Antigen

Antigen Class

Histone

Antigen

H3K4me3

Cell type

Cell type Class

Gonad

Cell type

Spermatocytes

MeSH Description

Male germ cells derived from SPERMATOGONIA. The euploid primary spermatocytes undergo MEIOSIS and give rise to the haploid secondary spermatocytes which in turn give rise to SPERMATIDS.

Sample

source_name

spermatocytes

cell type

spermatocyte

age

12 days post-partum

strain

CASTxB6 F1 Hybrid

chip antibody

H3K4me3 (Millipore/EMD, 07-473, lot 2155413)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Nuclei were isolated from cells using hypotonic lysis. Chromatin was fragmented either by Mnase digestion or sonication (PRDM9 ChIP). After high speed spin soluble chromatin was removed and used for ChIP Libraries were prepared for sequencing using Bioo Scientific's NEXTflex ChIP-Seq Kit (protocol version V11.11) without size selection. Amplification of the libraries was done using 14-18 cycles of PCR.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

44403771

Reads aligned (%)

83.8

Duplicates removed (%)

67.9

Number of peaks

48531 (qval < 1E-05)

mm9

Number of total reads

44403771

Reads aligned (%)

83.6

Duplicates removed (%)

68.0

Number of peaks

48522 (qval < 1E-05)