Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Smarca4

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
Primary fibroblasts
strain
C57BL/6J
age
E13.5-E14.5
genotype
wild-type
treatment
starved with 0.5% serum media
passage
3
chip antibody
Abcam ab4081 lot GR152856-1
cell line
Primary fibroblasts
serum stimulation
0hr

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Growth media was removed and MEFs were crosslinked in EGS for 30 minutes at room temperature, followed by 1% formaldehyde for 10 minutes at room temperature before quenching with glycine at a final concentration of 0.125M. Sonicated chromatin from isolated nuclei were used as input to ChIP. 2-40 ng of each ChIP sample was used to prepare ChIP-Seq libraries with the NuGEN Ovation Ultralow Library System v2 kit.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
32124916
Reads aligned (%)
94.3
Duplicates removed (%)
18.1
Number of peaks
20353 (qval < 1E-05)

mm9

Number of total reads
32124916
Reads aligned (%)
94.0
Duplicates removed (%)
18.1
Number of peaks
20411 (qval < 1E-05)

Base call quality data from DBCLS SRA