Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Embryonic fibroblast
Cell type
MEF-derived neural cells
NA
NA

Attributes by original data submitter

Sample

source_name
Input genomic DNA of tdMEFs at day 4 of M9-induced reprogramming
cell type
tdMEFs at day 4 of reprogramming
chip antibody
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells at indicated time points were cross-linked by 1% formaldehyde, quenched with 0.125 M glycine. The chromatin DNA was extracted and sheared into 200-400 bp, and immuoprecipitated using a EZ-ChIP kit (Millipore, 17-371), and indicated antibodies. Barcoded ChIP-Seq libraries were made from 1 to 10 ng of chromatin immunoprecipitated DNA (ChIP-DNA) using the NuGen Ovation Ultralow V2 kit. 13 cycles were used for PCR amplification of the libraries. Amplified libraries were checked for adapter artifacts by Agilent Bioanalyzer using DNA high sensitivity reagents and chips (Agilent). All libraries were quantified by qPCR using an Illumina Library Quantification kit (KAPA Biosystems). Libraries were pooled in equimolar amounts and run on the HiSeq 2500 sequencer with a single read 50 cycle run (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
29438120
Reads aligned (%)
96.7
Duplicates removed (%)
29.3
Number of peaks
380 (qval < 1E-05)

mm9

Number of total reads
29438120
Reads aligned (%)
96.5
Duplicates removed (%)
29.3
Number of peaks
415 (qval < 1E-05)

Base call quality data from DBCLS SRA