Antigen

Antigen Class

Histone

Antigen

H3K27ac

Cell type

Cell type Class

Gonad

Cell type

Seminoma

MeSH Description

A radiosensitive, malignant neoplasm of the testis, thought to be derived from primordial germ cells of the sexually undifferentiated embryonic gonad. There are three variants: classical (typical), the most common type; anaplastic; and spermatocytic. The classical seminoma is composed of fairly well differentiated sheets or cords of uniform polygonal or round cells (seminoma cells), each cell having abundant clear cytoplasm, distinct cell membranes, a centrally placed round nucleus, and one or more nucleoli. In the female, a grossly and histologically identical neoplasm, known as dysgerminoma, occurs. (Dorland, 27th ed)

Sample

source_name

FFPE seminoma

tissue type

testis

biopsy year

2006

storage years

13

sample collection

macrodissection

chip antibody

H3K27Ac (Diagenode, cat. no. C15410196, lot no. A1723-0041D)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

FFPE blocks were histologically examined and accordingly sectioned, macrodissected or cored. Samples were deparaffinized, rehydrated and homogenized by heating at 65C in 1% SDS detergent buffer overnight. Next samples were sonicated and solubilized chromatin was immunoprecipitated following a low-input protocol. Libraries were prepared with Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) or SMARTer® ThruPLEX® DNA-Seq Kit (Takara Bio USA Inc), amplified for 14 cycles.

Sequencing Platform

instrument_model

NextSeq 500

hg38

Number of total reads

20389342

Reads aligned (%)

95.8

Duplicates removed (%)

14.5

Number of peaks

3472 (qval < 1E-05)

hg19

Number of total reads

20389342

Reads aligned (%)

95.4

Duplicates removed (%)

15.5

Number of peaks

3525 (qval < 1E-05)