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
Mouse embryonic fibroblasts at passage 2
cell type
Fibroblast like cells
genotype
Strain (Nrl-GFP)

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Cells were harvested and frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were thawed in a 37oC water bath, pelleted, washed with cold PBS. Cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina) Tagmented DNA was purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter)

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
42786557
Reads aligned (%)
98.2
Duplicates removed (%)
11.6
Number of peaks
88948 (qval < 1E-05)

mm9

Number of total reads
42786557
Reads aligned (%)
98.1
Duplicates removed (%)
11.7
Number of peaks
88944 (qval < 1E-05)

Base call quality data from DBCLS SRA