Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Epidermis
Cell type
Skin
NA
NA

Attributes by original data submitter

Sample

source_name
Skin
genotype
wild type
tissue
Skin
background
C57BL/6
age
E16.5 days
chip antibody
Histone H3K4me3 antibody (Active Motif 39159)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Snap frozen skin samples from WT and Irf6-/- E16.5 mouse embryos (200 mg, n = 2 of each genotype) were sent to Active Motif for ChIP-Seq. ChIP was performed with validated antibodies against H3K27me3 (Active Motif 39155), H3K27Ac (Active Motif 39133) or H3K4me3 (Active Motif 39159). Illumina sequencing libraries were prepared from the ChIP and input DNA using the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation using Active Motif's custom liquid handling robotics pipeline. After the final 15 cycle PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500. Libraries were prepared using standard protocols for the Ovation Ultralow System. Briefly, samples were PCR-amplified and sized using the Agilent 2100Bioanalyzer. Barcoded libraries were sequenced 50 bp single end on HiSeq 2500 (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
32546866
Reads aligned (%)
94.2
Duplicates removed (%)
26.4
Number of peaks
23904 (qval < 1E-05)

mm9

Number of total reads
32546866
Reads aligned (%)
94.2
Duplicates removed (%)
26.4
Number of peaks
23885 (qval < 1E-05)

Base call quality data from DBCLS SRA