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
E12.5 Mouse embryonic fibroblasts
strain
FVB/NTac
tissue
E12.5 Mouse embryonic fibroblasts
number of cells
12.5k

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
For the ATACseq libraries, induced MEFs were trypsinized, washed, and resuspended in FACS sorting buffer. 12.5k GFP+ cells were sorted per replicate and transpostion reaction. In-house Tn5 transposase was used to insert sequencing adapters and fragmentate cDNA. Greenleaf primer sets (Buenrostro, J., 2015) were used to amplify the fragmented cDNA with 4-6 cycles (KAPA HiFi PCR Kits, catalog number KK2102). AMPure XP beads size selection was performed to recover fragments with length of 200 to 1000 bp.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
23295182
Reads aligned (%)
96.0
Duplicates removed (%)
7.9
Number of peaks
59600 (qval < 1E-05)

mm9

Number of total reads
23295182
Reads aligned (%)
96.0
Duplicates removed (%)
8.0
Number of peaks
59576 (qval < 1E-05)

Base call quality data from DBCLS SRA