Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KMT2D

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
keratinocytes
tissue
keratinocytes
chip antibody
anti-KMT2D (HPA035977) (Sigma-Aldrich)
genotype/variation
shSC

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP extracts were sonicated nine times for 5 min each round (30 sec of sonication with intermediate incubation of 30 sec per round) using a Bioruptor (Diagenode). All ChIPs were performed using 500 μg of extract and 2 μg of antibody per sample. ChIP DNA was also used to make sequencing libraries using NEBNext Ultra DNA library preparation kit for Illumina (New England Biolabs).

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
45901901
Reads aligned (%)
75.7
Duplicates removed (%)
19.5
Number of peaks
2284 (qval < 1E-05)

hg38

Number of total reads
45901901
Reads aligned (%)
77.5
Duplicates removed (%)
18.2
Number of peaks
2406 (qval < 1E-05)

Base call quality data from DBCLS SRA