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Status |
Public on Mar 06, 2024 |
Title |
small RNA guinea pig 1 |
Sample type |
SRA |
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Source name |
oocyte
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Organism |
Cavia porcellus |
Characteristics |
tissue: oocyte Sex: female Stage: GV genotype: wild type molecule subtype: small RNA
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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.
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Library strategy |
miRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina NovaSeq 6000 |
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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
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Submission date |
Apr 08, 2022 |
Last update date |
Mar 06, 2024 |
Contact name |
Wei Liu |
E-mail(s) |
liuwei2018@sibcb.ac.cn
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Organization name |
Chinese Academy of Sciences
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Department |
Institute of Biochemistry and Cell Biology
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Street address |
320 Yueyang Road
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City |
Shanghai |
State/province |
Shanghai |
ZIP/Postal code |
200031 |
Country |
China |
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Platform ID |
GPL28437 |
Series (1) |
GSE200470 |
Divergent composition and transposon-silencing activity of small RNAs in mammalian oocytes |
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Relations |
BioSample |
SAMN27462528 |
SRA |
SRX14786361 |
Supplementary data files not provided |
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Raw data are available in SRA |
Processed data are available on Series record |
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