Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Gata4

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
MEFs D0_Gata4_Gata4
cell type
Mouse embryonic fibroblast (MEF)
background strain
C57BL/6
treatment
Single Factor
induction time
2 days
development stage
2 days
antibody
Gata4 (Santa Cruz Biothechnology, sc1237)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
MEFs from E13.5-14.5 C57BL/6 mice were prepared as preciously described (Nam et al., 2014) and cultured in fibroblast growth medium (DMEM containing 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin) until experiments were performed. MEFs infected were induced using DMEM/199 (4:1), 10% FBS, 5% horse serum, 1% penicillin/streptomycin, 1% nonessential amino acids, 1% essential amino acids, 1% B-27, 1% insulin-selenium-transferrin, 1% vitamin mixture, and 1% sodium pyruvate (Invitrogen). The induction medium was replaced every other two or three days until experiments were performed. MEFs two or seven days after retroviral transduction were crosslinked with 1% formaldehyde in PBS for 30 min and neutralized by the addition of glycine to a final concentration of 0.125M for 5min. MEFs were then harvested and washed with cold PBS for ChIP. For mouse heart sample preparation, ChIP was performed as previously described (Huang et al., 2016; Xu et al., 2012), or by using ChIP-IT Express ChIP kits (Active Motif) following the vender's protocol. ChIP-seq libraries were generated using KAPA Hyper Prep Kit following the manufacturer's protocol (Kapa Biosystems).

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
17542142
Reads aligned (%)
91.6
Duplicates removed (%)
19.9
Number of peaks
6971 (qval < 1E-05)

mm9

Number of total reads
17542142
Reads aligned (%)
91.2
Duplicates removed (%)
19.8
Number of peaks
6965 (qval < 1E-05)

Base call quality data from DBCLS SRA