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run_metadata

9 rows where experiment.library_source = "TRANSCRIPTOMIC", experiment.library_strategy = "OTHER" and tissue_curation = "Gonad"

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experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Gonad · 9 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

  • OTHER · 9 ✖

experiment.library_source 1

  • TRANSCRIPTOMIC · 9 ✖

experiment.library_selection 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
29746 29746 SRR27467679 SRX23139227 SRS20090270 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary BS R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary BS rep2 EV02003 EV02003 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA NextSeq 500   SRP482074     EV02003.R1.fastq.gz EV02003.R2.fastq.gz fastq fastq 1031891720.0 3416860.0 EV02003.R1.fastq.gz 0:151 1:151 A:264464363;C:153440613;G:408557241;T:205367487;N:62016 151 151     264464363 153440613 408557241 205367487 62016 SRX23139227 SRS20090270 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 2 0.0 0.00019 0.0 0.00015 1.0 0.99993   1.0 151 151 T T mates < 9% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Adult Adult Gonad Reproductive System
29755 29755 SRR27467688 SRX23139218 SRS20090261 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary DM R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary DM rep2 EV02002 EV02002 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA NextSeq 500   SRP482074     EV02002.R1.fastq.gz EV02002.R2.fastq.gz fastq fastq 861320308.0 2852054.0 EV02002.R1.fastq.gz 0:151 1:151 A:205625519;C:162178974;G:334206312;T:159256900;N:52603 151 151     205625519 162178974 334206312 159256900 52603 SRX23139218 SRS20090261 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 2 2e-05 0.00049 0.0 0.00027 1.0 0.99947   0.44444 151 151 T T mates < 9% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Adult Adult Gonad Reproductive System
29756 29756 SRR27467689 SRX23139217 SRS20090260 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary mock R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary mock rep2 EV02001 EV02001 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA NextSeq 500   SRP482074     EV02001.R1.fastq.gz EV02001.R2.fastq.gz fastq fastq 520371066.0 1723083.0 EV02001.R1.fastq.gz 0:151 1:151 A:116107273;C:90896560;G:218652568;T:94682244;N:32421 151 151     116107273 90896560 218652568 94682244 32421 SRX23139217 SRS20090260 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 2 2e-05 0.00086 0.0 0.00078 0.99995 0.99981 0.0 0.61538 151 151 T T mates < 9% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Adult Adult Gonad Reproductive System
29765 29765 SRR27437485 SRX23109812 SRS20064566 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary BS R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary BS rep3 EV04017 EV04017 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04017.R1.fastq.gz fastq 576584540.0 4118461.0 EV04017.R1.fastq.gz 0:140 A:149516980;C:91163801;G:169046762;T:166831111;N:25886 140       149516980 91163801 169046762 166831111 25886 SRX23109812 SRS20064566 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Adult Adult Gonad Reproductive System
29776 29776 SRR27437496 SRX23109801 SRS20064555 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary DM R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary DM rep3 EV04016 EV04016 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04016.R1.fastq.gz fastq 635752880.0 4541092.0 EV04016.R1.fastq.gz 0:140 A:160072248;C:143996869;G:189137330;T:142516059;N:30374 140       160072248 143996869 189137330 142516059 30374 SRX23109801 SRS20064555 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 1e-05   0.0   0.99997   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Adult Adult Gonad Reproductive System
29777 29777 SRR27437497 SRX23109800 SRS20064554 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary mock R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary mock rep3 EV04015 EV04015 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04015.R1.fastq.gz fastq 489700680.0 3497862.0 EV04015.R1.fastq.gz 0:140 A:126641754;C:126582886;G:130564204;T:105889815;N:22021 140       126641754 126582886 130564204 105889815 22021 SRX23109800 SRS20064554 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 6e-05   0.0   0.99983   0.55555   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Adult Adult Gonad Reproductive System
29786 29786 SRR27435871 SRX23108225 SRS20063062 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary BS R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary BS rep4 EV08003 EV08003 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08003.R1.fastq.gz fastq 571689580.0 4083497.0 EV08003.R1.fastq.gz 0:140 A:141414131;C:88722455;G:138790445;T:202723075;N:39474 140       141414131 88722455 138790445 202723075 39474 SRX23108225 SRS20063062 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 3e-05   0.0   0.99991   0.75   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Adult Adult Gonad Reproductive System
29797 29797 SRR27435882 SRX23108214 SRS20063050 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary DM R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary DM rep4 EV08002 EV08002 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08002.R1.fastq.gz fastq 668593800.0 4775670.0 EV08002.R1.fastq.gz 0:140 A:164584224;C:175789134;G:175538168;T:152637106;N:45168 140       164584224 175789134 175538168 152637106 45168 SRX23108214 SRS20063050 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.00525   2e-05   0.99192   0.63501   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Adult Adult Gonad Reproductive System
29798 29798 SRR27435883 SRX23108213 SRS20063051 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary mock R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary mock rep4 EV08001 EV08001 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08001.R1.fastq.gz fastq 753247460.0 5380339.0 EV08001.R1.fastq.gz 0:140 A:183862675;C:196453674;G:197604061;T:175275086;N:51964 140       183862675 196453674 197604061 175275086 51964 SRX23108213 SRS20063051 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.00754   4e-05   0.98957   0.51048   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 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");;