Antigen

Antigen Class

Input control

Antigen

Input control

Cell type

Cell type Class

Epidermis

Cell type

Melanoma

MeSH Description

A malignant neoplasm derived from cells that are capable of forming melanin, which may occur in the skin of any part of the body, in the eye, or, rarely, in the mucous membranes of the genitalia, anus, oral cavity, or other sites. It occurs mostly in adults and may originate de novo or from a pigmented nevus or malignant lentigo. Melanomas frequently metastasize widely, and the regional lymph nodes, liver, lungs, and brain are likely to be involved. The incidence of malignant skin melanomas is rising rapidly in all parts of the world. (Stedman, 25th ed; from Rook et al., Textbook of Dermatology, 4th ed, p2445)

Sample

source_name

Melanoma_glutamine supplemented diet

tumor model

Melanoma PDX TM00702 model (Jackson Lab)

chip antibody

none

tissue

melanoma

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

10 mg of frozen tumor tissue was used for ChIP and pull down using H3K4me3 ChIP-seq libraries were prepared with Kapa DNA HyperPrep Kit (Cat No. KK 8700, Kapa) according to the manufacturer's protocol; A 10 cycles of PCR was performed on 5-10 ng of immunoprecipitated DNA to produce the final sequencing library. The libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit and quantified with Qubit.

Sequencing Platform

instrument_model

Illumina HiSeq 2500

hg38

Number of total reads

48163573

Reads aligned (%)

75.4

Duplicates removed (%)

5.3

Number of peaks

1456 (qval < 1E-05)

hg19

Number of total reads

48163573

Reads aligned (%)

74.7

Duplicates removed (%)

6.9

Number of peaks

1413 (qval < 1E-05)