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Sample GSM6034576 Query DataSets for GSM6034576
Status Public on Mar 06, 2024
Title small RNA Chinese hamster 2
Sample type SRA
 
Source name oocyte
Organism Cricetulus griseus
Characteristics tissue: oocyte
Sex: female
Stage: GV
genotype: wild type
molecule subtype: small RNA
Extracted molecule total RNA
Extraction 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.
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NovaSeq 6000
 
Data processing We used cutadapt to clip adaptor and filter low quality reads. Reads failing to match the adaptor or reads with lengths shorter than 17 nt were discarded. Redundant sequences were collapsed as useful reads and mapped to reference sequences by bowite. The useful reads were assigned to known miRNAs, tsRNA (tRNA-derived small non-coding RNA), rsRNA (rRNA-derived small non-coding RNA), small snoRNAs, lncRNA, and mRNA, successively. The reads that could not be mapped to these known small RNAs were used to predict piRNAs and endo-siRNAs successively. Sequences that were not annotated with any of the RNA categories above were classified as others.
We used trimmomatic to clip adaptor and filter low quality reads. The high quality reads were mapped to reference genomes by STAR. The expressed levels of genes were caculated in TPM (transcripts per kilobase of exon model per million mapped reads) by StringTie.
Assembly: GRCh38, GRCm38
Supplementary files format and content: tab-delimited text files include TPM values or raw counts for each Sample
 
Submission date Apr 08, 2022
Last update date Mar 06, 2024
Contact name Wei Liu
E-mail(s) [email protected]
Organization name Chinese Academy of Sciences
Department Institute of Biochemistry and Cell Biology
Street address 320 Yueyang Road
City Shanghai
State/province Shanghai
ZIP/Postal code 200031
Country China
 
Platform ID GPL27425
Series (1)
GSE200470 Divergent composition and transposon-silencing activity of small RNAs in mammalian oocytes
Relations
BioSample SAMN27462474
SRA SRX14786314

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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