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run_metadata

9 rows where experiment.library_selection = "RT-PCR", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Muscle"

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devstage_curation_coarse 3

devstage_curation 3

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Muscle · 9 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 9 ✖

experiment.library_selection 1

  • RT-PCR · 9 ✖
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
36665 36665 SRR800045 SRX257154 SRS405708 SRP020008 PRJNA193544 Danio rerio strain:Tubingen Epigenomics PRJNA193544 Other Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.   pubmed:23663776 Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper. Generic sample from Danio rerio muscle RNAseq totalRNARibominus   strain:Tubingen|label:PE: paired end SE: single end|development stage:muscle                 muscle RNAseq totalRNARibominus muscle RNAseq totalRNARibominus 9084X1 Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 1000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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> SRP020008     muscle_RNAseq_totalRNARibominus_SE_9084X1_120420_SN141_0500_AD0TG5ACXX_5.txt.gz Illumina native 3506573750.0 70131475.0 9084X1 120420 SN141 0500 AD0TG5ACXX 5 0:50 A:872717534;C:808774955;G:1036781008;T:777391447;N:10908806 50       872717534 808774955 1036781008 777391447 10908806 SRX257154 SRS405708 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.61428   0.09813   0.89305   0.6908   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2013-05-07 Undetermined Embryo Muscle Muscular System
63228 63228 SRR13674931 SRX10064377 SRS8226455 SRP305613 PRJNA701156 Zebrafish muscle transcriptome sequencing PRJNA701156 Other         RTL1 3 P5 FRAS192293744 1a   strain:AB|age:90.6 days|sex:male|tissue:muscle|treatment:transgened|BioSampleModel:Model organism or animal                 Danio rerio: adult male muscle P5 P5 Total?RNA?was?extracted?from?muscle?tissues?of?transgenic?zebrafish?at?60?and?90?dpf?using?Trizol?reagent?TaKaRa ?JP.?The?RNA?samples?of?control?and?Rtl1?transgenic?zebrafish?at?90?dpf?were?used?for?RNA?sequencing ?which?were?successively?checked?for?purity ?concentration?and?integrity?using?Nanodrop2000 ?Qubit?3.0?and?Agilent?2100?bioanalyzer?respectively.?The?150 bp?and?paired end?libraries?were?prepared?using?the?NEBNext?UltraTM?RNA?Library?Prep?kit?for?Illumina?NEB ?Beijing ?China.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA HiSeq X Ten   SRP305613     P5_FRAS192293744-1a_1.fq.gz P5_FRAS192293744-1a_2.fq.gz fastq fastq 6771953100.0 22573177.0 P5 FRAS192293744 1a 1.fq.gz 0:150 1:150 A:1754412294;C:1641284715;G:1642201960;T:1733881630;N:172501 150 150     1754412294 1641284715 1642201960 1733881630 172501 SRX10064377 SRS8226455 SRA1194342 Huazhong Agricultural University|College of Animal Science and Technology Huazhong Agricultural University 2 0.9658 0.96585 0.03234 0.03214 0.81235 0.81176 0.56443 0.56428 150 150 B B biological fallback assumption illumina hiseq_era unknown other nebnext bulk unknown unknown   China 2021-02-10 Adult Adult Muscle Muscular System
63229 63229 SRR13674932 SRX10064376 SRS8226454 SRP305613 PRJNA701156 Zebrafish muscle transcriptome sequencing PRJNA701156 Other         RTL1 2 P2 FRAS192293743 1a   strain:AB|age:90.8 days|sex:male|tissue:muscle|treatment:transgened|BioSampleModel:Model organism or animal                 Danio rerio: adult male muscle P2 P2 Total?RNA?was?extracted?from?muscle?tissues?of?transgenic?zebrafish?at?60?and?90?dpf?using?Trizol?reagent?TaKaRa ?JP.?The?RNA?samples?of?control?and?Rtl1?transgenic?zebrafish?at?90?dpf?were?used?for?RNA?sequencing ?which?were?successively?checked?for?purity ?concentration?and?integrity?using?Nanodrop2000 ?Qubit?3.0?and?Agilent?2100?bioanalyzer?respectively.?The?150 bp?and?paired end?libraries?were?prepared?using?the?NEBNext?UltraTM?RNA?Library?Prep?kit?for?Illumina?NEB ?Beijing ?China.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA HiSeq X Ten   SRP305613     P2_FRAS192293743-1a_1.fq.gz P2_FRAS192293743-1a_2.fq.gz fastq fastq 7086156600.0 23620522.0 P2 FRAS192293743 1a 1.fq.gz 0:150 1:150 A:1829494749;C:1728310792;G:1726602123;T:1801558967;N:189969 150 150     1829494749 1728310792 1726602123 1801558967 189969 SRX10064376 SRS8226454 SRA1194342 Huazhong Agricultural University|College of Animal Science and Technology Huazhong Agricultural University 2 0.94572 0.94586 0.03299 0.03368 0.8085 0.809 0.54521 0.54511 150 150 B B biological fallback assumption illumina hiseq_era unknown other nebnext bulk unknown unknown   China 2021-02-10 Adult Adult Muscle Muscular System
63230 63230 SRR13674933 SRX10064375 SRS8226453 SRP305613 PRJNA701156 Zebrafish muscle transcriptome sequencing PRJNA701156 Other         RTL1 1 P1 FRAS192293742 1a   strain:AB|age:90.2 days|sex:male|tissue:muscle|treatment:transgened|BioSampleModel:Model organism or animal                 Danio rerio: adult male muscle P1 P1 Total?RNA?was?extracted?from?muscle?tissues?of?transgenic?zebrafish?at?60?and?90?dpf?using?Trizol?reagent?TaKaRa ?JP.?The?RNA?samples?of?control?and?Rtl1?transgenic?zebrafish?at?90?dpf?were?used?for?RNA?sequencing ?which?were?successively?checked?for?purity ?concentration?and?integrity?using?Nanodrop2000 ?Qubit?3.0?and?Agilent?2100?bioanalyzer?respectively.?The?150 bp?and?paired end?libraries?were?prepared?using?the?NEBNext?UltraTM?RNA?Library?Prep?kit?for?Illumina?NEB ?Beijing ?China.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA HiSeq X Ten   SRP305613     P1_FRAS192293742-1a_1.fq.gz P1_FRAS192293742-1a_2.fq.gz fastq fastq 6459334500.0 21531115.0 P1 FRAS192293742 1a 1.fq.gz 0:150 1:150 A:1673495801;C:1568402960;G:1568786891;T:1648475694;N:173154 150 150     1673495801 1568402960 1568786891 1648475694 173154 SRX10064375 SRS8226453 SRA1194342 Huazhong Agricultural University|College of Animal Science and Technology Huazhong Agricultural University 2 0.9703 0.97063 0.03357 0.03364 0.81657 0.81765 0.57269 0.54967 150 150 B B biological fallback assumption illumina hiseq_era unknown other nebnext bulk unknown unknown   China 2021-02-10 Adult Adult Muscle Muscular System
63231 63231 SRR13674934 SRX10064374 SRS8226452 SRP305613 PRJNA701156 Zebrafish muscle transcriptome sequencing PRJNA701156 Other         Control 3 C4 FRAS192293741 1a   strain:AB|age:90.5 days|sex:male|tissue:muscle|treatment:no|BioSampleModel:Model organism or animal                 Danio rerio: adult male muscle C4 C4 Total?RNA?was?extracted?from?muscle?tissues?of?transgenic?zebrafish?at?60?and?90?dpf?using?Trizol?reagent?TaKaRa ?JP.?The?RNA?samples?of?control?and?Rtl1?transgenic?zebrafish?at?90?dpf?were?used?for?RNA?sequencing ?which?were?successively?checked?for?purity ?concentration?and?integrity?using?Nanodrop2000 ?Qubit?3.0?and?Agilent?2100?bioanalyzer?respectively.?The?150 bp?and?paired end?libraries?were?prepared?using?the?NEBNext?UltraTM?RNA?Library?Prep?kit?for?Illumina?NEB ?Beijing ?China.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA HiSeq X Ten   SRP305613     C4_FRAS192293741-1a_1.fq.gz C4_FRAS192293741-1a_2.fq.gz fastq fastq 7438432200.0 24794774.0 C4 FRAS192293741 1a 1.fq.gz 0:150 1:150 A:1873929323;C:1856432531;G:1861416319;T:1846451050;N:202977 150 150     1873929323 1856432531 1861416319 1846451050 202977 SRX10064374 SRS8226452 SRA1194342 Huazhong Agricultural University|College of Animal Science and Technology Huazhong Agricultural University 2 0.91395 0.91431 0.03002 0.0299 0.82546 0.82542 0.53591 0.5362 150 150 B B biological fallback assumption illumina hiseq_era unknown other nebnext bulk unknown unknown   China 2021-02-10 Adult Adult Muscle Muscular System
63232 63232 SRR13674935 SRX10064373 SRS8226451 SRP305613 PRJNA701156 Zebrafish muscle transcriptome sequencing PRJNA701156 Other         Control 2 C3 FRAS192293740 1a   strain:AB|age:90.1 days|sex:male|tissue:muscle|treatment:no|BioSampleModel:Model organism or animal                 Danio rerio: adult male muscle C3 C3 Total?RNA?was?extracted?from?muscle?tissues?of?transgenic?zebrafish?at?60?and?90?dpf?using?Trizol?reagent?TaKaRa ?JP.?The?RNA?samples?of?control?and?Rtl1?transgenic?zebrafish?at?90?dpf?were?used?for?RNA?sequencing ?which?were?successively?checked?for?purity ?concentration?and?integrity?using?Nanodrop2000 ?Qubit?3.0?and?Agilent?2100?bioanalyzer?respectively.?The?150 bp?and?paired end?libraries?were?prepared?using?the?NEBNext?UltraTM?RNA?Library?Prep?kit?for?Illumina?NEB ?Beijing ?China.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA HiSeq X Ten   SRP305613     C3_FRAS192293740-1a_1.fq.gz C3_FRAS192293740-1a_2.fq.gz fastq fastq 9010307400.0 30034358.0 C3 FRAS192293740 1a 1.fq.gz 0:150 1:150 A:2348033685;C:2178627989;G:2176071816;T:2307406587;N:167323 150 150     2348033685 2178627989 2176071816 2307406587 167323 SRX10064373 SRS8226451 SRA1194342 Huazhong Agricultural University|College of Animal Science and Technology Huazhong Agricultural University 2 0.96511 0.96401 0.03416 0.03393 0.80503 0.8056 0.56138 0.54155 150 150 B B biological fallback assumption illumina hiseq_era unknown other nebnext bulk unknown unknown   China 2021-02-10 Adult Adult Muscle Muscular System
63233 63233 SRR13674936 SRX10064372 SRS8226450 SRP305613 PRJNA701156 Zebrafish muscle transcriptome sequencing PRJNA701156 Other         Control 1 C1 FRAS192293739 1a   strain:AB|age:90.3 days|sex:male|tissue:muscle|treatment:no|BioSampleModel:Model organism or animal                 Danio rerio: adult male muscle C1 C1 Total?RNA?was?extracted?from?muscle?tissues?of?transgenic?zebrafish?at?60?and?90?dpf?using?Trizol?reagent?TaKaRa ?JP.?The?RNA?samples?of?control?and?Rtl1?transgenic?zebrafish?at?90?dpf?were?used?for?RNA?sequencing ?which?were?successively?checked?for?purity ?concentration?and?integrity?using?Nanodrop2000 ?Qubit?3.0?and?Agilent?2100?bioanalyzer?respectively.?The?150 bp?and?paired end?libraries?were?prepared?using?the?NEBNext?UltraTM?RNA?Library?Prep?kit?for?Illumina?NEB ?Beijing ?China.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA HiSeq X Ten   SRP305613     C1_FRAS192293739-1a_1.fq.gz C1_FRAS192293739-1a_2.fq.gz fastq fastq 7559059800.0 25196866.0 C1 FRAS192293739 1a 1.fq.gz 0:150 1:150 A:1953593854;C:1846045443;G:1843347399;T:1915927680;N:145424 150 150     1953593854 1846045443 1843347399 1915927680 145424 SRX10064372 SRS8226450 SRA1194342 Huazhong Agricultural University|College of Animal Science and Technology Huazhong Agricultural University 2 0.96353 0.96407 0.03092 0.03073 0.82142 0.82264 0.56714 0.5657 150 150 B B biological fallback assumption illumina hiseq_era unknown other nebnext bulk unknown unknown   China 2021-02-10 Adult Adult Muscle Muscular System
66710 66710 SRR16378894 SRX12656337 SRS10609555 SRP341786 PRJNA772011 Spatial transcriptome of zebrafish trunk section PRJNA772011 Other Spatial transcriptome sequencing data from sections of adult and larvae zebrafish trunk. Aiming to delineate the distribution of fast and slow muscle fibers in zebrafish by transcriptomic patterns and the regulation of muscle growth.         zebrafish larvae   strain:Riken wide type|age:1 month|sex:not applicable|tissue:muscle|birth location:Tokyo Japan|collection date:2020 08 20|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: larvae muscle zebrafish larva zebrafish larva Visium spatial transcriptomics     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA HiSeq X Ten   SRP341786     zebra_young_S1_L004_R1_001.fastq zebra_young_S1_L004_R2_001.fastq fastq fastq 2755287020.0 23349890.0 zebra young S1 L004 R1 001.fastq 0:28 1:90 A:775062912;C:621131964;G:654720744;T:704362634;N:8766 28 90     775062912 621131964 654720744 704362634 8766 SRX12656337 SRS10609555 SRA1312274 The University of Tokyo|Graduate School of Agriculture and Life Science The University of Tokyo 2 0.00167 0.91629 0.0005 0.02744 0.99707 0.85989 0.57777 0.51307 28 90 T B sc-like readlen illumina hiseq_era unknown other unknown bulk unknown unknown   Japan 2021-10-17 Juvenile Juvenile Muscle Muscular System
66711 66711 SRR16378895 SRX12656336 SRS10609554 SRP341786 PRJNA772011 Spatial transcriptome of zebrafish trunk section PRJNA772011 Other Spatial transcriptome sequencing data from sections of adult and larvae zebrafish trunk. Aiming to delineate the distribution of fast and slow muscle fibers in zebrafish by transcriptomic patterns and the regulation of muscle growth.         zebrafish aged   strain:Riken wide type|age:8 month|sex:male|tissue:muscle|birth location:Tokyo Japan|collection date:2020 08 20|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: adult male muscle zebrafish aged zebrafish aged Visium spatial transcriptomics     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA HiSeq X Ten   SRP341786     zebra_aged_S2_L004_R1_001.fastq zebra_aged_S2_L004_R2_001.fastq fastq fastq 21508079126.0 182271857.0 zebra aged S2 L004 R1 001.fastq 0:28 1:90 A:6446039227;C:4838400089;G:4527284151;T:5696286768;N:68891 28 90     6446039227 4838400089 4527284151 5696286768 68891 SRX12656336 SRS10609554 SRA1312274 The University of Tokyo|Graduate School of Agriculture and Life Science The University of Tokyo 2 0.00207 0.89769 0.00073 0.03196 0.99736 0.89688 0.49411 0.40762 28 90 T B sc-like readlen illumina hiseq_era unknown other unknown bulk unknown unknown   Japan 2021-10-17 Adult Adult Muscle Muscular 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");;