run_metadata
4 rows where experiment.platform = "ION_TORRENT" and tissue_curation_coarse = "Reproductive System"
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 15550 | 15550 | ERR647595 | ERX604031 | ERS557915 | ERP007147 | PRJEB7420 | Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq | ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622 | Other | There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization. | Egg | SAMEA2796300 | UNIVERSITY OF AMSTERDAM | Alias:Egg|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:29:23Z|INSDC status:public|SRA accession:ERS557915|Sample Name:ERS557915|Title:Zebrafish Egg samples|dev stage:Oocytes | Ion Torrent Proton sequencing | ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:25:29:391 1 | RID0024 | 1 | miRNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent Proton | ERP007147 | Ion Torrent Proton sequencing | ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16 | RID0024_016.fastq.gz | fastq | 6684767188.0 | 89052017.0 | ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:25:29:391 1 | 0:75.07 | A:1523328157;C:1795624453;G:1849675240;T:1516139338;N:0 | 75 | 1523328157 | 1795624453 | 1849675240 | 1516139338 | 0 | ERX604031 | ERS557915 | ERA363845 | UNIVERSITY OF AMSTERDAM | UNIVERSITY OF AMSTERDAM | 1 | 0.89536 | 0.15322 | 0.91421 | 0.69019 | 73 | B | usable mapping rate | ion_torrent | ion_torrent | unknown | small_rna | unknown | bulk | unknown | unknown | Netherlands | 2014-10-01 | Zygote | Embryo | Oocyte | Reproductive System | ||||||||||||||||||||||||
| 59512 | 59512 | SRR11924307 | SRX8469983 | SRS6770634 | SRP265951 | PRJNA637293 | The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites | GSE151797 | Other | A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate. | pubmed:32912962 | Unf egg 3 | GSM4591051 | source name:unfertilized egg|tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA | Unf egg 3 | Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. | unfertilized egg | Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description | tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA | GSM4591051 | GSM4591051: Unf egg 3; Danio rerio; OTHER | GSM4591051 | 1 | Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description | GEO Accession:GSM4591051 | OTHER | TRANSCRIPTOMIC | other | SINGLE | ION_TORRENT | Ion Torrent Proton | SRP265951 | intentional duplicate | GSE151797_Reference_sequence.fa Unf_egg_3.bam | bam bam | 149835556.0 | 5777340.0 | GSM4591051 r1 | 0:25.94 | A:27873539;C:50837956;G:37710769;T:33413292;N:0 | 25 | 27873539 | 50837956 | 37710769 | 33413292 | 0 | SRX8469983 | SRS6770634 | SRA1083099 | GEO | RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen | 1 | 0.74561 | 0.22616 | 0.89441 | 0.76897 | 34 | B | usable mapping rate | ion_torrent | ion_torrent | 5prime | small_rna | unknown | bulk | unknown | unknown | Denmark | 2020-06-04 | Zygote | Embryo | Oocyte | Reproductive System | ||||||||||||||||||
| 59513 | 59513 | SRR11924305 | SRX8469982 | SRS6770633 | SRP265951 | PRJNA637293 | The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites | GSE151797 | Other | A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate. | pubmed:32912962 | Unf egg 2 | GSM4591050 | source name:unfertilized egg|tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA | Unf egg 2 | Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. | unfertilized egg | Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description | tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA | GSM4591050 | GSM4591050: Unf egg 2; Danio rerio; OTHER | GSM4591050 | 1 | Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description | GEO Accession:GSM4591050 | OTHER | TRANSCRIPTOMIC | other | SINGLE | ION_TORRENT | Ion Torrent Proton | SRP265951 | intentional duplicate | GSE151797_Reference_sequence.fa Unf_egg_2.bam | bam bam | 235014832.0 | 8915586.0 | GSM4591050 r1 | 0:26.36 | A:43825969;C:79775479;G:60531219;T:50882165;N:0 | 26 | 43825969 | 79775479 | 60531219 | 50882165 | 0 | SRX8469982 | SRS6770633 | SRA1083099 | GEO | RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen | 1 | 0.78414 | 0.23044 | 0.90352 | 0.76934 | 40 | B | usable mapping rate | ion_torrent | ion_torrent | 5prime | small_rna | unknown | bulk | unknown | unknown | Denmark | 2020-06-04 | Zygote | Embryo | Oocyte | Reproductive System | ||||||||||||||||||
| 59514 | 59514 | SRR11924304 | SRX8469981 | SRS6770632 | SRP265951 | PRJNA637293 | The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites | GSE151797 | Other | A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate. | pubmed:32912962 | Unf egg 1 | GSM4591049 | source name:unfertilized egg|tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA | Unf egg 1 | Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. | unfertilized egg | Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description | tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA | GSM4591049 | GSM4591049: Unf egg 1; Danio rerio; OTHER | GSM4591049 | 1 | Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description | GEO Accession:GSM4591049 | OTHER | TRANSCRIPTOMIC | other | SINGLE | ION_TORRENT | Ion Torrent Proton | SRP265951 | intentional duplicate | GSE151797_Reference_sequence.fa Unf_egg_1.bam | bam bam | 245529952.0 | 9182415.0 | GSM4591049 r1 | 0:26.74 | A:46557080;C:80893860;G:66050448;T:52028564;N:0 | 26 | 46557080 | 80893860 | 66050448 | 52028564 | 0 | SRX8469981 | SRS6770632 | SRA1083099 | GEO | RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen | 1 | 0.87423 | 0.27943 | 0.91721 | 0.76816 | 37 | B | usable mapping rate | ion_torrent | ion_torrent | 5prime | small_rna | unknown | bulk | unknown | unknown | Denmark | 2020-06-04 | Zygote | Embryo | Oocyte | 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");;