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run_metadata

10 rows where experiment.library_selection = "RANDOM PCR" and tissue_curation_coarse = "Multi-system"

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tissue_curation 2

experiment.platform 2

experiment.library_layout 2

devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

  • Multi-system · 10 ✖

technology 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • RANDOM PCR · 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
71549 71549 SRR21700247 SRX17697774 SRS15228561 SRP399479 PRJNA884084 RNA Seq data of gmfg morphants and their control siblings PRJNA884084 Other To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.       biological replicate 3 gmfg atgMO 3   strain:not applicable|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:the dissected trunk and tail|collection date:2021 02 26|geo loc name:China:Shenzhen Guangdong|sample type:mo3|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio MO3 20210214 MO3 20210214 RNA seq of Danio rerio in different conditions     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE BGISEQ BGISEQ-500   SRP399479     MO_3_1.fq.gz fastq 1194263900.0 23885278.0 MO 3 1.fq.gz 0:50 1:0 A:315714579;C:274130504;G:282488713;T:321930104;N:0 50 0     315714579 274130504 282488713 321930104 0 SRX17697774 SRS15228561 SRA1506658 the First Affiliated Hospital, School of Medicine, Zhejiang University|BoneMarrow Transplantation Center the First Affiliated Hospital, School of Medicine, Zhejiang University 1 0.9415   0.07261   0.70701   0.47029   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2022-09-25 Pharyngula Embryo Multi-tissue Multi-system
71550 71550 SRR21700248 SRX17697773 SRS15228560 SRP399479 PRJNA884084 RNA Seq data of gmfg morphants and their control siblings PRJNA884084 Other To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.       biological replicate 2 gmfg atgMO 2   strain:not applicable|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:the dissected trunk and tail|collection date:2021 02 26|geo loc name:China:Shenzhen Guangdong|sample type:mo2|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio MO2 20210213 MO2 20210213 RNA seq of Danio rerio in different conditions     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE BGISEQ BGISEQ-500   SRP399479     MO_2_1.fq.gz fastq 1193697300.0 23873946.0 MO 2 1.fq.gz 0:50 1:0 A:316188077;C:272941933;G:282559962;T:322007328;N:0 50 0     316188077 272941933 282559962 322007328 0 SRX17697773 SRS15228560 SRA1506658 the First Affiliated Hospital, School of Medicine, Zhejiang University|BoneMarrow Transplantation Center the First Affiliated Hospital, School of Medicine, Zhejiang University 1 0.94144   0.07426   0.70715   0.47856   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2022-09-25 Pharyngula Embryo Multi-tissue Multi-system
71551 71551 SRR21700249 SRX17697772 SRS15228559 SRP399479 PRJNA884084 RNA Seq data of gmfg morphants and their control siblings PRJNA884084 Other To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.       biological replicate 1 gmfg atgMO 1   strain:not applicable|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:the dissected trunk and tail|collection date:2021 02 26|geo loc name:China:Shenzhen Guangdong|sample type:mo1|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio MO1 20210212 MO1 20210212 RNA seq of Danio rerio in different conditions     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE BGISEQ BGISEQ-500   SRP399479     MO_1_1.fq.gz fastq 1194311300.0 23886226.0 MO 1 1.fq.gz 0:50 1:0 A:317344841;C:272348188;G:281111904;T:323506367;N:0 50 0     317344841 272348188 281111904 323506367 0 SRX17697772 SRS15228559 SRA1506658 the First Affiliated Hospital, School of Medicine, Zhejiang University|BoneMarrow Transplantation Center the First Affiliated Hospital, School of Medicine, Zhejiang University 1 0.94366   0.07701   0.70274   0.47929   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2022-09-25 Pharyngula Embryo Multi-tissue Multi-system
71552 71552 SRR21700250 SRX17697771 SRS15228558 SRP399479 PRJNA884084 RNA Seq data of gmfg morphants and their control siblings PRJNA884084 Other To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.       biological replicate 3 ctl 3   strain:not applicable|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:the dissected trunk and tail|collection date:2021 02 26|geo loc name:China:Shenzhen Guangdong|sample type:ctl3|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio ctl3 20210211 ctl3 20210211 RNA seq of Danio rerio in different conditions     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE BGISEQ BGISEQ-500   SRP399479     ctl_3_1.fq.gz fastq 1190502850.0 23810057.0 ctl 3 1.fq.gz 0:50 1:0 A:314168919;C:272277792;G:283249731;T:320806408;N:0 50 0     314168919 272277792 283249731 320806408 0 SRX17697771 SRS15228558 SRA1506658 the First Affiliated Hospital, School of Medicine, Zhejiang University|BoneMarrow Transplantation Center the First Affiliated Hospital, School of Medicine, Zhejiang University 1 0.94354   0.08493   0.70228   0.48147   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2022-09-25 Pharyngula Embryo Multi-tissue Multi-system
71553 71553 SRR21700251 SRX17697770 SRS15228557 SRP399479 PRJNA884084 RNA Seq data of gmfg morphants and their control siblings PRJNA884084 Other To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.       biological replicate 2 ctl 2   strain:not applicable|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:the dissected trunk and tail|collection date:2021 02 26|geo loc name:China:Shenzhen Guangdong|sample type:ctl2|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio ctl2 20210210 ctl2 20210210 RNA seq of Danio rerio in different conditions     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE BGISEQ BGISEQ-500   SRP399479     ctl_2_1.fq.gz fastq 1193941900.0 23878838.0 ctl 2 1.fq.gz 0:50 1:0 A:315521033;C:273947671;G:281554279;T:322918917;N:0 50 0     315521033 273947671 281554279 322918917 0 SRX17697770 SRS15228557 SRA1506658 the First Affiliated Hospital, School of Medicine, Zhejiang University|BoneMarrow Transplantation Center the First Affiliated Hospital, School of Medicine, Zhejiang University 1 0.94073   0.08514   0.70281   0.4767   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2022-09-25 Pharyngula Embryo Multi-tissue Multi-system
71554 71554 SRR21700252 SRX17697769 SRS15228556 SRP399479 PRJNA884084 RNA Seq data of gmfg morphants and their control siblings PRJNA884084 Other To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.       biological replicate 1 ctl 1   strain:not applicable|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:the dissected trunk and tail|collection date:2021 02 26|geo loc name:China:Shenzhen Guangdong|sample type:ctl1|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio ctl1 20210209 ctl1 20210209 RNA seq of Danio rerio in different conditions     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE BGISEQ BGISEQ-500   SRP399479     ctl_1_1.fq.gz fastq 1194196300.0 23883926.0 ctl 1 1.fq.gz 0:50 1:0 A:315050496;C:273915045;G:282252071;T:322978688;N:0 50 0     315050496 273915045 282252071 322978688 0 SRX17697769 SRS15228556 SRA1506658 the First Affiliated Hospital, School of Medicine, Zhejiang University|BoneMarrow Transplantation Center the First Affiliated Hospital, School of Medicine, Zhejiang University 1 0.94272   0.08675   0.70234   0.47397   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2022-09-25 Pharyngula Embryo Multi-tissue Multi-system
72464 72464 SRR22574253 SRX18537350 SRS16001767 SRP411954 PRJNA909445 Danio rerio Raw sequence reads PRJNA909445 Other Whole transcriptome analysis       Model organism or animal sample from zebrafish zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish   strain:zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish|age:60dpf|sex:pooled male and female|tissue:tail|BioSampleModel:Model organism or animal                 wt 2 R1.fastq wt 2 R1.fastq wt 2 R1.fastq tail muscule     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP411954     wt_2_R1.fastq.gz wt_2_R2.fastq.gz fastq fastq 20138999100.0 67129997.0 wt 2 R1.fastq.gz 0:150 1:150 A:5269495885;C:4709732469;G:4941455861;T:5217751419;N:563466 150 150     5269495885 4709732469 4941455861 5217751419 563466 SRX18537350 SRS16001767 SRA1555446 Fisheries College of Huazhong Agricultural University|Fisheries College of Huazhong Agricultural Univers Fisheries College of Huazhong Agricultural University 2 0.95899 0.96368 0.14222 0.14005 0.82102 0.81862 0.43313 0.43965 150 150 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   China 2022-12-08 Juvenile Juvenile Tail Multi-system
72465 72465 SRR22574254 SRX18537349 SRS16001767 SRP411954 PRJNA909445 Danio rerio Raw sequence reads PRJNA909445 Other Whole transcriptome analysis       Model organism or animal sample from zebrafish zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish   strain:zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish|age:60dpf|sex:pooled male and female|tissue:tail|BioSampleModel:Model organism or animal                 wt 1 R1.fastq wt 1 R1.fastq wt 1 R1.fastq tail muscule     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP411954     wt_1_R1.fastq.gz wt_1_R2.fastq.gz fastq fastq 23358126000.0 77860420.0 wt 1 R1.fastq.gz 0:150 1:150 A:6038817592;C:5541964880;G:5789495907;T:5987202665;N:644956 150 150     6038817592 5541964880 5789495907 5987202665 644956 SRX18537349 SRS16001767 SRA1555446 Fisheries College of Huazhong Agricultural University|Fisheries College of Huazhong Agricultural Univers Fisheries College of Huazhong Agricultural University 2 0.95378 0.95798 0.14042 0.13872 0.82065 0.81809 0.45238 0.37872 150 150 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   China 2022-12-08 Juvenile Juvenile Tail Multi-system
72466 72466 SRR22574255 SRX18537348 SRS16001767 SRP411954 PRJNA909445 Danio rerio Raw sequence reads PRJNA909445 Other Whole transcriptome analysis       Model organism or animal sample from zebrafish zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish   strain:zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish|age:60dpf|sex:pooled male and female|tissue:tail|BioSampleModel:Model organism or animal                 mut 2 R1.fastq mut 2 R1.fastq mut 2 R1.fastq tail muscule     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP411954     mut_2_R1.fastq.gz mut_2_R2.fastq.gz fastq fastq 19326017700.0 64420059.0 mut 2 R1.fastq.gz 0:150 1:150 A:5060790268;C:4512966975;G:4744771851;T:5006953597;N:535009 150 150     5060790268 4512966975 4744771851 5006953597 535009 SRX18537348 SRS16001767 SRA1555446 Fisheries College of Huazhong Agricultural University|Fisheries College of Huazhong Agricultural Univers Fisheries College of Huazhong Agricultural University 2 0.95472 0.95941 0.14789 0.14566 0.81746 0.81509 0.46875 0.39789 150 150 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   China 2022-12-08 Juvenile Juvenile Tail Multi-system
72467 72467 SRR22574256 SRX18537347 SRS16001767 SRP411954 PRJNA909445 Danio rerio Raw sequence reads PRJNA909445 Other Whole transcriptome analysis       Model organism or animal sample from zebrafish zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish   strain:zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish|age:60dpf|sex:pooled male and female|tissue:tail|BioSampleModel:Model organism or animal                 mut 1 R1.fastq mut 1 R1.fastq mut 1 R1.fastq tail muscule     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP411954     mut_1_R1.fastq.gz mut_1_R2.fastq.gz fastq fastq 22794782400.0 75982608.0 mut 1 R1.fastq.gz 0:150 1:150 A:5961354939;C:5333450654;G:5606279874;T:5893060023;N:636910 150 150     5961354939 5333450654 5606279874 5893060023 636910 SRX18537347 SRS16001767 SRA1555446 Fisheries College of Huazhong Agricultural University|Fisheries College of Huazhong Agricultural Univers Fisheries College of Huazhong Agricultural University 2 0.9557 0.95853 0.14259 0.13878 0.81771 0.81533 0.45125 0.3948 150 150 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   China 2022-12-08 Juvenile Juvenile Tail Multi-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");;