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

testes

cell type

pachytene spermatocytes

days postpartum

adult

strain

C57BL/6

chip antibody

none

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

About 5 x 10^5 to 5 x 10^6 cells were crosslinked using formaldehyde (a final 1% (v/v); Sigma, F8775-500ML), followed by quenching with a Glycine (final 125 mM; Sigma, G8898-1KG), mixed well and incubated for another 10 min. Cells were pelleted and washed once with ice-cold 1x PBS. After removing the supernatant, the cell pellets were stored at -80°C or directly used for the following Hi-C experiments. For ATAC-seq, First, 5 × 10^4 cells were spun at 500 g for 5 min, 4 °C, which was followed by a wash using 50 μl of cold 1× PBS and centrifugation at 500 g for 5 min, 4 °C. Cells were resuspended in 50 μl cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% (v/v) Igepal CA-630) and centrifugation at 500 g for 10 min, 4 °C. Second, the pellet was resuspended in the transposase reaction mix (25 μl 2× TD buffer, 2.5 μl transposase (Illumina, FC-121-1030) and 22.5 μl nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C. Then, the samples were purified by using a Qiagen MinElute PCR Purification Kit (Qiagen, 28004) and amplified by PCR. After size selected by VAHTS DNA Clean Beads, the samples were sequenced by HiSeq X Ten at Novogene. ChIP-seq sequencing libraries were generated by Tn5 transposase and then PCR amplification and size selected by VAHTS DNA Clean Beads. Libraries were sent for high throughput sequencing with the HiSeq X Ten at Novogene.

Sequencing Platform

instrument_model

HiSeq X Ten

mm10

Number of total reads

35660517

Reads aligned (%)

93.4

Duplicates removed (%)

5.5

Number of peaks

276 (qval < 1E-05)

mm9

Number of total reads

35660517

Reads aligned (%)

93.3

Duplicates removed (%)

5.6

Number of peaks

240 (qval < 1E-05)