run_metadata: 69437

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rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
69437	SRR18685200	SRX14786394	SRS12545299	SRP368241	PRJNA824784	Divergent composition and transposon silencing activity of small RNAs in mammalian oocytes	GSE200470	Other	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' three prime 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.		pubmed:38532500		small RNA zebrafish 1	GSM6034592		source name:oocyte\|tissue:oocyte\|Sex:female\|Stage:MII\|genotype:wild type\|molecule subtype:small RNA\|geo loc name:missing\|collection date:missing	small RNA zebrafish 1	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	oocyte		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. post 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 post 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. post reverse transcription and PCR pre amplification cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.		tissue:oocyte\|Sex:female\|Stage:MII\|genotype:wild type\|molecule subtype:small RNA	GSM6034592	GSM6034592: small RNA zebrafish 1; Danio rerio; miRNA Seq	GSM6034592 r1	GSM6034592	1	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. post 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 post 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. post reverse transcription and PCR pre amplification cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.		miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP368241			Zebrafish1_combined_R1.fastq.gz	fastq	1096131600.0	7307544.0	GSM6034592 r1	0:150 1:0	A:172547981;C:159060763;G:590708513;T:173788947;N:25396	150	0			172547981	159060763	590708513	173788947	25396	SRX14786394	SRS12545299	SRA1400916	Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences	Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences	1	0.00016		0.0		0.99965		0.96551		150		T		under 1.2% mapping rate	illumina	novaseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown		China	2022-04-08	Zygote	Embryo	Oocyte	Reproductive System