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run_metadata

5 rows where experiment.library_selection = "size fractionation", experiment.library_strategy = "RNA-Seq" and tissue_curation_coarse = "Surface Structure"

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devstage_curation 5

experiment.library_layout 2

devstage_curation_coarse 2

tissue_curation_coarse 1

  • Surface Structure · 5 ✖

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

  • RNA-Seq · 5 ✖

experiment.library_source 1

experiment.library_selection 1

  • size fractionation · 5 ✖
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
36272 36272 SRR298567 SRX079845 SRS212651 SRP007331 PRJNA141525 Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. GSE29418 Transcriptome Analysis RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.   pubmed:21743441   ZiliIPTes GSM727524   tissue:RNA obtained from immunoprecipitation with Zili antibody|strain:TL ZiliIPTes three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. RNA obtained from immunoprecipitation with Zili antibody   Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 µl Dynabeads Invitrogen 3 or 6 testes and Zili antibody in a total volume of 500 µl. RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.   strain:TL GSM727524 GSM727524: ZiliIPTes GSM727524: ZiliIPTes GSM727524: ZiliIPTes 1   GEO Accession:GSM727524 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer II <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> SRP007331   read name barcode proc directive:ignore ZiliIPTes.fastq fastq 995759064.0 27659974.0 GSM727524 1 0:36   36                 SRX079845 SRS212651 SRA039167 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.0537   0.03117   0.95856   0.42091   36   B   usable mapping rate illumina early_illumina 5prime size_fractionation unknown bulk unknown unknown   Netherlands 2011-05-20 Undetermined Undetermined Trunk Surface Structure
36335 36335 SRR398322 SRX115580 SRS285697 SRP010291 PRJNA150927 miR 221 is required for endothelial tip cell behaviors during vascular development GSE35078 Transcriptome Analysis Through deep sequencing and functional screening in zebrafish we find that miR 221 is essential for angiogenesis. miR 221 knockdown phenocopied defects associated with loss of the tip cell expressed Flt4 receptor. Furthermore miR 221 was required for tip cell proliferation and migration as well as tip cell potential in mosaic blood vessels. miR 221 knockdown also prevented “hyper angiogenesis” defects associated with Notch deficiency and miR 221 expression was inhibited by Notch signaling. Finally miR 221 promoted tip cell behavior through repression of two targets: cyclin dependent kinase inhibitor 1b cdkn1b and phosphoinositide 3 kinase regulatory subunit 1 pik3r1. These results identify miR 221 as an important regulatory node through which tip cell migration and proliferation are controlled during angiogenesis. Overall design: Identification of endothelial expressed microRNA from FACS isolated zebrafish endothelial cells.   pubmed:22340502   miRNA GFP minus GSM861784   source name:whole zebrafish embryos at 24 hpf|age:24 hpf|development stage:embryo|tissue:whole body|cell type:all cell types miRNA GFP minus The standard Illumina pipeline was applied for base calls and quality scoring; sequence tags were subsequently analyzed using miR Deep2. whole zebrafish embryos at 24 hpf Tgkdrl:egfp embryos were dissociated at 24 hpf followed by fluorescence activated cell sorting to isolate GFP positive and negative cells. Small RNAs were isolated by polyacrylamide gel electrophoresis and ligated to RNA adapters followed by cDNA synthesis and amplification with Illumina primers.   age:24 hpf|developmental stage:embryo|tissue:whole body|cell type:all cell types GSM861784 GSM861784: miRNA GFP minus; Danio rerio; RNA Seq GSM861784 1 GSM861784: miRNA GFP minus 1   GEO Accession:GSM861784 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer <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> SRP010291     miRNA_CNTL_WT.fastq.gz fastq 295021332.0 8195037.0 GSM861784 r1 0:36 A:70414178;C:53495749;G:76994313;T:87833261;N:6283831 36       70414178 53495749 76994313 87833261 6283831 SRX115580 SRS285697 SRA049243 GEO Nathan Lawson Lab, PGFE, Umass Medical School 1 0.02832   0.02716   0.99957   0.43137   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   United States 2012-01-12 Pharyngula Embryo Trunk Surface Structure
48627 48627 SRR7280654 SRX4184228 SRS3395608 SRP149913 PRJNA474911 Origin and Evolution of Neural Microexons PRJNA474911 Other Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized "enhancer of microexon" eMIC protein domain     Pool of one hundred 2hpf embryos 2hpf embryos Embr 2hpf   strain:AB|dev stage:2hpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: 2hpf embryos Embr 2hpf Embr 2hpf RNA extracted from a pool of one hundred embryos     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2500   SRP149913     Embr_2hpf_R2-125.fq.gz Embr_2hpf_R1-125.fq.gz fastq fastq 17109578000.0 68438312.0 Embr 2hpf R1 125.fq.gz 0:125 1:125 A:4536550134;C:4009266695;G:4076560218;T:4484964079;N:2236874 125 125     4536550134 4009266695 4076560218 4484964079 2236874 SRX4184228 SRS3395608 SRA717220 Centre for Genomic Regulation|Systems Biology Department Centre for Genomic Regulation 2 0.96221 0.96458 0.02765 0.02716 0.77116 0.77325 0.48649 0.4853 125 125 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Spain 2019-01-22 Cleavage Embryo Trunk Surface Structure
48628 48628 SRR7280655 SRX4184227 SRS3395607 SRP149913 PRJNA474911 Origin and Evolution of Neural Microexons PRJNA474911 Other Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized "enhancer of microexon" eMIC protein domain     Pool of one hundred 8hpf embryos 8hpf embryos Embr 8hpf   strain:AB|dev stage:8hpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: 8hpf embryos Embr 8hpf Embr 8hpf RNA extracted from a pool of one hundred embryos     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2500   SRP149913     Embr_8hpf_R1-125.fq.gz Embr_8hpf_R2-125.fq.gz fastq fastq 20486524750.0 81946099.0 Embr 8hpf R2 125.fq.gz 0:125 1:125 A:5437735333;C:4808439456;G:4859422420;T:5377132981;N:3794560 125 125     5437735333 4808439456 4859422420 5377132981 3794560 SRX4184227 SRS3395607 SRA717220 Centre for Genomic Regulation|Systems Biology Department Centre for Genomic Regulation 2 0.96373 0.95763 0.07096 0.0702 0.75937 0.75866 0.48455 0.484 125 125 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Spain 2019-01-22 Gastrula Embryo Trunk Surface Structure
48629 48629 SRR7280656 SRX4184226 SRS3395606 SRP149913 PRJNA474911 Origin and Evolution of Neural Microexons PRJNA474911 Other Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized "enhancer of microexon" eMIC protein domain     Pool of one hundred 12hpf embryos 12hpf embryos Embr 12hpf   strain:AB|dev stage:12hpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: 12hpf embryos Embr 12hpf Embr 12hpf RNA extracted from a pool of one hundred embryos     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2500   SRP149913     Embr_12hpf_R2-125.fq.gz Embr_12hpf_R1-125.fq.gz fastq fastq 22366284500.0 89465138.0 Embr 12hpf R1 125.fq.gz 0:125 1:125 A:5886492098;C:5284016845;G:5382041408;T:5809628253;N:4105896 125 125     5886492098 5284016845 5382041408 5809628253 4105896 SRX4184226 SRS3395606 SRA717220 Centre for Genomic Regulation|Systems Biology Department Centre for Genomic Regulation 2 0.96226 0.96763 0.06393 0.06451 0.74355 0.74472 0.48233 0.48387 125 125 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Spain 2019-01-22 Segmentation Embryo Trunk Surface Structure

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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");;