GSM3074500: SpragueDawley_oocyte_RNAseq_rep1; Rattus norvegicus; RNA-... - SRA

SRX3875402: GSM3074500: SpragueDawley_oocyte_RNAseq_rep1; Rattus norvegicus; RNA-Seq
1 ILLUMINA (NextSeq 500) run: 56.3M spots, 8.5G bases, 3.3Gb downloads

Submitted by: NCBI (GEO)

Study: LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation

PRJNA448528 • SRP136995 • All experiments • All runs

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De novo DNA methylation (DNAme) occurs coincident with transcription during mouse oogenesis. As many oocyte transcripts originate in Long Terminal Repeats (LTRs), which are divergent across species, we examined whether polymorphic LTR-initiated transcription units (LITs) shape the oocyte methylome. We identified thousands of syntenic regions in mouse, rat and human, including CpG islands (CGIs), that show divergent DNAme associated with polymorphic LITs. Notably, many CGI promoters methylated exclusively in mouse and/or rat are embedded within rodent-specific LITs, and show persistent maternal methylation in the blastocyst. Polymorphic LITs are also responsible for divergent methylation of CGI promoters in distantly related mouse strains, revealing that LITs also promote intra-species diversification of promoter DNAme. Overall design: Total RNA-seq in mouse and rat oocytes; H3K36me3 ChIP-seq in mouse oocytes

Sample: SpragueDawley_oocyte_RNAseq_rep1

SAMN08848929 • SRS3115878 • All experiments • All runs

Organism: Rattus norvegicus

Library:

Instrument: NextSeq 500

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Construction protocol: RNA-seq: total RNA was isolated from 100-200 mouse or rat oocytes using TriReagent, and ribosomal RNA was depleted using NEB Next rRNA Depletion kit according to manufacturer's instruction. Double stranded cDNA was synthesized using NEB Next first strand and second strand synthesis modules. Libraries were constructed using a custom protocol (Brind'Amour et al. 2015) and amplified for 10-12 PCR cycles (RNA) or 15 PCR cycles (ChIP). 75 bp or 100bp paired-end libraries were sequenced on the NextSeq 500 or HiSeq 2500 platform an according to manufacturer's protocols.

Experiment attributes:

GEO Accession: GSM3074500

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 56.3M spots, 8.5G bases, 3.3Gb

Run	# of Spots	# of Bases	Size	Published
SRR6929782	56,254,114	8.5G	3.3Gb	2018-07-06

ID:: 5327926

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