Antigen

Antigen Class

Input control

Antigen

Input control

Cell type

Cell type Class

Gonad

Cell type

Oocytes

MeSH Description

Female germ cells derived from OOGONIA and termed OOCYTES when they enter MEIOSIS. The primary oocytes begin meiosis but are arrested at the diplotene state until OVULATION at PUBERTY to give rise to haploid secondary oocytes or ova (OVUM).

Sample

source_name

fully grown oocytes

strain

C57BL/6

developmental stage

fully grown oocytes

genotype

wildtype

chip antibody

none

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Total RNA was extracted from pooled FGOs and 2-cell embryos using Trizol reagent (Thermo Fisher Scientific). ULI-NChIP-seq libraries were prepared from about 200 FGOs based on previous reports (Brind'Amour et al., 2015). ChIP was performed with 0.15 μg of anti-H3K9me2 (abcam ab1220) in 200-μl NChIP buffer. WGBS libraries were constructed using the post-bisulfite adapter tagging method (Miura et al., 2012). Pooled GOs, FGOs, MII oocytes, 2-cell embryos and blastocysts were spiked with 1% unmethylated lambda phage DNA (Promega). Libraries were amplified with KAPA library amplification kit (KAPA) for 4 cycles using primers AATGATACGGCGACCACCGAGATCTACAC and CAAGCAGAAGACGGCATACGAGAT. For RNA-seq, libraries were constructed using NEBNext® rRNA Depletion Kit (Human/Mouse/Rat), NEBNext® RNA First Strand Synthesis Module, NEBNext® Ultra Directional RNA Second Strand Synthesis Module, and NEBNext® Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer's protocols. Libraries were amplified by PCR for 10 cycles. WGBS libraries were sequenced on HiSeq 1500 or 2500 (Illumina) (FGOs and blastocysts: HCS v2.0.5 and RTA v1.17.20; MII oocytes and 2-cell embryos: HCS v2.2.68 and RTA v1.18.66.3) using TruSeq SBS kit v3-HS and HiSeq Rapid SBS Kit v2 (Illumina) according to manufacturer's protocols. For ULI-ChIP-seq and RNA-seq, libraries were sequenced on NextSeq 500, HiSeq 1500, or HiSeq 2500 (Illumina) according to manufacturer's protocols.

Sequencing Platform

instrument_model

NextSeq 500

mm10

Number of total reads

66842070

Reads aligned (%)

90.7

Duplicates removed (%)

39.6

Number of peaks

157 (qval < 1E-05)

mm9

Number of total reads

66842070

Reads aligned (%)

90.6

Duplicates removed (%)

39.8

Number of peaks

145 (qval < 1E-05)