Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Epidermis
Cell type
NHEK
Tissue
skin
Lineage
ectoderm
Description
epidermal keratinocytes

Attributes by original data submitter

Sample

source_name
Primary human epidermal keratinocytes (NHEK)
antibody
H3K4me3
antibody vendor/catalog
millipore 07-473

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the respective histone antibodies. Sequencing libraries were generated for the H3K27ac, H3K4me1, and H3K4me3 samples (samples were divided in half, and two libraries made for each using different multiplexed adaptors) Clustering and 50-cycle single end sequencing were performed on the Illumina Illumina HiSeq 2000 Genome Analyzer. Libraries were sequenced on the Illumina Illumina HiSeq 2000, with 50bp single end sequencing

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
45353645
Reads aligned (%)
83.8
Duplicates removed (%)
42.5
Number of peaks
29423 (qval < 1E-05)

hg19

Number of total reads
45353645
Reads aligned (%)
83.6
Duplicates removed (%)
42.8
Number of peaks
29251 (qval < 1E-05)

Base call quality data from DBCLS SRA