Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

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
H3K4me1 at day 0 of M9-induced reprogramming
cell type
tdMEFs at day 0 of reprogramming
chip antibody
H3K4me1 (Abcam, ab8895, lot GR193727-1)

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
41531966
Reads aligned (%)
80.1
Duplicates removed (%)
24.7
Number of peaks
735 (qval < 1E-05)

mm9

Number of total reads
41531966
Reads aligned (%)
79.9
Duplicates removed (%)
24.8
Number of peaks
727 (qval < 1E-05)

Base call quality data from DBCLS SRA