic Fibroblast

Attributes by original data submitter

Sample

source_name
Fibroblast
genotype/variation
Atoh1::nGFP
developmental stage
embryonic day 14
tissue
Fibroblast

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Cells were collected by FACS purification into cold PBS, and centrifuged 500 xg for 15 min. Cell pellet were resuspended with 50 ul transposition buffer consisting of 10mM Tris-HCL pH8.0, 5 mM MgCl2, 10% DMF, 0.2% NP40, and home-made transposase Tn5. Transposition was performed at 37 degree for 20 min. DNA was collected immediately after transposition using Qiagen Mini-elute kit. Library was prepared using primers from Illumina Nextera DNA Library Preparation Kit.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
34013527
Reads aligned (%)
96.5
Duplicates removed (%)
18.4
Number of peaks
43518 (qval < 1E-05)

mm9

Number of total reads
34013527
Reads aligned (%)
96.4
Duplicates removed (%)
18.6
Number of peaks
43477 (qval < 1E-05)

Base call quality data from DBCLS SRA