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run_metadata

12 rows where experiment.library_selection = "unspecified" and tissue_curation_coarse = "Reproductive System"

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tissue_curation_coarse 1

  • Reproductive System · 12 ✖

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • unspecified · 12 ✖

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 1

Link 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
37921 37921 SRR1554495 SRX685396 SRS686645 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF4Ovary1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Ovary2 ZF4Ovary2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF4_Ovary_3.fq.gz fastq 1225610154.0 12134754.0 Ovary2 Run3 0:101 A:347141358;C:303255805;G:280185540;T:294456010;N:571441 101       347141358 303255805 280185540 294456010 571441 SRX685396 SRS686645 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 2e-05   1e-05   1.0       101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37922 37922 SRR1554492 SRX685395 SRS686644 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Testis1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Testis2 ZF2Testis2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF2_Testis_3.fq.gz fastq 1192024422.0 11802222.0 Testis2 Run3 0:101 A:373380865;C:276125943;G:251033102;T:290931637;N:552875 101       373380865 276125943 251033102 290931637 552875 SRX685395 SRS686644 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 3e-05   1e-05   0.99997   0.0   101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37925 37925 SRR1554483 SRX685391 SRS686559 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF3Ovary1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Ovary1 ZF3Ovary2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF3_Ovary_3.fq.gz fastq 347516154.0 3440754.0 Ovary1 Run3 0:101 A:107805981;C:80183725;G:73617313;T:85763181;N:145954 101       107805981 80183725 73617313 85763181 145954 SRX685391 SRS686559 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 5e-05   4e-05   1.0       101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37926 37926 SRR1554480 SRX685390 SRS686542 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Testis1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Testis1 ZF1Testis2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF1_Testis_3.fq.gz fastq 1184228636.0 11725036.0 Testis1 Run3 0:101 A:340636900;C:278505979;G:259975802;T:304564724;N:545231 101       340636900 278505979 259975802 304564724 545231 SRX685390 SRS686542 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 1e-05   0.0   1.0       101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37929 37929 SRR1554493 SRX683354 SRS686645 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF4Ovary1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Ovary2 ZF4Ovary1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF4_Ovary_1.fq.gz fastq 476104278.0 9335378.0 Ovary2 Run1 0:51 A:111060704;C:120863975;G:129849761;T:114224677;N:105161 51       111060704 120863975 129849761 114224677 105161 SRX683354 SRS686645 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.00027   8e-05   0.99945   0.8125   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37930 37930 SRR1554494 SRX683354 SRS686645 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF4Ovary1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Ovary2 ZF4Ovary1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF4_Ovary_2.fq.gz fastq 561956352.0 11018752.0 Ovary2 Run2 0:51 A:129925815;C:148479658;G:148478706;T:132824290;N:2247883 51       129925815 148479658 148478706 132824290 2247883 SRX683354 SRS686645 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.00022   0.0001   0.99967   0.6875   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37931 37931 SRR1554490 SRX683353 SRS686644 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Testis1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Testis2 ZF2Testis1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF2_Testis_1.fq.gz fastq 586152231.0 11493181.0 Testis2 Run1 0:51 A:145360493;C:148943988;G:151402108;T:140286245;N:159397 51       145360493 148943988 151402108 140286245 159397 SRX683353 SRS686644 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 8e-05   2e-05   0.99985   0.57142   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37932 37932 SRR1554491 SRX683353 SRS686644 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Testis1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Testis2 ZF2Testis1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF2_Testis_2.fq.gz fastq 697016337.0 13666987.0 Testis2 Run2 0:51 A:172082858;C:184634425;G:173370430;T:163527914;N:3400710 51       172082858 184634425 173370430 163527914 3400710 SRX683353 SRS686644 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 8e-05   2e-05   0.99985   0.57142   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37937 37937 SRR1554481 SRX683080 SRS686559 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF3Ovary1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Ovary1 ZF3Ovary1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF3_Ovary_1.fq.gz fastq 116086965.0 2276215.0 Ovary1 Run1 0:51 A:29237121;C:30235277;G:29264328;T:27320814;N:29425 51       29237121 30235277 29264328 27320814 29425 SRX683080 SRS686559 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.00022   9e-05   0.99967   0.65   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37938 37938 SRR1554482 SRX683080 SRS686559 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF3Ovary1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Ovary1 ZF3Ovary1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF3_Ovary_2.fq.gz fastq 138905844.0 2723644.0 Ovary1 Run2 0:51 A:34695180;C:38015933;G:33434207;T:32057083;N:703441 51       34695180 38015933 33434207 32057083 703441 SRX683080 SRS686559 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.00016   5e-05   0.99977   0.42857   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37939 37939 SRR1554478 SRX683062 SRS686542 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Testis1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Testis1 ZF1Testis1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF1_Testis_1.fq.gz fastq 655515750.0 12853250.0 Testis1 Run1 0:51 A:152422885;C:163771947;G:179144090;T:159997538;N:179290 51       152422885 163771947 179144090 159997538 179290 SRX683062 SRS686542 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.0011   0.00053   0.99829   0.67777   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37940 37940 SRR1554479 SRX683062 SRS686542 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Testis1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Testis1 ZF1Testis1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF1_Testis_2.fq.gz fastq 777594399.0 15246949.0 Testis1 Run2 0:51 A:180116528;C:202508153;G:204833105;T:186435696;N:3700917 51       180116528 202508153 204833105 186435696 3700917 SRX683062 SRS686542 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.00073   0.00032   0.99898   0.62745   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad 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");;