Antigen

Antigen Class

Input control

Antigen

Input control

Cell type

Cell type Class

Gonad

Cell type

Testis

MeSH Description

The male gonad containing two functional parts: the SEMINIFEROUS TUBULES for the production and transport of male germ cells (SPERMATOGENESIS) and the interstitial compartment containing LEYDIG CELLS that produce ANDROGENS.

Sample

source_name

Testes

strain

C57BL/6J

chip antibody

none, input

agent

Atrazine

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Lysates from testis cells were sonicated, clarified and DNA protein complexes were isolated with anti H3K4me3 antibodies. Immunoprecipitated DNA was purified from proteins.The DNA concentration was measured with Quantus Fluoremeter (E6150, Promega), using Quantiflor dsDNA system, (E2670, Promega). The libraries were prepared from 50 ng of ChiP and Input material using NEBNext Ultra DNA library Prep Kit for Illumina (NEB #E7370S). Library selection was done using excision fragments from 2% agarose gel including GelGreen stain (Gentaur, 41005), 180-220 bp fragments were excised using Dark reader transilluminator (Clare Chemical research, Dr-46B). The Illumina Hiseq2000 Genome Analyzer was used to perform massively parallel 51 bp sequencing in Single End mode. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

104558758

Reads aligned (%)

90.4

Duplicates removed (%)

21.5

Number of peaks

583 (qval < 1E-05)

mm9

Number of total reads

104558758

Reads aligned (%)

90.1

Duplicates removed (%)

21.4

Number of peaks

704 (qval < 1E-05)