run_metadata
3 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "other" and tissue_curation = "Gonad"
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 36285 | 36285 | SRR363985 | SRX105298 | SRS270141 | SRP009275 | PRJNA148581 | Hen1 analysis in zebrafish | GSE33582 | Transcriptome Analysis | small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel the small RNA libraries wre made. | pubmed:20859253 | wildtype ligation | GSM830247 | source name:testis|strain:TL|genotype/variation:Hen1 wildtype|tissue:testis|small rna library prep method:adapter ligation | wildtype ligation | three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8 | testis | Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. Adaptors were ligated to the five prime and three prime ends of the isolated RNA and the product was converted to cDNA using a primer on the three prime adaptor. post 15 cycles PCR amplification of the library the product was gel purified and sequenced on a Solexa platform. | strain:TL|genotype/variation:Hen1 wildtype|tissue:testis|small rna library prep method:adapter ligation | GSM830247 | GSM830247: wildtype ligation | GSM830247: wildtype ligation | GSM830247: wildtype ligation | 1 | GEO Accession:GSM830247 | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina Genome Analyzer II | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>46</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> | SRP009275 | read name barcode proc directive:ignore | WTTESTIS.fastq | fastq | 395791130.0 | 8604155.0 | GSM830247 1 | 0:46 | A:79045664;C:90489917;G:99082007;T:127024229;N:149313 | 46 | 79045664 | 90489917 | 99082007 | 127024229 | 149313 | SRX105298 | SRS270141 | SRA047996 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.00021 | 0.00015 | 0.99989 | 0.0 | 46 | T | under 1.2% mapping rate | illumina | early_illumina | 5prime | poly_a | unknown | bulk | unknown | unknown | Netherlands | 2011-11-09 | Undetermined | Undetermined | Gonad | Reproductive System | |||||||||||||||||
| 36286 | 36286 | SRR363984 | SRX105297 | SRS270140 | SRP009275 | PRJNA148581 | Hen1 analysis in zebrafish | GSE33582 | Transcriptome Analysis | small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel the small RNA libraries wre made. | pubmed:20859253 | hen1 mutant ligation | GSM830246 | source name:testis|strain:TL|genotype/variation:Hen1 mutant|tissue:testis|small rna library prep method:adapter ligation | hen1 mutant ligation | three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8 | testis | Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. Adaptors were ligated to the five prime and three prime ends of the isolated RNA and the product was converted to cDNA using a primer on the three prime adaptor. post 15 cycles PCR amplification of the library the product was gel purified and sequenced on a Solexa platform. | strain:TL|genotype/variation:Hen1 mutant|tissue:testis|small rna library prep method:adapter ligation | GSM830246 | GSM830246: hen1 mutant ligation | GSM830246: hen1 mutant ligation | GSM830246: hen1 mutant ligation | 1 | GEO Accession:GSM830246 | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina Genome Analyzer II | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>46</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> | SRP009275 | read name barcode proc directive:ignore | HEN1TESTIS.fastq | fastq | 440876374.0 | 9584269.0 | GSM830246 1 | 0:46 | A:91693980;C:99515953;G:105634029;T:143841954;N:190458 | 46 | 91693980 | 99515953 | 105634029 | 143841954 | 190458 | SRX105297 | SRS270140 | SRA047996 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.00039 | 0.00033 | 0.99995 | 0.0 | 46 | T | under 1.2% mapping rate | illumina | early_illumina | 5prime | poly_a | unknown | bulk | unknown | unknown | Netherlands | 2011-11-09 | Undetermined | Undetermined | Gonad | Reproductive System | |||||||||||||||||
| 36287 | 36287 | SRR363983 | SRX105296 | SRS270139 | SRP009275 | PRJNA148581 | Hen1 analysis in zebrafish | GSE33582 | Transcriptome Analysis | small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel the small RNA libraries wre made. | pubmed:20859253 | wildtype polyA | GSM830245 | source name:testis|strain:TL|genotype/variation:Hen1 wildtype|tissue:testis|small rna library prep method:polyA tailing | wildtype polyA | three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8 | testis | Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. RNA was polyA tailed using polyA polymerase followed by ligation of a RNA adaptor to the five prime phosphate of the small RNAs. First strand cDNA synthesis was performed using an oligodT linker primer and M MLV RNase H reverse transcriptase. post amplification the cDNA was sent for sequencing on an Illumina/Solexa platform. | strain:TL|genotype/variation:Hen1 wildtype|tissue:testis|small rna library prep method:polyA tailing | GSM830245 | GSM830245: wildtype polyA | GSM830245: wildtype polyA | GSM830245: wildtype polyA | 1 | GEO Accession:GSM830245 | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | ILLUMINA | Illumina Genome Analyzer II | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>44</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> | SRP009275 | read name barcode proc directive:ignore | VASAGFPHEN1plusMALE.fastq | fastq | 167344144.0 | 3803276.0 | GSM830245 1 | 0:44 | A:87935982;C:21182538;G:19081938;T:34474815;N:4668871 | 44 | 87935982 | 21182538 | 19081938 | 34474815 | 4668871 | SRX105296 | SRS270139 | SRA047996 | GEO | European Research Institute for the Biology of Ageing, University Medical Center Groningen | 1 | 0.06642 | 0.05042 | 0.99226 | 0.38346 | 44 | B | usable mapping rate | illumina | early_illumina | unknown | poly_a | unknown | bulk | unknown | unknown | Netherlands | 2011-11-09 | Undetermined | Undetermined | 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");;