Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

Cell type Class
Epidermis
Cell type
Keratinocytes
MeSH Description
Epidermal cells which synthesize keratin and undergo characteristic changes as they move upward from the basal layers of the epidermis to the cornified (horny) layer of the skin. Successive stages of differentiation of the keratinocytes forming the epidermal layers are basal cell, spinous or prickle cell, and the granular cell.

Attributes by original data submitter

Sample

source_name
DMSO H3K4me1
cell type
Normal Human Epidermal Keratinocyte
passages
6-8
treatment
DMSO
chip antibody
Rabbit polyclonal anti-Histone 3 (monomethyl K4) (Abcam, Cat# ab8895) RRID: AB_306847

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq was performed as described previously (Capell et al., 2016; Lin-Shiao et al., 2018). Briefly, keratinocytes cultured in 10-cm2 dishes were fixed in 1% formaldehyde for 5 min, and fixation was quenched with the addition of glycine to 125 mM for an additional 5 min. Cells were harvested by scraping from plates and washed twice in 1× PBS before storage at −80°C. ChIP extracts were sonicated for 15 minutes in a Covaris sonicator. All ChIPs were performed using 500 µg of extract and 2 µg of antibody per sample. Thirty microliters of Protein G Dynabeads was used per ChIP. Libraries were prepared according to NEBNext Ultra DNA library preparation kit for Illumina instructions.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
47132303
Reads aligned (%)
98.1
Duplicates removed (%)
2.7
Number of peaks
22099 (qval < 1E-05)

hg19

Number of total reads
47132303
Reads aligned (%)
97.8
Duplicates removed (%)
3.2
Number of peaks
21715 (qval < 1E-05)

Base call quality data from DBCLS SRA