RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

24 rows where experiment.library_selection = "RT-PCR", technology = "unknown" and tissue_curation = "Trunk"

✎ View and edit SQL

This data as json, CSV (advanced)

devstage_curation_coarse 3

devstage_curation 3

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Trunk · 24 ✖

technology 1

  • unknown · 24 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • RT-PCR · 24 ✖
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
45033 45033 SRR6466457 SRX3556410 SRS2829758 SRP128941 PRJNA428924 Danio rerio breed:TU Transcriptome or Gene expression PRJNA428924 Transcriptome Analysis In order to know about more basic knowledge of none/less gut adhesive strain L. casei BL23 induce on the developmental profile and immunity education in zebrafish     pooled of 30 whole body larvae fish at 14 dpf old.   Control 14   breed:TU|age:14 dpf|sex:pooled male and female|tissue:whole body|treatment:Control|BioSampleModel:Model organism or animal                 RNA seq of zebrafish larvae with or without xxx administration Ctl 14 Ctl 14 Total RNA were isolated from pooled samples of larvae whole body or juvenile s intestines with TRIzol Tian Gen Beijing China following the manufacturer s specifications. The RNA was treated with amplification grade DNase I 1 U/ g RNA; Invitrogen USA. RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. All the RNA RIN values were bigger than 9.5 as analyzed by Bioanalyzer 2100 system. For mRNAseq equal volume and amount 1 g of total RNA from 4 sample pools of each treatment group were mixed as a sequencing sample.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP128941     ZF_CK_1.fq.gz ZF_CK_2.fq.gz fastq fastq 3194379750.0 12777519.0 ZF CK 1.fq.gz 0:125 1:125 A:843962375;C:752856573;G:753886188;T:843555573;N:119041 125 125     843962375 752856573 753886188 843555573 119041 SRX3556410 SRS2829758 SRA646164 Chinese Academy of Agricultural Sciences|Key Laboratory for Feed Biotechnology of the Minis Chinese Academy of Agricultural Sciences 2 0.94377 0.94754 0.06883 0.06783 0.67442 0.67844 0.46844 0.472 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2018-01-12 Larval Larval Trunk Surface Structure
45034 45034 SRR6466458 SRX3556409 SRS2829757 SRP128941 PRJNA428924 Danio rerio breed:TU Transcriptome or Gene expression PRJNA428924 Transcriptome Analysis In order to know about more basic knowledge of none/less gut adhesive strain L. casei BL23 induce on the developmental profile and immunity education in zebrafish     pooled of 30 larvae of fish at 14 dpf with L. casei BL23 administration   BL23 14   breed:TU|age:14 dpf|sex:pooled male and female|tissue:whole body|treatment:BL23 administration|BioSampleModel:Model organism or animal                 RNA seq of zebrafish larvae with or without xxx administration BL23 14 BL23 14 Total RNA were isolated from pooled samples of larvae whole body or juvenile s intestines with TRIzol Tian Gen Beijing China following the manufacturer s specifications. The RNA was treated with amplification grade DNase I 1 U/ g RNA; Invitrogen USA. RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. All the RNA RIN values were bigger than 9.5 as analyzed by Bioanalyzer 2100 system. For mRNAseq equal volume and amount 1 g of total RNA from 4 sample pools of each treatment group were mixed as a sequencing sample.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP128941     ZF_BL23_1.fq.gz ZF_BL23_2.fq.gz fastq fastq 3720774000.0 14883096.0 ZF BL23 2.fq.gz 0:125 1:125 A:974128380;C:885422072;G:887959104;T:973126100;N:138344 125 125     974128380 885422072 887959104 973126100 138344 SRX3556409 SRS2829757 SRA646164 Chinese Academy of Agricultural Sciences|Key Laboratory for Feed Biotechnology of the Minis Chinese Academy of Agricultural Sciences 2 0.94399 0.94862 0.0635 0.06328 0.66898 0.67243 0.48704 0.48297 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2018-01-12 Larval Larval Trunk Surface Structure
47611 47611 SRR6671794 SRX3648486 SRS2913085 SRP132190 PRJNA432942 Zebrafish genes regulated in response to Mucor circinelloides infection PRJNA432942 Other Determination of the genes that can be important for the defense of the host to infection for Mucorales fungi using zebrafish and the fungus Mucor circinelloides as host and pathogen model respectively. Total RNA was sequenced RNA seq from abdominal organs of infected fish.         PBS2   strain:AB|dev stage:Adult|sex:not determined|tissue:Abdomen|treatment:Control innoculated with PBS|BioSampleModel:Model organism or animal                 RNA seq of Darnio rerio: uninffected PBS2 PBS2 Total RNA isolated from uninfected abdominal tissue was used to generate the library using truseq kit     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP132190     PBS2_GCCAAT_L001_R1_001_BH8U70ADXX.filt.fastq.gz fastq 792892359.0 15546909.0 PBS2 GCCAAT L001 R1 001 BH8U70ADXX.filt.fastq.gz 0:51 A:207417646;C:188867370;G:187996499;T:208448675;N:162169 51       207417646 188867370 187996499 208448675 162169 SRX3648486 SRS2913085 SRA655550 University of Murcia|Genetics and Microbiology University of Murcia 1 0.92826   0.02642   0.72815   0.45776   51   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Spain 2018-09-28 Adult Adult Trunk Surface Structure
47612 47612 SRR6671795 SRX3648485 SRS2913084 SRP132190 PRJNA432942 Zebrafish genes regulated in response to Mucor circinelloides infection PRJNA432942 Other Determination of the genes that can be important for the defense of the host to infection for Mucorales fungi using zebrafish and the fungus Mucor circinelloides as host and pathogen model respectively. Total RNA was sequenced RNA seq from abdominal organs of infected fish.         RDRZ   strain:AB|dev stage:Adult|sex:not determined|tissue:Abdomen|treatment:Infected with Mucor circinelloides spores|BioSampleModel:Model organism or animal                 RNA seq of Darnio rerio: infected with Mucor circinelloides RDRZ RDRZ Total RNA isolated from abdominal tissue infected with Mucor circinelloides was used to generate the library using truseq kit     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP132190     RDRZ_TGACCA_L001_R1_001_BH8U70ADXX.filt.fastq.gz fastq 741005418.0 14529518.0 RDRZ TGACCA L001 R1 001 BH8U70ADXX.filt.fastq.gz 0:51 A:192330774;C:178252917;G:175501754;T:194766886;N:153087 51       192330774 178252917 175501754 194766886 153087 SRX3648485 SRS2913084 SRA655550 University of Murcia|Genetics and Microbiology University of Murcia 1 0.91685   0.03703   0.70873   0.49947   51   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Spain 2018-09-28 Adult Adult Trunk Surface Structure
49248 49248 SRR7881079 SRX4719723 SRS3804945 SRP162200 PRJNA492186 Danio rerio Genome sequencing PRJNA492186 Other The transcriptome of zebrafish mutant and wt embryos.       wt wt   strain:TU|age:30h|sex:not determined|tissue:whole body|phenotype:normal body|BioSampleModel:Model organism or animal                 RNA Seq data of wt RNA Seq data of wt RNA Seq data of wt For each sample mRNA was extracted from the whole body of one individual and the standard RNA Seq library was constructed and subjected to Illumina PE125 sequencing     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP162200     WT-blu_L5_I392.R1.clean.fastq.gz WT-blu_L5_I392.R2.clean.fastq.gz fastq fastq 3703694250.0 14814777.0 WT blu L5 I392.R2.clean.fastq.gz 0:125 1:125 A:966446794;C:893928928;G:885838907;T:957360869;N:118752 125 125     966446794 893928928 885838907 957360869 118752 SRX4719723 SRS3804945 SRA779493 Ocean University of China|College of Marine Life Sciences Ocean University of China 2 0.97308 0.97256 0.07482 0.07588 0.70431 0.70595 0.49836 0.5007 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2018-09-20 Pharyngula Embryo Trunk Surface Structure
49249 49249 SRR7881080 SRX4719722 SRS3804946 SRP162200 PRJNA492186 Danio rerio Genome sequencing PRJNA492186 Other The transcriptome of zebrafish mutant and wt embryos.       mutant zmynd10 mutant   strain:TU|age:30h|sex:not determined|tissue:whole body|phenotype:curve body|BioSampleModel:Model organism or animal                 RNA Seq data of zmynd10 mutant RNA Seq data of zmynd10 mutant RNA Seq data of zmynd10 mutant For each sample mRNA was extracted from the whole body of one individual and the standard RNA Seq library was constructed and subjected to Illumina PE125 sequencing     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP162200     MT-blu_L5_I393.R1.clean.fastq.gz MT-blu_L5_I393.R2.clean.fastq.gz fastq fastq 4156063750.0 16624255.0 MT blu L5 I393.R2.clean.fastq.gz 0:125 1:125 A:1084666899;C:1001943643;G:994799272;T:1074520227;N:133709 125 125     1084666899 1001943643 994799272 1074520227 133709 SRX4719722 SRS3804946 SRA779493 Ocean University of China|College of Marine Life Sciences Ocean University of China 2 0.97259 0.97221 0.07667 0.0775 0.70084 0.70199 0.4768 0.48903 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2018-09-20 Pharyngula Embryo Trunk Surface Structure
52281 52281 SRR9077085 SRX5852372 SRS4776365 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       body2 mock s11   breed:zebrafish|dev stage:adult|sex:NA|tissue:body6|BioSampleModel:Model organism or animal                 body2 mock WC TC 060 WC TC 060 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_060_S11.R2.fastq.gz WC_TC_060_S11.R1.fastq.gz fastq fastq 6570204104.0 43225027.0 WC TC 060 S11.R1.fastq.gz 0:101 1:51 A:1688920476;C:1591936403;G:1547543861;T:1736945913;N:4857451 101 51     1688920476 1591936403 1547543861 1736945913 4857451 SRX5852372 SRS4776365 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.96893 0.96531 0.06012 0.06428 0.74002 0.74308 0.44405 0.45056 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Trunk Surface Structure
52282 52282 SRR9077086 SRX5852371 SRS4776364 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       body2 control s12   breed:zebrafish|dev stage:adult|sex:NA|tissue:body7|BioSampleModel:Model organism or animal                 body2 control WC TC 061 WC TC 061 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_061_S12.R1.fastq.gz WC_TC_061_S12.R2.fastq.gz fastq fastq 5298115192.0 34856021.0 WC TC 061 S12.R1.fastq.gz 0:101 1:51 A:1365002199;C:1284749208;G:1236476294;T:1407970678;N:3916813 101 51     1365002199 1284749208 1236476294 1407970678 3916813 SRX5852371 SRS4776364 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.96855 0.96437 0.06631 0.06978 0.72819 0.73158 0.43805 0.4516 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Trunk Surface Structure
52283 52283 SRR9077087 SRX5852370 SRS4776363 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       body2 kd s13   breed:zebrafish|dev stage:adult|sex:NA|tissue:body8|BioSampleModel:Model organism or animal                 body2 kd WC TC 062 WC TC 062 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_062_S13.R1.fastq.gz WC_TC_062_S13.R2.fastq.gz fastq fastq 6381036304.0 41980502.0 WC TC 062 S13.R1.fastq.gz 0:101 1:51 A:1647560028;C:1537878827;G:1499984084;T:1690940053;N:4673312 101 51     1647560028 1537878827 1499984084 1690940053 4673312 SRX5852370 SRS4776363 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.96684 0.96194 0.06383 0.06747 0.73608 0.74052 0.45347 0.4621 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Trunk Surface Structure
52284 52284 SRR9077088 SRX5852369 SRS4776362 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       body2 kd+wt s14   breed:zebrafish|dev stage:adult|sex:NA|tissue:body9|BioSampleModel:Model organism or animal                 body2 kd+wt WC TC 063 WC TC 063 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_063_S14.R1.fastq.gz WC_TC_063_S14.R2.fastq.gz fastq fastq 5465511120.0 35957310.0 WC TC 063 S14.R1.fastq.gz 0:101 1:51 A:1414511882;C:1316966059;G:1276815442;T:1453177754;N:4039983 101 51     1414511882 1316966059 1276815442 1453177754 4039983 SRX5852369 SRS4776362 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.96743 0.96269 0.06264 0.06717 0.73768 0.74002 0.43946 0.44951 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Trunk Surface Structure
52289 52289 SRR9077093 SRX5852364 SRS4776357 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       body1 mock s6   breed:zebrafish|dev stage:adult|sex:NA|tissue:body1|BioSampleModel:Model organism or animal                 body1 mock WC TC 055 WC TC 055 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_055_S6.R1.fastq.gz WC_TC_055_S6.R2.fastq.gz fastq fastq 5140707792.0 33820446.0 WC TC 055 S6.R1.fastq.gz 0:101 1:51 A:1316539385;C:1252228375;G:1214956681;T:1353162802;N:3820549 101 51     1316539385 1252228375 1214956681 1353162802 3820549 SRX5852364 SRS4776357 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.97114 0.96587 0.05961 0.06293 0.73596 0.73979 0.43233 0.4586 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Trunk Surface Structure
52290 52290 SRR9077094 SRX5852363 SRS4776356 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       body1 control s7   breed:zebrafish|dev stage:adult|sex:NA|tissue:body2|BioSampleModel:Model organism or animal                 body1 control WC TC 056 WC TC 056 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_056_S7.R1.fastq.gz WC_TC_056_S7.R2.fastq.gz fastq fastq 5020859136.0 33031968.0 WC TC 056 S7.R1.fastq.gz 0:101 1:51 A:1291539287;C:1214422587;G:1184146239;T:1327013927;N:3737096 101 51     1291539287 1214422587 1184146239 1327013927 3737096 SRX5852363 SRS4776356 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.96884 0.96505 0.0623 0.06643 0.73572 0.73904 0.44643 0.45988 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Trunk Surface Structure
52291 52291 SRR9077095 SRX5852362 SRS4776355 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       body1 kd+wt s9   breed:zebrafish|dev stage:adult|sex:NA|tissue:body4|BioSampleModel:Model organism or animal                 body1 kd+wt WC TC 058 WC TC 058 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_058_S9.R1.fastq.gz WC_TC_058_S9.R2.fastq.gz fastq fastq 6018676056.0 39596553.0 WC TC 058 S9.R1.fastq.gz 0:101 1:51 A:1548315021;C:1452922375;G:1413529417;T:1599423213;N:4486030 101 51     1548315021 1452922375 1413529417 1599423213 4486030 SRX5852362 SRS4776355 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.96912 0.96439 0.06373 0.06781 0.73612 0.73988 0.44769 0.46236 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Trunk Surface Structure
52293 52293 SRR9077097 SRX5852360 SRS4776353 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       body1 kd+mt s10   breed:zebrafish|dev stage:adult|sex:NA|tissue:body5|BioSampleModel:Model organism or animal                 body1 kd+mt WC TC 059 WC TC 059 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_059_S10.R2.fastq.gz WC_TC_059_S10.R1.fastq.gz fastq fastq 6271465432.0 41259641.0 WC TC 059 S10.R1.fastq.gz 0:101 1:51 A:1629820249;C:1502782160;G:1459060597;T:1675172643;N:4629783 101 51     1629820249 1502782160 1459060597 1675172643 4629783 SRX5852360 SRS4776353 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.96576 0.96033 0.06782 0.07173 0.73547 0.74014 0.45453 0.45359 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Trunk Surface Structure
52294 52294 SRR9077098 SRX5852359 SRS4776352 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       body1 kd s8   breed:zebrafish|dev stage:adult|sex:NA|tissue:body3|BioSampleModel:Model organism or animal                 body1 kd WC TC 057 WC TC 057 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_057_S8.R1.fastq.gz WC_TC_057_S8.R2.fastq.gz fastq fastq 4742849768.0 31202959.0 WC TC 057 S8.R1.fastq.gz 0:101 1:51 A:1229413754;C:1139873278;G:1110810068;T:1259324043;N:3428625 101 51     1229413754 1139873278 1110810068 1259324043 3428625 SRX5852359 SRS4776352 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.96593 0.96237 0.06455 0.06966 0.73618 0.74126 0.45216 0.4641 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Trunk Surface Structure
52295 52295 SRR9077099 SRX5852358 SRS4776351 SRP198708 PRJNA543385 mRNA sequence of zebrafish head and body PRJNA543385 Other RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing       body2 kd+mt s15   breed:zebrafish|dev stage:adult|sex:NA|tissue:body|BioSampleModel:Model organism or animal                 body2 kd+mt WC TC 064 WC TC 064 TRUEseq standardised protocol     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP198708     WC_TC_064_S15.R2.fastq.gz WC_TC_064_S15.R1.fastq.gz fastq fastq 5256312456.0 34581003.0 WC TC 064 S15.R1.fastq.gz 0:101 1:51 A:1366908192;C:1258394092;G:1221379603;T:1405741204;N:3889365 101 51     1366908192 1258394092 1221379603 1405741204 3889365 SRX5852358 SRS4776351 SRA887738 Southern University of Science and Technology|Department of Biology Southern University of Science and Technology 2 0.96533 0.96121 0.06858 0.07356 0.73547 0.7387 0.46254 0.46106 101 51 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk unknown unknown   China 2019-10-08 Adult Adult Trunk Surface Structure
69631 69631 SRR19025949 SRX15097731 SRS12843022 SRP373069 PRJNA833575 RNA sequencing analysis of wildtype and trmt5 knock out zebrafish PRJNA833575 Other Having clarified the alternated histological properties in trmt5 null zebrafish we were curious about the differences at the molecular level induced by trmt5 depletion. Whole body total RNAs samples were prepared from trmt5 / mutants and wide type siblings larvae at 16 dpf and RNA sequencing analysis was performed.       trmt5 knock out zebrafish trmt5 / 1   isolate:total RNAs isolated from trmt5 knock out zebrafish|age:16 dpf|dev stage:larval stage|sex:N1|tissue:whole body|replicate:replicate1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish 66ff83cdf42005466331679c80f92d12 66ff83cdf42005466331679c80f92d12 trmt5 knock out zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP373069     hom_1_Clean_Data2.fq.gz hom_1_Clean_Data1.fq.gz fastq fastq 6169235123.0 21958377.0 hom 1 Clean Data1.fq.gz 0:140.50 1:140.46 A:1560853223;C:1511690807;G:1520013294;T:1576470786;N:207013 140 140     1560853223 1511690807 1520013294 1576470786 207013 SRX15097731 SRS12843022 SRA1412777 Zhejiang University|Division of Medical Genetics and Genomics Zhejiang University 2 0.96859 0.96977 0.0392 0.03772 0.70658 0.70751 0.49243 0.49647 141 141 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2022-05-02 Larval Larval Trunk Surface Structure
69632 69632 SRR19025950 SRX15097730 SRS12843021 SRP373069 PRJNA833575 RNA sequencing analysis of wildtype and trmt5 knock out zebrafish PRJNA833575 Other Having clarified the alternated histological properties in trmt5 null zebrafish we were curious about the differences at the molecular level induced by trmt5 depletion. Whole body total RNAs samples were prepared from trmt5 / mutants and wide type siblings larvae at 16 dpf and RNA sequencing analysis was performed.       wild type zebrafish trmt5+/+ 4   isolate:total RNAs isolated from WT zebrafish|age:16 dpf|dev stage:larval stage|sex:N1|tissue:whole body|replicate:replicate4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish d919fe9c401838b06040e4ee1638981e d919fe9c401838b06040e4ee1638981e wild type zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP373069     wt_4_Clean_Data1.fq.gz wt_4_Clean_Data2.fq.gz fastq fastq 6033250663.0 21483270.0 wt 4 Clean Data1.fq.gz 0:140.44 1:140.40 A:1538261833;C:1466011430;G:1475787704;T:1552985419;N:204277 140 140     1538261833 1466011430 1475787704 1552985419 204277 SRX15097730 SRS12843021 SRA1412777 Zhejiang University|Division of Medical Genetics and Genomics Zhejiang University 2 0.96586 0.96804 0.04584 0.04451 0.68698 0.68688 0.46575 0.44961 141 141 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2022-05-02 Larval Larval Trunk Surface Structure
69633 69633 SRR19025951 SRX15097729 SRS12843020 SRP373069 PRJNA833575 RNA sequencing analysis of wildtype and trmt5 knock out zebrafish PRJNA833575 Other Having clarified the alternated histological properties in trmt5 null zebrafish we were curious about the differences at the molecular level induced by trmt5 depletion. Whole body total RNAs samples were prepared from trmt5 / mutants and wide type siblings larvae at 16 dpf and RNA sequencing analysis was performed.       wild type zebrafish trmt5+/+ 3   isolate:total RNAs isolated from WT zebrafish|age:16 dpf|dev stage:larval stage|sex:N1|tissue:whole body|replicate:replicate3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish d0459b1dac26131278f334c9290f1d2b d0459b1dac26131278f334c9290f1d2b wild type zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP373069     wt_3_Clean_Data2.fq.gz wt_3_Clean_Data1.fq.gz fastq fastq 5891772865.0 20970124.0 wt 3 Clean Data1.fq.gz 0:140.50 1:140.46 A:1502638659;C:1431652346;G:1439973482;T:1517318614;N:189764 140 140     1502638659 1431652346 1439973482 1517318614 189764 SRX15097729 SRS12843020 SRA1412777 Zhejiang University|Division of Medical Genetics and Genomics Zhejiang University 2 0.96668 0.96871 0.04432 0.04253 0.6887 0.68842 0.46997 0.45735 141 141 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2022-05-02 Larval Larval Trunk Surface Structure
69634 69634 SRR19025952 SRX15097728 SRS12843019 SRP373069 PRJNA833575 RNA sequencing analysis of wildtype and trmt5 knock out zebrafish PRJNA833575 Other Having clarified the alternated histological properties in trmt5 null zebrafish we were curious about the differences at the molecular level induced by trmt5 depletion. Whole body total RNAs samples were prepared from trmt5 / mutants and wide type siblings larvae at 16 dpf and RNA sequencing analysis was performed.       wild type zebrafish trmt5+/+ 2   isolate:total RNAs isolated from WT zebrafish|age:16 dpf|dev stage:larval stage|sex:N1|tissue:whole body|replicate:replicate2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish 9dbee5750238db2822304d9f2e0edea9 9dbee5750238db2822304d9f2e0edea9 wild type zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP373069     wt_2_Clean_Data1.fq.gz wt_2_Clean_Data2.fq.gz fastq fastq 5766006501.0 20521262.0 wt 2 Clean Data1.fq.gz 0:140.51 1:140.47 A:1470465676;C:1400491025;G:1410148993;T:1484706149;N:194658 140 140     1470465676 1400491025 1410148993 1484706149 194658 SRX15097728 SRS12843019 SRA1412777 Zhejiang University|Division of Medical Genetics and Genomics Zhejiang University 2 0.96644 0.9675 0.04557 0.04323 0.68832 0.68842 0.4676 0.4602 141 141 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2022-05-02 Larval Larval Trunk Surface Structure
69635 69635 SRR19025953 SRX15097727 SRS12843018 SRP373069 PRJNA833575 RNA sequencing analysis of wildtype and trmt5 knock out zebrafish PRJNA833575 Other Having clarified the alternated histological properties in trmt5 null zebrafish we were curious about the differences at the molecular level induced by trmt5 depletion. Whole body total RNAs samples were prepared from trmt5 / mutants and wide type siblings larvae at 16 dpf and RNA sequencing analysis was performed.       trmt5 knock out zebrafish trmt5 / 4   isolate:total RNAs isolated from trmt5 knock out zebrafish|age:16 dpf|dev stage:larval stage|sex:N1|tissue:whole body|replicate:replicate4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish 7a076bcf71269def10954f4107bf1124 7a076bcf71269def10954f4107bf1124 trmt5 knock out zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP373069     hom_4_Clean_Data1.fq.gz hom_4_Clean_Data2.fq.gz fastq fastq 6241361550.0 22218760.0 hom 4 Clean Data1.fq.gz 0:140.47 1:140.43 A:1577557316;C:1530905024;G:1539141855;T:1593551612;N:205743 140 140     1577557316 1530905024 1539141855 1593551612 205743 SRX15097727 SRS12843018 SRA1412777 Zhejiang University|Division of Medical Genetics and Genomics Zhejiang University 2 0.97042 0.97147 0.03889 0.03706 0.71035 0.71062 0.48557 0.50047 141 141 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2022-05-02 Larval Larval Trunk Surface Structure
69636 69636 SRR19025954 SRX15097726 SRS12843017 SRP373069 PRJNA833575 RNA sequencing analysis of wildtype and trmt5 knock out zebrafish PRJNA833575 Other Having clarified the alternated histological properties in trmt5 null zebrafish we were curious about the differences at the molecular level induced by trmt5 depletion. Whole body total RNAs samples were prepared from trmt5 / mutants and wide type siblings larvae at 16 dpf and RNA sequencing analysis was performed.       trmt5 knock out zebrafish trmt5 / 3   isolate:total RNAs isolated from trmt5 knock out zebrafish|age:16 dpf|dev stage:larval stage|sex:N1|tissue:whole body|replicate:replicate3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish 5689e7391d2921855b4759bcdc123378 5689e7391d2921855b4759bcdc123378 trmt5 knock out zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP373069     hom_3_Clean_Data1.fq.gz hom_3_Clean_Data2.fq.gz fastq fastq 6051656240.0 21549593.0 hom 3 Clean Data1.fq.gz 0:140.43 1:140.39 A:1531682742;C:1482500631;G:1490088770;T:1547184370;N:199727 140 140     1531682742 1482500631 1490088770 1547184370 199727 SRX15097726 SRS12843017 SRA1412777 Zhejiang University|Division of Medical Genetics and Genomics Zhejiang University 2 0.96902 0.97138 0.03966 0.03849 0.71208 0.71244 0.49461 0.4851 141 141 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2022-05-02 Larval Larval Trunk Surface Structure
69637 69637 SRR19025955 SRX15097725 SRS12843016 SRP373069 PRJNA833575 RNA sequencing analysis of wildtype and trmt5 knock out zebrafish PRJNA833575 Other Having clarified the alternated histological properties in trmt5 null zebrafish we were curious about the differences at the molecular level induced by trmt5 depletion. Whole body total RNAs samples were prepared from trmt5 / mutants and wide type siblings larvae at 16 dpf and RNA sequencing analysis was performed.       trmt5 knock out zebrafish trmt5 / 2   isolate:total RNAs isolated from trmt5 knock out zebrafish|age:16 dpf|dev stage:larval stage|sex:N1|tissue:whole body|replicate:replicate2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish 8b1e5ab49c8be853af71803609cb227c 8b1e5ab49c8be853af71803609cb227c trmt5 knock out zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP373069     hom_2_Clean_Data1.fq.gz hom_2_Clean_Data2.fq.gz fastq fastq 6212537192.0 22136506.0 hom 2 Clean Data1.fq.gz 0:140.34 1:140.31 A:1573896925;C:1526845773;G:1529170873;T:1582416723;N:206898 140 140     1573896925 1526845773 1529170873 1582416723 206898 SRX15097725 SRS12843016 SRA1412777 Zhejiang University|Division of Medical Genetics and Genomics Zhejiang University 2 0.96821 0.96875 0.03881 0.03757 0.71259 0.71285 0.48811 0.48638 141 141 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2022-05-02 Larval Larval Trunk Surface Structure
69638 69638 SRR19025956 SRX15097724 SRS12843015 SRP373069 PRJNA833575 RNA sequencing analysis of wildtype and trmt5 knock out zebrafish PRJNA833575 Other Having clarified the alternated histological properties in trmt5 null zebrafish we were curious about the differences at the molecular level induced by trmt5 depletion. Whole body total RNAs samples were prepared from trmt5 / mutants and wide type siblings larvae at 16 dpf and RNA sequencing analysis was performed.       wild type zebrafish trmt5+/+ 1   isolate:total RNAs isolated from WT zebrafish|age:16 dpf|dev stage:larval stage|sex:N1|tissue:whole body|replicate:replicate1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish acd6771912bd9a4423df64fa4898e484 acd6771912bd9a4423df64fa4898e484 wild type zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP373069     wt_1_Clean_Data1.fq.gz wt_1_Clean_Data2.fq.gz fastq fastq 6143077598.0 21878233.0 wt 1 Clean Data1.fq.gz 0:140.41 1:140.38 A:1578226894;C:1486538531;G:1490138396;T:1587966031;N:207746 140 140     1578226894 1486538531 1490138396 1587966031 207746 SRX15097724 SRS12843015 SRA1412777 Zhejiang University|Division of Medical Genetics and Genomics Zhejiang University 2 0.96278 0.96429 0.05204 0.05046 0.67817 0.67978 0.45055 0.43833 141 141 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2022-05-02 Larval Larval Trunk Surface Structure

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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");;