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10 rows where experiment.library_selection = "other", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation_coarse = "Undetermined"

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experiment.platform 3

experiment.library_strategy 3

experiment.library_layout 2

devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

  • Undetermined · 10 ✖

tissue_curation 1

technology 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 10 ✖

experiment.library_selection 1

  • other · 10 ✖
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
33123 33123 SRR29672615 SRX25176099 SRS21866000 SRP517393 PRJNA1130538 ac4C transcriptomes of Zebrafish and Worm GSE271258 Other ac4C modification appears in mutilple model organisms including Zebrafish and Worm Overall design: To investigate whether ac4C modification is involved in evolution we performed ac4C RIP seq on Zebrafish and Worm.       Zebrafish ac4C GSM8372406   tissue:Animal organ cells|cell type:Animal organ cells|genotype:Wild type|rip antibody:anti ac4C Abcam catalog No. ab252215|geo loc name:missing|collection date:missing Zebrafish ac4C The raw ac4C RIP seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for ac4C modification peak calling and the significant methylation was identified by exomepeak2 and the ac4C peak calling can be visualized by IGV software. The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME was used to determine if the ac4C peaks contained the consensus of ac4C motif sequences. For mRNA seq the mRNA expression level was analyzed by StringTie and differentially expressed mRNAs were calculated by DEseq. The substrates of ac4C regulators were obtained from starBase v2.0. The statistical enrichment analysis of Gene Ontology GO and Kyoto Encyclopedia of Genes and Genomes KEGG pathway for differentially expressed genes DEGs and differentially methylated mRNAs were applied by DAVID. Assembly: danRer10 or WBcel235 Supplementary files format and content: The processed data files is in CSV format containing the expression levels and ac4C status changes for each gene. Animal organ cells   Total RNA was extracted according to manufacturer’s instruction. The stranded RNA sequencing library was constructed by KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules. The library products corresponding to 200 500 bps were enriched   cell type:Animal organ cells|genotype:Wild type|rip antibody:anti ac4C Abcam catalog No. ab252215 GSM8372406 GSM8372406: Zebrafish ac4C; Danio rerio; RIP Seq GSM8372406 r1 GSM8372406 1 Total RNA was extracted according to manufacturer's instruction. The stranded RNA sequencing library was constructed by KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules. The library products corresponding to 200 500 bps were enriched   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP517393     Fish_IP.clean.R2.fastq.gz Fish_IP.clean.R1.fastq.gz fastq fastq 816231517.0 3830403.0 GSM8372406 r1 0:102.34 1:110.76 A:199381841;C:207571478;G:205740791;T:203535549;N:1858 102 110     199381841 207571478 205740791 203535549 1858 SRX25176099 SRS21866000 SRA1914369 Fujian Medical University Fujian Medical University 2 0.60415 0.60545 0.08824 0.08794 0.78796 0.78733 0.43432 0.43842 126 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-07-01 Undetermined Undetermined Undetermined Undetermined
52210 52210 SRR9021058 SRX5799154 SRS4730324 SRP195685 PRJNA541367 Global transcriptomic analysis of zebrafish glucagon receptor mutant PRJNA541367 Other We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.         WT 1   replicate:biological replicate 1|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal                 Diano rerio transcriptome WT 1 20190506 1 WT 1 20190506 1 RNA seq of WT Diano rerio     RNA-Seq TRANSCRIPTOMIC other SINGLE BGISEQ BGISEQ-500   SRP195685   loader:fastq load.py WT1.1.fq fastq 1094498950.0 21889979.0 WT1.1.fq 0:50 A:291195764;C:255539280;G:262638316;T:284737693;N:387897 50       291195764 255539280 262638316 284737693 387897 SRX5799154 SRS4730324 SRA883435 Xiamen University|School of Pharmaceutical Sciences Xiamen University 1 0.94195   0.09713   0.66689   0.47749   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-18 Larval Larval Undetermined Undetermined
52211 52211 SRR9021059 SRX5799153 SRS4730323 SRP195685 PRJNA541367 Global transcriptomic analysis of zebrafish glucagon receptor mutant PRJNA541367 Other We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.         WT 2   replicate:biological replicate 2|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal                 Diano rerio transcriptome WT 2 20190506 2 WT 2 20190506 2 RNA seq of WT Diano rerio     RNA-Seq TRANSCRIPTOMIC other SINGLE BGISEQ BGISEQ-500   SRP195685   loader:fastq load.py WT2.1.fq fastq 1095133200.0 21902664.0 WT2.1.fq 0:50 A:290594757;C:255644044;G:259681140;T:288014102;N:1199157 50       290594757 255644044 259681140 288014102 1199157 SRX5799153 SRS4730323 SRA883435 Xiamen University|School of Pharmaceutical Sciences Xiamen University 1 0.93368   0.09166   0.67085   0.46523   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-18 Larval Larval Undetermined Undetermined
52212 52212 SRR9021060 SRX5799152 SRS4730322 SRP195685 PRJNA541367 Global transcriptomic analysis of zebrafish glucagon receptor mutant PRJNA541367 Other We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.         WT 3   replicate:biological replicate 3|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal                 Diano rerio transcriptome WT 3 20190506 3 WT 3 20190506 3 RNA seq of WT Diano rerio     RNA-Seq TRANSCRIPTOMIC other SINGLE BGISEQ BGISEQ-500   SRP195685   loader:fastq load.py WT3.1.fq fastq 1096083900.0 21921678.0 WT3.1.fq 0:50 A:290332094;C:256993500;G:263043956;T:285349722;N:364628 50       290332094 256993500 263043956 285349722 364628 SRX5799152 SRS4730322 SRA883435 Xiamen University|School of Pharmaceutical Sciences Xiamen University 1 0.94147   0.10157   0.66135   0.47301   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-18 Larval Larval Undetermined Undetermined
52213 52213 SRR9021061 SRX5799151 SRS4730320 SRP195685 PRJNA541367 Global transcriptomic analysis of zebrafish glucagon receptor mutant PRJNA541367 Other We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.         gcgr 1   replicate:biological replicate 1|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal                 Diano rerio transcriptome gcgr 1 20190506 1 gcgr 1 20190506 1 RNA seq of Diano rerio with gcgr mutant     RNA-Seq TRANSCRIPTOMIC other SINGLE BGISEQ BGISEQ-500   SRP195685   loader:fastq load.py gcgr1.1.fq fastq 1096307200.0 21926144.0 gcgr1.1.fq 0:50 A:288839446;C:258297625;G:264630675;T:284199738;N:339716 50       288839446 258297625 264630675 284199738 339716 SRX5799151 SRS4730320 SRA883435 Xiamen University|School of Pharmaceutical Sciences Xiamen University 1 0.94131   0.09307   0.67574   0.46993   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-18 Larval Larval Undetermined Undetermined
52214 52214 SRR9021062 SRX5799150 SRS4730321 SRP195685 PRJNA541367 Global transcriptomic analysis of zebrafish glucagon receptor mutant PRJNA541367 Other We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.         gcgr 2   replicate:biological replicate 2|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal                 Diano rerio transcriptome gcgr 2 20190506 2 gcgr 2 20190506 2 RNA seq of Diano rerio with gcgr mutant     RNA-Seq TRANSCRIPTOMIC other SINGLE BGISEQ BGISEQ-500   SRP195685   loader:fastq load.py gcgr2.1.fq fastq 1094410100.0 21888202.0 gcgr2.1.fq 0:50 A:290062779;C:256358687;G:264488431;T:282812212;N:687991 50       290062779 256358687 264488431 282812212 687991 SRX5799150 SRS4730321 SRA883435 Xiamen University|School of Pharmaceutical Sciences Xiamen University 1 0.94074   0.09337   0.67633   0.46861   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-18 Larval Larval Undetermined Undetermined
52215 52215 SRR9021063 SRX5799149 SRS4730319 SRP195685 PRJNA541367 Global transcriptomic analysis of zebrafish glucagon receptor mutant PRJNA541367 Other We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.         gcgr 3   replicate:biological replicate 3|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal                 Diano rerio transcriptome gcgr 3 20190506 3 gcgr 3 20190506 3 RNA seq of Diano rerio with gcgr mutant     RNA-Seq TRANSCRIPTOMIC other SINGLE BGISEQ BGISEQ-500   SRP195685   loader:fastq load.py gcgr3.1.fq fastq 1094284800.0 21885696.0 gcgr3.1.fq 0:50 A:289313514;C:257096636;G:264011408;T:283143600;N:719642 50       289313514 257096636 264011408 283143600 719642 SRX5799149 SRS4730319 SRA883435 Xiamen University|School of Pharmaceutical Sciences Xiamen University 1 0.94222   0.09557   0.67521   0.46664   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-18 Larval Larval Undetermined Undetermined
59503 59503 SRR11924320 SRX8469993 SRS6770644 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   PM 3 GSM4591060   source name:protruding mouth stage|tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA PM 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. protruding mouth stage   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:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA GSM4591060 GSM4591060: PM 3; Danio rerio; OTHER GSM4591060   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:GSM4591060 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent Proton   SRP265951   intentional duplicate GSE151797_Reference_sequence.fa PM_3.bam bam bam 215125332.0 6403488.0 GSM4591060 r1 0:33.60 A:50202267;C:65116674;G:52637331;T:47169060;N:0 33       50202267 65116674 52637331 47169060 0 SRX8469993 SRS6770644 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.73594   0.21617   0.86251   0.68892   42   B   usable mapping rate ion_torrent ion_torrent 5prime small_rna unknown bulk unknown unknown   Denmark 2020-06-04 Larval Larval Undetermined Undetermined
59504 59504 SRR11924318 SRX8469992 SRS6770643 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   PM 2 GSM4591059   source name:protruding mouth stage|tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA PM 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. protruding mouth stage   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:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA GSM4591059 GSM4591059: PM 2; Danio rerio; OTHER GSM4591059   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:GSM4591059 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent Proton   SRP265951   intentional duplicate GSE151797_Reference_sequence.fa PM_2.bam bam bam 426315355.0 12915702.0 GSM4591059 r1 0:33.01 A:92276988;C:141702085;G:104175159;T:88161123;N:0 33       92276988 141702085 104175159 88161123 0 SRX8469992 SRS6770643 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.76385   0.1921   0.87207   0.71495   40   B   usable mapping rate ion_torrent ion_torrent 5prime small_rna unknown bulk unknown unknown   Denmark 2020-06-04 Larval Larval Undetermined Undetermined
59505 59505 SRR11924317 SRX8469990 SRS6770641 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   PM 1 GSM4591058   source name:protruding mouth stage|tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA PM 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. protruding mouth stage   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:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA GSM4591058 GSM4591058: PM 1; Danio rerio; OTHER GSM4591058   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:GSM4591058 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent Proton   SRP265951   intentional duplicate GSE151797_Reference_sequence.fa PM_1.bam bam bam 130388595.0 5124384.0 GSM4591058 r1 0:25.44 A:27290253;C:42592303;G:31075292;T:29430747;N:0 25       27290253 42592303 31075292 29430747 0 SRX8469990 SRS6770641 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.78884   0.23004   0.85113   0.67571   38   B   usable mapping rate ion_torrent ion_torrent 5prime small_rna unknown bulk unknown unknown   Denmark 2020-06-04 Larval Larval Undetermined Undetermined

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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");;