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14 rows where experiment.library_selection = "PolyA" and experiment.platform = "ION_TORRENT"

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tissue_curation_coarse 1

tissue_curation 1

technology 1

experiment.platform 1

  • ION_TORRENT · 14 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • PolyA · 14 ✖

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
40984 40984 SRR3521412 SRX1763130 SRS1437887 SRP075186 PRJNA321644 Danio rerio RNA structure PRJNA321644 Whole Genome Sequencing RNA structure of Danio rerio to understand role of secondary structure dynamics       Danio rerio transcriptome secondary structure ASWT RNA structure   strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal                 Structure dynamics of zebrafish transcriptome using PAR CLIP RNA structure of Danio rerio: S1 data S1 1     OTHER TRANSCRIPTOMIC PolyA SINGLE ION_TORRENT Ion Torrent Proton <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP075186     S1_replicate1.fq.gz fastq 3198275111.0 46580204.0 S1 replicate 1 0:4 1:64.66 A:903404566;C:767156853;G:800702475;T:727011217;N:0 4 64     903404566 767156853 800702475 727011217 0 SRX1763130 SRS1437887 SRA425688 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 1 0.72262   0.05785   0.76552   0.50263   61   B   usable mapping rate ion_torrent ion_torrent unknown poly_a unknown bulk unknown unknown   India 2016-05-17 Pharyngula Embryo Whole Organism All anatomical structures
40985 40985 SRR3521413 SRX1763130 SRS1437887 SRP075186 PRJNA321644 Danio rerio RNA structure PRJNA321644 Whole Genome Sequencing RNA structure of Danio rerio to understand role of secondary structure dynamics       Danio rerio transcriptome secondary structure ASWT RNA structure   strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal                 Structure dynamics of zebrafish transcriptome using PAR CLIP RNA structure of Danio rerio: S1 data S1 1     OTHER TRANSCRIPTOMIC PolyA SINGLE ION_TORRENT Ion Torrent Proton <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP075186     S1_replicate2.fq.gz fastq 3458893385.0 48723018.0 S1 replicate 2 0:4 1:66.99 A:1012209805;C:783264940;G:815198929;T:848219711;N:0 4 66     1012209805 783264940 815198929 848219711 0 SRX1763130 SRS1437887 SRA425688 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 1 0.80213   0.06798   0.76836   0.50977   64   B   usable mapping rate ion_torrent ion_torrent unknown poly_a unknown bulk unknown unknown   India 2017-05-16 Pharyngula Embryo Whole Organism All anatomical structures
40986 40986 SRR3521414 SRX1763130 SRS1437887 SRP075186 PRJNA321644 Danio rerio RNA structure PRJNA321644 Whole Genome Sequencing RNA structure of Danio rerio to understand role of secondary structure dynamics       Danio rerio transcriptome secondary structure ASWT RNA structure   strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal                 Structure dynamics of zebrafish transcriptome using PAR CLIP RNA structure of Danio rerio: S1 data S1 1     OTHER TRANSCRIPTOMIC PolyA SINGLE ION_TORRENT Ion Torrent Proton <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP075186     S1_replicate3.fq.gz fastq 2246373759.0 27629374.0 S1 replicate 3 0:4 1:77.30 A:680882972;C:506454752;G:543187806;T:515848229;N:0 4 77     680882972 506454752 543187806 515848229 0 SRX1763130 SRS1437887 SRA425688 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 1 0.75362   0.08102   0.80874   0.50576   43   B   usable mapping rate ion_torrent ion_torrent unknown poly_a unknown bulk unknown unknown   India 2016-05-17 Pharyngula Embryo Whole Organism All anatomical structures
40987 40987 SRR3521415 SRX1763130 SRS1437887 SRP075186 PRJNA321644 Danio rerio RNA structure PRJNA321644 Whole Genome Sequencing RNA structure of Danio rerio to understand role of secondary structure dynamics       Danio rerio transcriptome secondary structure ASWT RNA structure   strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal                 Structure dynamics of zebrafish transcriptome using PAR CLIP RNA structure of Danio rerio: S1 data S1 1     OTHER TRANSCRIPTOMIC PolyA SINGLE ION_TORRENT Ion Torrent Proton <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP075186         3113059012.0 39573890.0 S1 replicate 4 0:4 1:74.66 A:917116196;C:724979517;G:776099987;T:694863312;N:0 4 74     917116196 724979517 776099987 694863312 0 SRX1763130 SRS1437887 SRA425688 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 1 0.75652   0.07876   0.81385   0.50701   69   B   usable mapping rate ion_torrent ion_torrent unknown poly_a unknown bulk unknown unknown   India 2016-05-17 Pharyngula Embryo Whole Organism All anatomical structures
40988 40988 SRR3521416 SRX1763130 SRS1437887 SRP075186 PRJNA321644 Danio rerio RNA structure PRJNA321644 Whole Genome Sequencing RNA structure of Danio rerio to understand role of secondary structure dynamics       Danio rerio transcriptome secondary structure ASWT RNA structure   strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal                 Structure dynamics of zebrafish transcriptome using PAR CLIP RNA structure of Danio rerio: S1 data S1 1     OTHER TRANSCRIPTOMIC PolyA SINGLE ION_TORRENT Ion Torrent Proton <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP075186     S1_replicate5.fq.gz fastq 3997589784.0 50540637.0 S1 replicate 5 0:4 1:75.10 A:1185172057;C:921610580;G:981479162;T:909327985;N:0 4 75     1185172057 921610580 981479162 909327985 0 SRX1763130 SRS1437887 SRA425688 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 1 0.77298   0.08278   0.80196   0.50419   122   B   usable mapping rate ion_torrent ion_torrent unknown poly_a unknown bulk unknown unknown   India 2016-05-17 Pharyngula Embryo Whole Organism All anatomical structures
40989 40989 SRR3521417 SRX1763130 SRS1437887 SRP075186 PRJNA321644 Danio rerio RNA structure PRJNA321644 Whole Genome Sequencing RNA structure of Danio rerio to understand role of secondary structure dynamics       Danio rerio transcriptome secondary structure ASWT RNA structure   strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal                 Structure dynamics of zebrafish transcriptome using PAR CLIP RNA structure of Danio rerio: S1 data S1 1     OTHER TRANSCRIPTOMIC PolyA SINGLE ION_TORRENT Ion Torrent Proton <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP075186   loader:fastq load.py S1_nonCodingRNA1.fq.gz fastq 2515453735.0 26514293.0 S1 non coding RNA 1 0:94.87 A:545495988;C:609885515;G:774432484;T:585639748;N:0 94       545495988 609885515 774432484 585639748 0 SRX1763130 SRS1437887 SRA425688 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 1 0.00845   0.0053   0.9976   0.34551   112   T   under 1.2% mapping rate ion_torrent ion_torrent unknown poly_a unknown bulk unknown unknown   India 2017-10-02 Pharyngula Embryo Whole Organism All anatomical structures
40990 40990 SRR3521418 SRX1763130 SRS1437887 SRP075186 PRJNA321644 Danio rerio RNA structure PRJNA321644 Whole Genome Sequencing RNA structure of Danio rerio to understand role of secondary structure dynamics       Danio rerio transcriptome secondary structure ASWT RNA structure   strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal                 Structure dynamics of zebrafish transcriptome using PAR CLIP RNA structure of Danio rerio: S1 data S1 1     OTHER TRANSCRIPTOMIC PolyA SINGLE ION_TORRENT Ion Torrent Proton <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP075186   loader:fastq load.py     923856697.0 17302758.0 S1 non coding RNA 2 0:53.39 A:249661089;C:215235054;G:243253253;T:215639847;N:67454 53       249661089 215235054 243253253 215639847 67454 SRX1763130 SRS1437887 SRA425688 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 1 0.10161   0.02132   0.98435   0.29096   51   B   usable mapping rate ion_torrent ion_torrent unknown poly_a unknown bulk unknown unknown   India 2017-10-02 Pharyngula Embryo Whole Organism All anatomical structures
40991 40991 SRR3521419 SRX1763130 SRS1437887 SRP075186 PRJNA321644 Danio rerio RNA structure PRJNA321644 Whole Genome Sequencing RNA structure of Danio rerio to understand role of secondary structure dynamics       Danio rerio transcriptome secondary structure ASWT RNA structure   strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal                 Structure dynamics of zebrafish transcriptome using PAR CLIP RNA structure of Danio rerio: S1 data S1 1     OTHER TRANSCRIPTOMIC PolyA SINGLE ION_TORRENT Ion Torrent Proton <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP075186         797557294.0 14312934.0 S1 non coding RNA 3 0:4 1:51.72 A:215288442;C:189620793;G:209773713;T:182874346;N:0 4 51     215288442 189620793 209773713 182874346 0 SRX1763130 SRS1437887 SRA425688 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 1 0.09688   0.01835   0.98027   0.29048   75   B   usable mapping rate ion_torrent ion_torrent unknown poly_a unknown bulk unknown unknown   India 2016-05-17 Pharyngula Embryo Whole Organism All anatomical structures
40992 40992 SRR3521405 SRX1763129 SRS1437887 SRP075186 PRJNA321644 Danio rerio RNA structure PRJNA321644 Whole Genome Sequencing RNA structure of Danio rerio to understand role of secondary structure dynamics       Danio rerio transcriptome secondary structure ASWT RNA structure   strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal                 Structure dynamics of zebrafish transcriptome using PAR CLIP RNA structure of Danio rerio V1 1     OTHER TRANSCRIPTOMIC PolyA SINGLE ION_TORRENT Ion Torrent Proton <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP075186     V1_replicate1.fq.gz fastq 4530127185.0 55155258.0 V1 replicate 1 0:4 1:78.13 A:1262427584;C:1070775955;G:1144547430;T:1052376216;N:0 4 78     1262427584 1070775955 1144547430 1052376216 0 SRX1763129 SRS1437887 SRA425688 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 1 0.74907   0.09071   0.7876   0.57031   5   B   usable mapping rate ion_torrent ion_torrent unknown poly_a unknown bulk unknown unknown   India 2016-05-17 Pharyngula Embryo Whole Organism All anatomical structures
40993 40993 SRR3521406 SRX1763129 SRS1437887 SRP075186 PRJNA321644 Danio rerio RNA structure PRJNA321644 Whole Genome Sequencing RNA structure of Danio rerio to understand role of secondary structure dynamics       Danio rerio transcriptome secondary structure ASWT RNA structure   strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal                 Structure dynamics of zebrafish transcriptome using PAR CLIP RNA structure of Danio rerio V1 1     OTHER TRANSCRIPTOMIC PolyA SINGLE ION_TORRENT Ion Torrent Proton <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP075186     V1_replicate2.fq.gz fastq 1189043570.0 25178053.0 V1 replicate 2 0:4 1:43.23 A:319718349;C:286808587;G:313734800;T:268781834;N:0 4 43     319718349 286808587 313734800 268781834 0 SRX1763129 SRS1437887 SRA425688 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 1 0.45251   0.06891   0.80385   0.50742   143   B   usable mapping rate ion_torrent ion_torrent unknown poly_a unknown bulk unknown unknown   India 2016-05-17 Pharyngula Embryo Whole Organism All anatomical structures
40994 40994 SRR3521407 SRX1763129 SRS1437887 SRP075186 PRJNA321644 Danio rerio RNA structure PRJNA321644 Whole Genome Sequencing RNA structure of Danio rerio to understand role of secondary structure dynamics       Danio rerio transcriptome secondary structure ASWT RNA structure   strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal                 Structure dynamics of zebrafish transcriptome using PAR CLIP RNA structure of Danio rerio V1 1     OTHER TRANSCRIPTOMIC PolyA SINGLE ION_TORRENT Ion Torrent Proton <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP075186     V1_replicate3.fq.gz fastq 3554365020.0 38155820.0 V1 replicate 3 0:4 1:89.15 A:1029602890;C:801334700;G:876594681;T:846832749;N:0 4 89     1029602890 801334700 876594681 846832749 0 SRX1763129 SRS1437887 SRA425688 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 1 0.68437   0.09576   0.81688   0.53109   94   B   usable mapping rate ion_torrent ion_torrent unknown poly_a unknown bulk unknown unknown   India 2017-05-16 Pharyngula Embryo Whole Organism All anatomical structures
40995 40995 SRR3521408 SRX1763129 SRS1437887 SRP075186 PRJNA321644 Danio rerio RNA structure PRJNA321644 Whole Genome Sequencing RNA structure of Danio rerio to understand role of secondary structure dynamics       Danio rerio transcriptome secondary structure ASWT RNA structure   strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal                 Structure dynamics of zebrafish transcriptome using PAR CLIP RNA structure of Danio rerio V1 1     OTHER TRANSCRIPTOMIC PolyA SINGLE ION_TORRENT Ion Torrent Proton <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP075186         4005348870.0 44573054.0 V1 replicate 4 0:4 1:85.86 A:1152986833;C:913529601;G:1003588263;T:935244173;N:0 4 85     1152986833 913529601 1003588263 935244173 0 SRX1763129 SRS1437887 SRA425688 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 1 0.65253   0.09144   0.82726   0.52272   87   B   usable mapping rate ion_torrent ion_torrent unknown poly_a unknown bulk unknown unknown   India 2016-05-17 Pharyngula Embryo Whole Organism All anatomical structures
40996 40996 SRR3521409 SRX1763129 SRS1437887 SRP075186 PRJNA321644 Danio rerio RNA structure PRJNA321644 Whole Genome Sequencing RNA structure of Danio rerio to understand role of secondary structure dynamics       Danio rerio transcriptome secondary structure ASWT RNA structure   strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal                 Structure dynamics of zebrafish transcriptome using PAR CLIP RNA structure of Danio rerio V1 1     OTHER TRANSCRIPTOMIC PolyA SINGLE ION_TORRENT Ion Torrent Proton <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP075186     V1_replicate5.fq.gz fastq 3724196991.0 41897201.0 V1 replicate 5 0:4 1:84.89 A:1058600798;C:857924228;G:938831956;T:868840009;N:0 4 84     1058600798 857924228 938831956 868840009 0 SRX1763129 SRS1437887 SRA425688 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 1 0.6539   0.08809   0.82264   0.525   60   B   usable mapping rate ion_torrent ion_torrent unknown poly_a unknown bulk unknown unknown   India 2017-05-16 Pharyngula Embryo Whole Organism All anatomical structures
40997 40997 SRR3521410 SRX1763129 SRS1437887 SRP075186 PRJNA321644 Danio rerio RNA structure PRJNA321644 Whole Genome Sequencing RNA structure of Danio rerio to understand role of secondary structure dynamics       Danio rerio transcriptome secondary structure ASWT RNA structure   strain:Wild Type|breed:ASWT|age:24 hpf stage:24hpf|sex:not determined|tissue:Whole embryo|biomaterial provider:CSIR IGIB|BioSampleModel:Model organism or animal                 Structure dynamics of zebrafish transcriptome using PAR CLIP RNA structure of Danio rerio V1 1     OTHER TRANSCRIPTOMIC PolyA SINGLE ION_TORRENT Ion Torrent Proton <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>0</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP075186   loader:fastq load.py V1_nonCodingRNA.fq.gz fastq 1824118507.0 29210555.0 V1 non coding RNA 0:62.45 A:473289902;C:444879325;G:490109158;T:415840122;N:0 62       473289902 444879325 490109158 415840122 0 SRX1763129 SRS1437887 SRA425688 CSIR-IGIB CSIR- Institute of Genomics and Integrative Biology 1 0.08263   0.01578   0.98021   0.34484   62   B   usable mapping rate ion_torrent ion_torrent unknown poly_a unknown bulk unknown unknown   India 2017-10-02 Pharyngula Embryo Whole Organism All anatomical structures

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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");;