Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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
cells_3T9_input
cell line
3T9
cell type
immortalized embryonic fibroblasts
genotype
3T9MycER
chip antibody
IgG (Santa Cruz, sc-2027)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were immunoprecipitated using different antibodies. For Myc, TEAD, Histone Marks, RNAPol2 ChIP, 3T9 fibroblasts or dissected liver/tumors were fixed with 1% formaldehyde. For YAP ChIP, fixation was performed by a double step approach with 0.5 M DSG (Di-(N-succinimidyl)-glutarate) and 1% formaldehyde (FA). Libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
99889816
Reads aligned (%)
95.7
Duplicates removed (%)
18.0
Number of peaks
691 (qval < 1E-05)

mm9

Number of total reads
99889816
Reads aligned (%)
95.4
Duplicates removed (%)
17.9
Number of peaks
848 (qval < 1E-05)

Base call quality data from DBCLS SRA