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run_metadata

4 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "size fractionation" and experiment.library_strategy = "OTHER"

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tissue_curation_coarse 2

tissue_curation 2

devstage_curation_coarse 2

devstage_curation 2

technology 1

experiment.platform 1

experiment.library_strategy 1

  • OTHER · 4 ✖

experiment.library_source 1

experiment.library_selection 1

  • size fractionation · 4 ✖

experiment.library_layout 1

  • PAIRED · 4 ✖
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
40707 40707 SRR3502888 SRX1760541 SRS1436386 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.       Zebrafish tRNA at 6hpf tRNA AB 6h   strain:TUAB|age:6hpf|dev stage:Shield|sex:pooled male and female|tissue:Whole animal|collected by:Ariel Bazzini|genotype:WT|BioSampleModel:Model organism or animal                 Zebrafish tRNAs at 6hpf tRNA 6hpf zebrafish TGIRT tRNA Library 1     OTHER TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP072296     AB-tRNA_S9_R1_001.fastq.gz AB-tRNA_S9_R2_001.fastq.gz fastq fastq 7860522000.0 26201740.0 tRNA zebrafish 6hpf 0:150 1:150 A:1945184302;C:2012637521;G:2171934357;T:1730625218;N:140602 150 150     1945184302 2012637521 2171934357 1730625218 140602 SRX1760541 SRS1436386 SRA395141 Yale University|Giraldez Lab Yale University 2 0.04186 0.04313 0.00633 0.00639 0.96834 0.96913 0.53967 0.5329 150 150 T T mates < 9% mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   United States 2016-06-17 Gastrula 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");;