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
ChIP_input_D3
strain background
C57BL/6
genotype/variation background
transgenic carrying the tetO-OSKM transgene and Oct4-GFP/Rosa26-M2rtTA
cell type
reprogrammable mouse embryonic fibroblasts (MEFs)
induced with
doxycycline (Dox) (1ug/ml) for 3 days
reprogramming stage
day3
dox-induced genes
OSKM+Obox1
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For RNA-seq, the cells were lysed using RLT buffer supplemented with β-mercaptoethanol and processed using the RNeasy mini kit (Cat. 74104).For ChIP-seq, the cells were cross-linked with 37% formaldehyde in serum-free medium at room temperature for 10 min in room temperature (RT). Glycine was added to stop the cross-linking at final concentration of 0.125 M and the cells were rinsed in PBS. Then the cells were re-suspended in lysis buffer containing protease inhibitors and chromatin was sonicated to 100-400 bp with Covaris M220 system. RNA-seq: KAPA Stranded mRNA-Seq Kit (KK8420) ChIP-seq: KAPA HyperPlus Library Preparation kit (KAPA KK8510)

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
20376161
Reads aligned (%)
99.0
Duplicates removed (%)
4.6
Number of peaks
585 (qval < 1E-05)

mm9

Number of total reads
20376161
Reads aligned (%)
98.8
Duplicates removed (%)
4.7
Number of peaks
555 (qval < 1E-05)

Base call quality data from DBCLS SRA