metadata: run_metadata: 5 rows where experiment.library_strategy = "miRNA-Seq" and tissue

5 rows where experiment.library_strategy = "miRNA-Seq" and tissue_curation = "Oocyte"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	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.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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
15550	15550	ERR647595	ERX604031	ERS557915	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.		Egg	SAMEA2796300	UNIVERSITY OF AMSTERDAM	Alias:Egg\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:29:23Z\|INSDC status:public\|SRA accession:ERS557915\|Sample Name:ERS557915\|Title:Zebrafish Egg samples\|dev stage:Oocytes							Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:25:29:391 1	RID0024	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0024_016.fastq.gz	fastq	6684767188.0	89052017.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:25:29:391 1	0:75.07	A:1523328157;C:1795624453;G:1849675240;T:1516139338;N:0	75		1523328157	1795624453	1849675240	1516139338	0	ERX604031	ERS557915	ERA363845	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.89536	0.15322	0.91421	0.69019	73	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Zygote	Embryo	Oocyte	Reproductive System
38256	38256	SRR1596061	SRX719267	SRS715451	SRP048591	PRJNA262865	Identification and Characterization of MicroRNAs in Zebrafish Spermatozoa by Illumina Sequencing	GSE61984	Other	MicroRNAs miRNAs are involved in nearly every biological process examined to date. Mounting evidence show that some spermatozoa specific miRNAs play important roles in the regulation of spermatogenesis and germ cells development but little is known of the exact identity and function of miRNA in sperm cells or their potential involvement in spermatogenesis and germ cells development. Here we investigated the spermatozoa miRNA profiles using illumina deep sequencing combined with bioinformatic analysis using zebrafish as a model system. Deep sequencing of small RNAs yielded 12 million raw reads from zebrafish spermatozoa. Analysis showed that the noncoding RNA of the spermatozoa included tRNA rRNA snRNA snoRNA and miRNA. By mapping to the zebrafish genome we identified 400 novel and 204 conserved miRNAs which could be grouped into 104 families including zebrafish specific families such as mir 731 mir 724 mir 725 mir 729 and mir 2185. We report the first characterization of the miRNAs profiling in zebrafish spermatozoa. The obtained spermatozoa miRNAs profiling will serve as valuable resources to systematically study spermatogenesis in fish and vertebrate. Overall design: Examination of small RNA populations in zebrafish spermatozoa	pubmed:26418264	zebrafish sperm	GSM1517943		tissue:Zebrafish Spermatozoa\|cell type:Spermatozoa\|strain:AB wild type	zebrafish sperm	The sequencing data were analyzed as described previously by Xu et al 2014. The low quality reads were filtered to remove reads without xxx 3’ adaptor 5’ adaptor contaminant reads reads without xxx insert fragment reads containing polyA stretches and reads of less than 18 nt. Next the remaining sequences clean reads were mapped to the zebrafish genome using SOAP with a tolerance of one mismatch to analyze their distribution The sequences were aligned against known miRNA precursors and mature miRNAs deposited in the miRBase 20.0 to identify conserved miRNAs. The clean reads were compared against the sRNAs rRNAs tRNAs snRNAs snoRNA miRNA deposited in the GenBank and Rfam http://www.sanger.ac.uk/resources/databases/rfam.html databases to annotate the sRNA sequences. Because some sRNA tags might map to more than one category we used priority rules to ensure that every unique sRNA was mapped to only one annotation as follows: rRNA etc. GenBank >Rfam >known miRNA >repeat >exon >intron. Genome build: miRBase 20.0 Supplementary files format and content: zebrafish miRNA count.txt include RPKM values of each known miRNA in this sample	Zebrafish Spermatozoa	Total RNA was isolated from sample using Trizol reagent Invitrogen USA in accordance with the manufacturer’s protocol. RNA integrity was confirmed using the 2100 Bioanalyzer Agilent Technologies. RNA samples that passed the quality check were sent to BGI Shenzhen China for sRNA library construction and Solexa sequencing using standard protocols on the Illumina Hiseq 2000 platform.	cell type:Spermatozoa\|strain:AB wild type	GSM1517943	GSM1517943: zebrafish sperm; Danio rerio; miRNA Seq	GSM1517943		1	Total RNA was isolated from sample using Trizol reagent Invitrogen USA in accordance with the manufacturer’s protocol. RNA integrity was confirmed using the 2100 Bioanalyzer Agilent Technologies. RNA samples that passed the quality check were sent to BGI Shenzhen China for sRNA library construction and Solexa sequencing using standard protocols on the Illumina Hiseq 2000 platform.	GEO Accession:GSM1517943	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP048591			zebrafish-sperm5.fq.bz2	fastq	588000000.0	12000000.0	GSM1517943 r1	0:49	A:122673394;C:136175879;G:140377184;T:188702650;N:70893	49		122673394	136175879	140377184	188702650	70893	SRX719267	SRS715451	SRA188511	GEO	SUN YAT-SEN UNIVERSITY	1	2e-05	0.0	0.99997	1.0	49	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2014-10-02	Zygote	Embryo	Oocyte	Reproductive System
69435	69435	SRR18685198	SRX14786396	SRS12545301	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 3	GSM6034594		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 3	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	GSM6034594	GSM6034594: small RNA zebrafish 3; Danio rerio; miRNA Seq	GSM6034594 r1	GSM6034594	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			Zebrafish3_combined_R1.fastq.gz	fastq	687816450.0	4585443.0	GSM6034594 r1	0:150 1:0	A:94948683;C:106096224;G:367933691;T:118821697;N:16155	150	0	94948683	106096224	367933691	118821697	16155	SRX14786396	SRS12545301	SRA1400916	Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences	Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences	1	2e-05	0.0	0.99993	0.66666	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
69436	69436	SRR18685199	SRX14786395	SRS12545300	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 2	GSM6034593		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 2	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	GSM6034593	GSM6034593: small RNA zebrafish 2; Danio rerio; miRNA Seq	GSM6034593 r1	GSM6034593	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			Zebrafish2_combined_R1.fastq.gz	fastq	354830850.0	2365539.0	GSM6034593 r1	0:150 1:0	A:48935028;C:57418354;G:192263153;T:56206000;N:8315	150	0	48935028	57418354	192263153	56206000	8315	SRX14786395	SRS12545300	SRA1400916	Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences	Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences	1	0.00026	0.0	0.99967	1.0	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
69437	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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;