Antigen

Antigen Class

TFs and others

Antigen

Dmc1

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

Anti-DMC1 S3K_testis_SSDS_1

strain

C57BL/6N

tissue

Testis

genotype

Stag3 -/-

chip antibody

Anti-DMC1 (C-20); vendor: Santa Cruz; sc-8973

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

To determine the sites and frequencies of double-stranded breaks in mouse spermatocytes ChIP was performed on 2-month old testis samples using anti-DMC1 antibody which specifically recognizes single-stranded end protruding from germ cell-specific double-stranded ends as per Brick et. al. 2012. Germ cells were isolated from the desired genotypes using Dounce Homogenizer, crosslinked, sonicated and immunoprecipitated with anti-DMC1(C-20) antibody. The libraries were prepared using adapters from TruSeq DNA LT sample prep kit. Libraries were prepared according to the prescribed protocols and amplified for 12 cycles. Size selection of library fragments of 150 - 250 bp was performed after PCR amplification. SSDS samples were denatured and quickly renatured before adapter ligation. The amount of DNA after PCR is low to reduce background. Important comments: The samples were run on Bioanalyzer for quality control. Libraries were sequenced on an Illumina® HiSeq 2500, with 75 bp paired-end reads.

Sequencing Platform

instrument_model

Illumina HiSeq 2500

mm10

Number of total reads

46363052

Reads aligned (%)

30.7

Duplicates removed (%)

27.9

Number of peaks

4337 (qval < 1E-05)

mm9

Number of total reads

46363052

Reads aligned (%)

30.7

Duplicates removed (%)

28.0

Number of peaks

4303 (qval < 1E-05)