Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Epidermis
Cell type
Melanocytes
MeSH Description
Mammalian pigment cells that produce MELANINS, pigments found mainly in the EPIDERMIS, but also in the eyes and the hair, by a process called melanogenesis. Coloration can be altered by the number of melanocytes or the amount of pigment produced and stored in the organelles called MELANOSOMES. The large non-mammalian melanin-containing cells are called MELANOPHORES.

Attributes by original data submitter

Sample

source_name
Melanocyte
sirna
siSCR
antibody
H3K4me3

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were prepared from sonicated cells and histone-DNA complexes were isolated with antibody. Illumina sequencing libraries were prepared from ChIP DNA using the NEBNext ChIP-seq library prep reagent set for Illumina (New England Biolabs) as per manufacturer's protocol with the following modifications: DNA purification with Qiaquick PCR purification or Minelute PCR purification kits, 2% agarose gel DNA size selection, custom indexed adapters, and 18 cycles of PCR amplification. The libraries were sequenced on an Illumina HiSeq 2000 (single-end, 75 bp).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
82796342
Reads aligned (%)
96.7
Duplicates removed (%)
49.7
Number of peaks
41899 (qval < 1E-05)

hg19

Number of total reads
82796342
Reads aligned (%)
96.4
Duplicates removed (%)
50.1
Number of peaks
41713 (qval < 1E-05)

Base call quality data from DBCLS SRA