run_metadata
3 rows where devstage_curation = "Adult" and tissue_curation = "Tail"
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| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 36478 | 36478 | SRR527835 | SRX171222 | SRS352108 | SRP014596 | PRJNA171539 | Transcriptomic analysis of zebrafish during development and homeostasis | GSE39703 | Transcriptome Analysis | Sequencing libraries were generated from total RNA samples following the mRNAseq protocol for the generation of single end 16 hpf 36 hpf 5 day larvae adult head and adult tail or paired end 24 hpf libraries Illumina. Single end reads of 36 nucleotides and paired end reads 2 x 76 nucleotides were obtained with a GAIIx Illumina. Gene expression at the different stages/tissu was assessed by cufflinks and HTseq. Overall design: RNAseq on 5 differents samples: 24hpf embryos pool of 16 hour to 36 hour embryos 5 dpf larvea adult head and adult tail | pubmed:23684812 | tail | GSM977960 | tissue:entire adult tail|genotype:Wild type|strain:AB|Stage:adult tail | tail | Basecalls performed using CASAVA version 1.4 Reads aligned to zebrafish genome Zv9 Ensembl with Tophat v 1.4.1 and Bowtie v 0.12.7 options: butterfly search coverage search microexon search min anchor length 5 G GTF Determination of raw reads aligned to ZV9 with HTSeq v0.5.3p3 and gtf file ensembl zv9 release 60 Determination of RPKM/FPKM with cufflinks v 1.3.0 with the options u b M rRNA/Mtgenes mask G gtf Genome build: Zv9 v 60 Supplementary files format and content: *.count file are the output of Htseq reads quantification. *.fpkm files are the output of cufflinks quantification | entire adult tail | Extraction of total RNA with Trizol following manufacturer's instruction. Generation of mRNA libraries with Trueseq RNA kit following Illumina's instructions | genotype:Wild type|strain:AB|Stage:adult tail | GSM977960 | GSM977960: tail; Danio rerio; RNA Seq | GSM977960 1 | GSM977960: tail | 1 | GEO Accession:GSM977960 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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> | SRP014596 | 534897504.0 | 14858264.0 | GSM977960 r1 | 0:36 | A:144900139;C:122639505;G:130189210;T:136990883;N:177767 | 36 | 144900139 | 122639505 | 130189210 | 136990883 | 177767 | SRX171222 | SRS352108 | SRA056408 | GEO | ITG | 1 | 0.89933 | 0.04578 | 0.71254 | 0.41668 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Unknown | 2012-07-27 | Adult | Adult | Tail | Multi-system | ||||||||||||||||||||
| 41418 | 41418 | SRR4423118 | SRX2245302 | SRS1745860 | SRP091534 | PRJNA347637 | Danio rerio and Xenopus laevis Raw sequence reads | PRJNA347637 | Other | To study the transcriptome during development | Adult FT Dr | strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:female|tissue:tail|BioSampleModel:Model organism or animal | miRNA Seq of Zebrafish: Adult female tail | 172 5 | 172 5 | Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol. | miRNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent Proton | SRP091534 | femaletailRID0172BC05smallZF.fastq | fastq | 491055734.0 | 7690105.0 | femaletailRID0172BC05smallZF.fastq | 0:63.86 | A:114732043;C:132287469;G:130972143;T:113064079;N:0 | 63 | 114732043 | 132287469 | 130972143 | 113064079 | 0 | SRX2245302 | SRS1745860 | SRA485147 | Universiteit van Amsterdam|SILS | Universiteit van Amsterdam | 1 | 0.82246 | 0.13521 | 0.91303 | 0.63226 | 43 | B | usable mapping rate | ion_torrent | ion_torrent | unknown | small_rna | unknown | bulk | unknown | unknown | Netherlands | 2016-10-19 | Adult | Adult | Tail | Multi-system | ||||||||||||||||||||||||||||
| 41419 | 41419 | SRR4423117 | SRX2245301 | SRS1745860 | SRP091534 | PRJNA347637 | Danio rerio and Xenopus laevis Raw sequence reads | PRJNA347637 | Other | To study the transcriptome during development | Adult FT Dr | strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:female|tissue:tail|BioSampleModel:Model organism or animal | RNA Seq of Zebrafish: Adult female tail | 172 3 | 172 3 | Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent Proton | SRP091534 | femaletailRID0172BC03largeZF.fastq | fastq | 1414932187.0 | 9757587.0 | femaletailRID0172BC03largeZF.fastq | 0:145.01 | A:343007105;C:362895564;G:422320111;T:286709407;N:0 | 145 | 343007105 | 362895564 | 422320111 | 286709407 | 0 | SRX2245301 | SRS1745860 | SRA485147 | Universiteit van Amsterdam|SILS | Universiteit van Amsterdam | 1 | 0.96057 | 0.21796 | 0.95177 | 0.76663 | 141 | B | usable mapping rate | ion_torrent | ion_torrent | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Netherlands | 2016-10-19 | Adult | Adult | Tail | Multi-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");;