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SRX14786305: GSM6034567: small RNA mouse 5; Mus musculus; miRNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 15.5M spots, 2.3G bases, 765.9Mb downloads

External Id: GSM6034567_r1
Submitted by: Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences
Study: Divergent composition and transposon-silencing activity of small RNAs in mammalian oocytes
show Abstracthide Abstract
We found piRNAs with different lengths represented the predominant small RNA species in oocytes from the 12 explored species, except mouse. We found endo-siRNAs resulted from the truncated Dicer isoform were mouse-specific, and os-piRNAs associating with PIWIL3 in human oocytes are widespread in mammals and are typically with low levels of the 2'-3'-O-methylation. The sequences of many highly expressed piRNA clusters are fast-evolving compared with their syntenic genomic locations, and the TE families distributing in the conserved piRNA clusters are various between species. Overall design: Profiling small RNAs and mRNA in oocytes from 12 animals.
Sample: small RNA mouse 5
SAMN27462503 • SRS12545210 • All experiments • All runs
Organism: Mus musculus
Library:
Name: GSM6034567
Instrument: Illumina NovaSeq 6000
Strategy: miRNA-Seq
Source: TRANSCRIPTOMIC
Selection: size fractionation
Layout: SINGLE
Construction protocol: Total RNA from oocytes of different species were extracted with TRIzol Reagent (Ambion, USA), respectively. Small RNA library construction. Briefly, the single oocytes were incubated at 72 °C for 3 min then cooled in ice. After 3′ adapter ligation, the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de-adenylates. Small RNAs were reverse-transcribed after 5′ adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel. mRNA library construction. In brief, single oocytes were incubated at 72 °C for 3 min and then cooled on ice. For every single oocyte, 1 μl of a 1/500,000-1/50,000 dilution of the ERCC RNA Spike-In Mix (Invitrogen, 4456740) was added. After reverse transcription and PCR pre-amplification, cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.
Runs: 1 run, 15.5M spots, 2.3G bases, 765.9Mb
Run# of Spots# of BasesSizePublished
SRR1868528915,519,6442.3G765.9Mb2024-03-06

ID:
21169209

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