Antigen

Antigen Class

Input control

Antigen

Input control

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

Isolated pachytene spermatocytes

genotype/variation

Wild-type

strain

C57BL/6

chip antibody

none (input)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

For ChIP-seq of crosslink samples, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibodies. For ChIP-seq of MNase samples, lysate was digested with Mnase and Histone-DNA complexes were isolated with antibodies. For RNA-seq, RNA was purified using RNeasy mini kit. DNA library for ChIP-seq (both crosslink and MNase samples) was prepared with NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® (NEB) and Agencourt AMPure XP (Beckman Coulter). For RNA-seq, TruSeq™ RNA Sample Prep Kit v2 -Set A was used for library construction.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

39134473

Reads aligned (%)

96.3

Duplicates removed (%)

14.7

Number of peaks

628 (qval < 1E-05)

mm9

Number of total reads

39134473

Reads aligned (%)

96.0

Duplicates removed (%)

14.6

Number of peaks

674 (qval < 1E-05)