{"database": "metadata", "table": "run_metadata", "rows": [[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.", null, "pubmed:38532500", null, "small RNA zebrafish 1", "GSM6034592", null, "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", null, "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 \u00b0C for 3 min then cooled in ice. post 3\u2032 adapter ligation  the samples were incubated with 5 U of lambda exonuclease and 25 U of 5\u2032 de adenylates. Small RNAs were reverse transcribed post 5\u2032 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 \u00b0C for 3 min and then cooled on ice. For every single oocyte  1 \u03bcl 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.", null, "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 \u00b0C for 3 min then cooled in ice. post 3\u2032 adapter ligation  the samples were incubated with 5 U of lambda exonuclease and 25 U of 5\u2032 de adenylates. Small RNAs were reverse transcribed post 5\u2032 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 \u00b0C for 3 min and then cooled on ice. For every single oocyte  1 \u03bcl 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.", null, "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP368241", null, null, "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, null, null, 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, null, 0.0, null, 0.99965, null, 0.96551, null, 150, null, "T", null, "under 1.2% mapping rate", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-08", "Zygote", "Embryo", "Oocyte", "Reproductive System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["69437"], "units": {}, "query_ms": 11.049310000089463}