Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Sox2

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
SKM secondary MEF
sample stage
Day 2 of SKM reprogramming
chip antibody
Sox2 (Millipore, AB5603)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatins were cross-linked by 1% formaldehyde and extracted using EZ-ChIP Chromatin Immunoprecipitation kit (Millipore, 17-371). The chromatin was then sonicated to an average DNA fragment length of 100-500 bp on Covaris S2 . Sequencing libraries were generated, according to the manufacturer's instructions. Briefly, 4 ng of ChIP product was used for each library preparation. The NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645) was used to ligate adapters and for barcoding and amplification. Libraries was purified using SPRIselect® Reagent magnetic beads (Beckman Coulter, Inc. #B23317), quality-controlled by the Bioanalyzer, and quantified by qPCR.

Sequencing Platform

instrument_model
NextSeq 550

mm10

Number of total reads
40427815
Reads aligned (%)
95.7
Duplicates removed (%)
15.3
Number of peaks
518 (qval < 1E-05)

mm9

Number of total reads
40427815
Reads aligned (%)
95.5
Duplicates removed (%)
15.2
Number of peaks
599 (qval < 1E-05)

Base call quality data from DBCLS SRA