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22 rows where experiment.library_source = "TRANSCRIPTOMIC", experiment.platform = "BGISEQ" and tissue_curation_coarse = "Reproductive System"

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experiment.library_selection 3

experiment.library_layout 2

devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

  • Reproductive System · 22 ✖

tissue_curation 1

technology 1

experiment.platform 1

  • BGISEQ · 22 ✖

experiment.library_strategy 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 22 ✖
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
48812 48812 SRR7341816 SRX4215318 SRS3417596 SRP150521 PRJNA476105 Transcriptome analysis of wildtype and sox3 / zebrafish adult ovary GSE115806 Transcriptome Analysis The goals of this study are to compare the differentially expressed genes between wildtype and sox3 / zebrafish ovaries based on RNA seq data and some of these genes were validated by qRT–PCR. Further the differentially expressed genes were devided into up regulated and down regulated genes for GO and KEGG analysis. Overall design: Ovary mRNA profiles of adult wildtype and sox3 / zebrafish were generated by deep sequencing.   pubmed:30588557   KO mix GSM3190267   source name:Ovary|strain:AB|tissue:Ovary|age:Adult KO mix Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz10 whole genome using HISAT mapped to genes using Bowtie2. fragments per kilo bases per million fragments FPKM were calculated using RSEM. Genome build: GRCz10 Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample. Ovary   Ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.   strain:AB|tissue:Ovary|age:Adult GSM3190267 GSM3190267: KO mix; Danio rerio; RNA Seq GSM3190267   1 Ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols. GEO Accession:GSM3190267 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP150521     KO-ovary.fq.gz fastq 1173123100.0 23462462.0 GSM3190267 r1 0:50 1:0 A:308426188;C:271468505;G:292019086;T:300532126;N:677195 50 0     308426188 271468505 292019086 300532126 677195 SRX4215318 SRS3417596 SRA721702 GEO Wuhan university 1 0.93261   0.02261   0.76132   0.4585   50   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2018-06-14 Adult Adult Gonad Reproductive System
48813 48813 SRR7341815 SRX4215317 SRS3417595 SRP150521 PRJNA476105 Transcriptome analysis of wildtype and sox3 / zebrafish adult ovary GSE115806 Transcriptome Analysis The goals of this study are to compare the differentially expressed genes between wildtype and sox3 / zebrafish ovaries based on RNA seq data and some of these genes were validated by qRT–PCR. Further the differentially expressed genes were devided into up regulated and down regulated genes for GO and KEGG analysis. Overall design: Ovary mRNA profiles of adult wildtype and sox3 / zebrafish were generated by deep sequencing.   pubmed:30588557   WT mix GSM3190266   source name:Ovary|strain:AB|tissue:Ovary|age:Adult WT mix Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz10 whole genome using HISAT mapped to genes using Bowtie2. fragments per kilo bases per million fragments FPKM were calculated using RSEM. Genome build: GRCz10 Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample. Ovary   Ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.   strain:AB|tissue:Ovary|age:Adult GSM3190266 GSM3190266: WT mix; Danio rerio; RNA Seq GSM3190266   1 Ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols. GEO Accession:GSM3190266 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP150521     WT-ovary.fq.gz fastq 1176463600.0 23529272.0 GSM3190266 r1 0:50 1:0 A:311869864;C:270650722;G:289863261;T:303489229;N:590524 50 0     311869864 270650722 289863261 303489229 590524 SRX4215317 SRS3417595 SRA721702 GEO Wuhan university 1 0.93489   0.02765   0.75627   0.46875   50   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2018-06-14 Adult Adult Gonad Reproductive System
58533 58533 SRR11355387 SRX7957249 SRS6343356 SRP253408 PRJNA613558 Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture PRJNA613558 Other As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study combined with antibiotics bioaccumulated in ovary we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish and thus affect egg production and survival. Therefore ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0 1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.       C2 3 C2 3   strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 RNA seq of zebrafish C2 320200327 C2 320200327 RNA seq of zebrafish in different conditions     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED BGISEQ BGISEQ-500   SRP253408     C2_3_1.fq.gz C2_3_2.fq.gz fastq fastq 6857650800.0 45717672.0 C2 3 1.fq.gz 0:150 1:150 A:1826466263;C:1599272942;G:1580689630;T:1851144875;N:77090 150 150     1826466263 1599272942 1580689630 1851144875 77090 SRX7957249 SRS6343356 SRA1056819 Southern University of Science and Technology|School of Environmental Science and Engineering Southern University of Science and Technology 1 0.93222   0.02854   0.75138   0.50759   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-03-20 Undetermined Adult Gonad Reproductive System
58534 58534 SRR11355388 SRX7957248 SRS6343355 SRP253408 PRJNA613558 Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture PRJNA613558 Other As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study combined with antibiotics bioaccumulated in ovary we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish and thus affect egg production and survival. Therefore ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0 1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.       C2 2 C2 2   strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 RNA seq of zebrafish C2 220200326 C2 220200326 RNA seq of zebrafish in different conditions     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED BGISEQ BGISEQ-500   SRP253408     C2_2_1.fq.gz C2_2_2.fq.gz fastq fastq 6859954800.0 45733032.0 C2 2 1.fq.gz 0:150 1:150 A:1836618967;C:1591135182;G:1572318102;T:1859806048;N:76501 150 150     1836618967 1591135182 1572318102 1859806048 76501 SRX7957248 SRS6343355 SRA1056819 Southern University of Science and Technology|School of Environmental Science and Engineering Southern University of Science and Technology 1 0.93237   0.03248   0.74663   0.5081   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-03-20 Undetermined Adult Gonad Reproductive System
58535 58535 SRR11355389 SRX7957247 SRS6343354 SRP253408 PRJNA613558 Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture PRJNA613558 Other As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study combined with antibiotics bioaccumulated in ovary we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish and thus affect egg production and survival. Therefore ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0 1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.       C2 1 C2 1   strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 RNA seq of zebrafish C2 120200325 C2 120200325 RNA seq of zebrafish in different conditions     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED BGISEQ BGISEQ-500   SRP253408     C2_1_1.fq.gz C2_1_2.fq.gz fastq fastq 6618974400.0 44126496.0 C2 1 1.fq.gz 0:150 1:150 A:1774116288;C:1533828286;G:1511526952;T:1799423408;N:79466 150 150     1774116288 1533828286 1511526952 1799423408 79466 SRX7957247 SRS6343354 SRA1056819 Southern University of Science and Technology|School of Environmental Science and Engineering Southern University of Science and Technology 1 0.9326   0.02973   0.75426   0.50678   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-03-20 Undetermined Adult Gonad Reproductive System
58536 58536 SRR11355390 SRX7957246 SRS6343353 SRP253408 PRJNA613558 Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture PRJNA613558 Other As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study combined with antibiotics bioaccumulated in ovary we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish and thus affect egg production and survival. Therefore ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0 1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.       C1 3 C1 3   strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 RNA seq of zebrafish C1 320200324 C1 320200324 RNA seq of zebrafish in different conditions     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED BGISEQ BGISEQ-500   SRP253408     C1_3_1.fq.gz C1_3_2.fq.gz fastq fastq 6837729600.0 45584864.0 C1 3 1.fq.gz 0:150 1:150 A:1831266308;C:1587032733;G:1565071069;T:1853950421;N:409069 150 150     1831266308 1587032733 1565071069 1853950421 409069 SRX7957246 SRS6343353 SRA1056819 Southern University of Science and Technology|School of Environmental Science and Engineering Southern University of Science and Technology 1 0.93541   0.03212   0.74681   0.50268   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-03-20 Undetermined Adult Gonad Reproductive System
58537 58537 SRR11355391 SRX7957245 SRS6343352 SRP253408 PRJNA613558 Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture PRJNA613558 Other As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study combined with antibiotics bioaccumulated in ovary we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish and thus affect egg production and survival. Therefore ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0 1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.       C1 2 C1 2   strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 RNA seq of zebrafish C1 220200323 C1 220200323 RNA seq of zebrafish in different conditions     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED BGISEQ BGISEQ-500   SRP253408     C1_2_2.fq.gz C1_2_1.fq.gz fastq fastq 6860328000.0 45735520.0 C1 2 1.fq.gz 0:150 1:150 A:1838176072;C:1591277709;G:1569605888;T:1861063734;N:204597 150 150     1838176072 1591277709 1569605888 1861063734 204597 SRX7957245 SRS6343352 SRA1056819 Southern University of Science and Technology|School of Environmental Science and Engineering Southern University of Science and Technology 1 0.93763   0.033   0.74617   0.50287   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-03-20 Undetermined Adult Gonad Reproductive System
58538 58538 SRR11355392 SRX7957244 SRS6343351 SRP253408 PRJNA613558 Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture PRJNA613558 Other As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study combined with antibiotics bioaccumulated in ovary we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish and thus affect egg production and survival. Therefore ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0 1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.       C1 1 C1 1   strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 RNA seq of zebrafish C1 120200322 C1 120200322 RNA seq of zebrafish in different conditions     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED BGISEQ BGISEQ-500   SRP253408     C1_1_1.fq.gz C1_1_2.fq.gz fastq fastq 6865547700.0 45770318.0 C1 1 1.fq.gz 0:150 1:150 A:1841774713;C:1591288582;G:1570400871;T:1861867728;N:215806 150 150     1841774713 1591288582 1570400871 1861867728 215806 SRX7957244 SRS6343351 SRA1056819 Southern University of Science and Technology|School of Environmental Science and Engineering Southern University of Science and Technology 1 0.93567   0.03152   0.74653   0.50239   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-03-20 Undetermined Adult Gonad Reproductive System
58539 58539 SRR11355393 SRX7957243 SRS6343350 SRP253408 PRJNA613558 Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture PRJNA613558 Other As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study combined with antibiotics bioaccumulated in ovary we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish and thus affect egg production and survival. Therefore ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0 1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.       C0 3 C0 3   strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 RNA seq of zebrafish C0 320200321 C0 320200321 RNA seq of zebrafish in different conditions     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED BGISEQ BGISEQ-500   SRP253408     C0_3_1.fq.gz C0_3_2.fq.gz fastq fastq 6824622600.0 45497484.0 C0 3 1.fq.gz 0:150 1:150 A:1833660953;C:1578510104;G:1558095174;T:1854128169;N:228200 150 150     1833660953 1578510104 1558095174 1854128169 228200 SRX7957243 SRS6343350 SRA1056819 Southern University of Science and Technology|School of Environmental Science and Engineering Southern University of Science and Technology 1 0.93758   0.0323   0.75024   0.50852   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-03-20 Undetermined Adult Gonad Reproductive System
58540 58540 SRR11355394 SRX7957242 SRS6343349 SRP253408 PRJNA613558 Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture PRJNA613558 Other As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study combined with antibiotics bioaccumulated in ovary we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish and thus affect egg production and survival. Therefore ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0 1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.       C0 2 C0 2   strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 RNA seq of zebrafish C0 220200320 C0 220200320 RNA seq of zebrafish in different conditions     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED BGISEQ BGISEQ-500   SRP253408     C0_2_2.fq.gz C0_2_1.fq.gz fastq fastq 6819326400.0 45462176.0 C0 2 1.fq.gz 0:150 1:150 A:1837661215;C:1571877614;G:1550458835;T:1859103408;N:225328 150 150     1837661215 1571877614 1550458835 1859103408 225328 SRX7957242 SRS6343349 SRA1056819 Southern University of Science and Technology|School of Environmental Science and Engineering Southern University of Science and Technology 1 0.93697   0.0339   0.74793   0.5035   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-03-20 Undetermined Adult Gonad Reproductive System
58541 58541 SRR11355395 SRX7957241 SRS6343348 SRP253408 PRJNA613558 Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture PRJNA613558 Other As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study combined with antibiotics bioaccumulated in ovary we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish and thus affect egg production and survival. Therefore ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0 1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.       C0 1 C0 1   strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 RNA seq of zebrafish C0 120200319 C0 120200319 RNA seq of zebrafish in different conditions     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED BGISEQ BGISEQ-500   SRP253408     C0_1_1.fq.gz C0_1_2.fq.gz fastq fastq 7030804800.0 46872032.0 C0 1 1.fq.gz 0:150 1:150 A:1891469955;C:1624531422;G:1603124564;T:1911444454;N:234405 150 150     1891469955 1624531422 1603124564 1911444454 234405 SRX7957241 SRS6343348 SRA1056819 Southern University of Science and Technology|School of Environmental Science and Engineering Southern University of Science and Technology 1 0.93519   0.0328   0.74602   0.48272   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-03-20 Undetermined Adult Gonad Reproductive System
74160 74160 SRR23576624 SRX19463433 SRS16856056 SRP423783 PRJNA937311 Telomere elongation in the gut extends systemic healthspan of zebrafish PRJNA937311 Other Telomere shortening is a hallmark of aging and is counteracted by telomerase. zebrafish gut is one of the organs with the fastest rate of telomere decline. However whether telomere dependent aging of an individual organ the gut causes systemic aging remains unknown. Here we show that preventing telomere shortening in the gut through tissue specific telomerase expression rescues premature aging of tert / . Conclusively we show that gut specific telomerase expression extends lifespan of tert / by 40 % while ameliorating natural aging. Our work demonstrates that delaying telomere shortening in the gut is sufficient to systemically counteract aging in zebrafish.         T1B   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:testis|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:testis tert no Cre R1|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male testis T1B T1B RNA Seq of Danio rerio : adult male testis     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     T1B_1.fq.gz T1B_2.fq.gz fastq fastq 12301883400.0 123018834.0 T1B 1.fq.gz 0:100 1:100 A:3241228917;C:2853095411;G:2904960052;T:3302599020;N:0 100 100     3241228917 2853095411 2904960052 3302599020 0 SRX19463433 SRS16856056 SRA1593824 Sun Yat-sen University Cancer Center|State Key Laboratory of Oncology in South China Sun Yat-sen University Cancer Center Miguel Godinho Ferreira 1 0.95272   0.09396   0.68469   0.54489   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Gonad Reproductive System
74177 74177 SRR23576641 SRX19463416 SRS16856039 SRP423783 PRJNA937311 Telomere elongation in the gut extends systemic healthspan of zebrafish PRJNA937311 Other Telomere shortening is a hallmark of aging and is counteracted by telomerase. zebrafish gut is one of the organs with the fastest rate of telomere decline. However whether telomere dependent aging of an individual organ the gut causes systemic aging remains unknown. Here we show that preventing telomere shortening in the gut through tissue specific telomerase expression rescues premature aging of tert / . Conclusively we show that gut specific telomerase expression extends lifespan of tert / by 40 % while ameliorating natural aging. Our work demonstrates that delaying telomere shortening in the gut is sufficient to systemically counteract aging in zebrafish.         T9   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:testis|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:testis WT R3|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male testis T9 T9 RNA Seq of Danio rerio : adult male testis     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     T9_1.fq.gz T9_2.fq.gz fastq fastq 12386772800.0 123867728.0 T9 1.fq.gz 0:100 1:100 A:3400599530;C:2772066139;G:2813890387;T:3400216744;N:0 100 100     3400599530 2772066139 2813890387 3400216744 0 SRX19463416 SRS16856039 SRA1593824 Sun Yat-sen University Cancer Center|State Key Laboratory of Oncology in South China Sun Yat-sen University Cancer Center Miguel Godinho Ferreira 1 0.93775   0.12024   0.63838   0.49765   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Gonad Reproductive System
74178 74178 SRR23576642 SRX19463415 SRS16856037 SRP423783 PRJNA937311 Telomere elongation in the gut extends systemic healthspan of zebrafish PRJNA937311 Other Telomere shortening is a hallmark of aging and is counteracted by telomerase. zebrafish gut is one of the organs with the fastest rate of telomere decline. However whether telomere dependent aging of an individual organ the gut causes systemic aging remains unknown. Here we show that preventing telomere shortening in the gut through tissue specific telomerase expression rescues premature aging of tert / . Conclusively we show that gut specific telomerase expression extends lifespan of tert / by 40 % while ameliorating natural aging. Our work demonstrates that delaying telomere shortening in the gut is sufficient to systemically counteract aging in zebrafish.         T8   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:testis|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:testis WT R2|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male testis T8 T8 RNA Seq of Danio rerio : adult male testis     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     T8_1.fq.gz T8_2.fq.gz fastq fastq 12176715600.0 121767156.0 T8 1.fq.gz 0:100 1:100 A:3287270041;C:2775700062;G:2808469679;T:3305275818;N:0 100 100     3287270041 2775700062 2808469679 3305275818 0 SRX19463415 SRS16856037 SRA1593824 Sun Yat-sen University Cancer Center|State Key Laboratory of Oncology in South China Sun Yat-sen University Cancer Center Miguel Godinho Ferreira 1 0.94261   0.12625   0.63838   0.49901   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Gonad Reproductive System
74179 74179 SRR23576643 SRX19463414 SRS16856038 SRP423783 PRJNA937311 Telomere elongation in the gut extends systemic healthspan of zebrafish PRJNA937311 Other Telomere shortening is a hallmark of aging and is counteracted by telomerase. zebrafish gut is one of the organs with the fastest rate of telomere decline. However whether telomere dependent aging of an individual organ the gut causes systemic aging remains unknown. Here we show that preventing telomere shortening in the gut through tissue specific telomerase expression rescues premature aging of tert / . Conclusively we show that gut specific telomerase expression extends lifespan of tert / by 40 % while ameliorating natural aging. Our work demonstrates that delaying telomere shortening in the gut is sufficient to systemically counteract aging in zebrafish.         T7   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:testis|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:testis WT R1|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male testis T7 T7 RNA Seq of Danio rerio : adult male testis     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     T7_1.fq.gz T7_2.fq.gz fastq fastq 12172655600.0 121726556.0 T7 1.fq.gz 0:100 1:100 A:3248593263;C:2809119242;G:2855399333;T:3259543762;N:0 100 100     3248593263 2809119242 2855399333 3259543762 0 SRX19463414 SRS16856038 SRA1593824 Sun Yat-sen University Cancer Center|State Key Laboratory of Oncology in South China Sun Yat-sen University Cancer Center Miguel Godinho Ferreira 1 0.94602   0.10229   0.63603   0.48805   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Gonad Reproductive System
74180 74180 SRR23576644 SRX19463413 SRS16856036 SRP423783 PRJNA937311 Telomere elongation in the gut extends systemic healthspan of zebrafish PRJNA937311 Other Telomere shortening is a hallmark of aging and is counteracted by telomerase. zebrafish gut is one of the organs with the fastest rate of telomere decline. However whether telomere dependent aging of an individual organ the gut causes systemic aging remains unknown. Here we show that preventing telomere shortening in the gut through tissue specific telomerase expression rescues premature aging of tert / . Conclusively we show that gut specific telomerase expression extends lifespan of tert / by 40 % while ameliorating natural aging. Our work demonstrates that delaying telomere shortening in the gut is sufficient to systemically counteract aging in zebrafish.         T6   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:testis|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:testis tert Cre R3|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male testis T6 T6 RNA Seq of Danio rerio : adult male testis     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     T6_1.fq.gz T6_2.fq.gz fastq fastq 12378860000.0 123788600.0 T6 1.fq.gz 0:100 1:100 A:3314969512;C:2848487369;G:2903637904;T:3311765215;N:0 100 100     3314969512 2848487369 2903637904 3311765215 0 SRX19463413 SRS16856036 SRA1593824 Sun Yat-sen University Cancer Center|State Key Laboratory of Oncology in South China Sun Yat-sen University Cancer Center Miguel Godinho Ferreira 1 0.94452   0.10777   0.62422   0.49742   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Gonad Reproductive System
74181 74181 SRR23576645 SRX19463412 SRS16856034 SRP423783 PRJNA937311 Telomere elongation in the gut extends systemic healthspan of zebrafish PRJNA937311 Other Telomere shortening is a hallmark of aging and is counteracted by telomerase. zebrafish gut is one of the organs with the fastest rate of telomere decline. However whether telomere dependent aging of an individual organ the gut causes systemic aging remains unknown. Here we show that preventing telomere shortening in the gut through tissue specific telomerase expression rescues premature aging of tert / . Conclusively we show that gut specific telomerase expression extends lifespan of tert / by 40 % while ameliorating natural aging. Our work demonstrates that delaying telomere shortening in the gut is sufficient to systemically counteract aging in zebrafish.         T5   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:testis|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:testis tert Cre R2|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male testis T5 T5 RNA Seq of Danio rerio : adult male testis     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     T5_1.fq.gz T5_2.fq.gz fastq fastq 12128636200.0 121286362.0 T5 1.fq.gz 0:100 1:100 A:3365971947;C:2671909728;G:2726788212;T:3363966313;N:0 100 100     3365971947 2671909728 2726788212 3363966313 0 SRX19463412 SRS16856034 SRA1593824 Sun Yat-sen University Cancer Center|State Key Laboratory of Oncology in South China Sun Yat-sen University Cancer Center Miguel Godinho Ferreira 1 0.93852   0.14946   0.63747   0.52613   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Gonad Reproductive System
74182 74182 SRR23576646 SRX19463411 SRS16856032 SRP423783 PRJNA937311 Telomere elongation in the gut extends systemic healthspan of zebrafish PRJNA937311 Other Telomere shortening is a hallmark of aging and is counteracted by telomerase. zebrafish gut is one of the organs with the fastest rate of telomere decline. However whether telomere dependent aging of an individual organ the gut causes systemic aging remains unknown. Here we show that preventing telomere shortening in the gut through tissue specific telomerase expression rescues premature aging of tert / . Conclusively we show that gut specific telomerase expression extends lifespan of tert / by 40 % while ameliorating natural aging. Our work demonstrates that delaying telomere shortening in the gut is sufficient to systemically counteract aging in zebrafish.         T4   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:testis|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:testis tert Cre R1|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male testis T4 T4 RNA Seq of Danio rerio : adult male testis     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     T4_1.fq.gz T4_2.fq.gz fastq fastq 12162901400.0 121629014.0 T4 1.fq.gz 0:100 1:100 A:3278648055;C:2767244505;G:2825703918;T:3291304922;N:0 100 100     3278648055 2767244505 2825703918 3291304922 0 SRX19463411 SRS16856032 SRA1593824 Sun Yat-sen University Cancer Center|State Key Laboratory of Oncology in South China Sun Yat-sen University Cancer Center Miguel Godinho Ferreira 1 0.94511   0.11642   0.63258   0.4913   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Gonad Reproductive System
74183 74183 SRR23576647 SRX19463410 SRS16856035 SRP423783 PRJNA937311 Telomere elongation in the gut extends systemic healthspan of zebrafish PRJNA937311 Other Telomere shortening is a hallmark of aging and is counteracted by telomerase. zebrafish gut is one of the organs with the fastest rate of telomere decline. However whether telomere dependent aging of an individual organ the gut causes systemic aging remains unknown. Here we show that preventing telomere shortening in the gut through tissue specific telomerase expression rescues premature aging of tert / . Conclusively we show that gut specific telomerase expression extends lifespan of tert / by 40 % while ameliorating natural aging. Our work demonstrates that delaying telomere shortening in the gut is sufficient to systemically counteract aging in zebrafish.         T3   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:testis|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:testis tert no Cre R3|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male testis T3 T3 RNA Seq of Danio rerio : adult male testis     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     T3_1.fq.gz T3_2.fq.gz fastq fastq 12163321600.0 121633216.0 T3 1.fq.gz 0:100 1:100 A:3285334843;C:2767357208;G:2816394061;T:3294235488;N:0 100 100     3285334843 2767357208 2816394061 3294235488 0 SRX19463410 SRS16856035 SRA1593824 Sun Yat-sen University Cancer Center|State Key Laboratory of Oncology in South China Sun Yat-sen University Cancer Center Miguel Godinho Ferreira 1 0.9415   0.11969   0.62666   0.50292   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Gonad Reproductive System
74184 74184 SRR23576648 SRX19463409 SRS16856033 SRP423783 PRJNA937311 Telomere elongation in the gut extends systemic healthspan of zebrafish PRJNA937311 Other Telomere shortening is a hallmark of aging and is counteracted by telomerase. zebrafish gut is one of the organs with the fastest rate of telomere decline. However whether telomere dependent aging of an individual organ the gut causes systemic aging remains unknown. Here we show that preventing telomere shortening in the gut through tissue specific telomerase expression rescues premature aging of tert / . Conclusively we show that gut specific telomerase expression extends lifespan of tert / by 40 % while ameliorating natural aging. Our work demonstrates that delaying telomere shortening in the gut is sufficient to systemically counteract aging in zebrafish.         T2B   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:testis|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:testis tert no Cre R2|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male testis T2B T2B RNA Seq of Danio rerio : adult male testis     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     T2B_1.fq.gz T2B_2.fq.gz fastq fastq 12317978600.0 123179786.0 T2B 1.fq.gz 0:100 1:100 A:3182137355;C:2913584264;G:2974241242;T:3248015739;N:0 100 100     3182137355 2913584264 2974241242 3248015739 0 SRX19463409 SRS16856033 SRA1593824 Sun Yat-sen University Cancer Center|State Key Laboratory of Oncology in South China Sun Yat-sen University Cancer Center Miguel Godinho Ferreira 1 0.95364   0.08029   0.6882   0.53887   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Gonad Reproductive System
74613 74613 SRR23868264 SRX19680348 SRS17049789 SRP427394 PRJNA944944 Comparative transcriptome analysis of testes and ovaries reveals sex biased genes and pathways in zebrafish GSE227389 Transcriptome Analysis The goals of this study are to compare the differentially expressed genes between testes and ovaries of zebrafish based on RNA seq data and some of these genes were validated by qRT–PCR.Further the differentially expressed genes were devided into up regulated and down regulated genes for GO and KEGG analysis. Overall design: Testes and ovaries mRNA profiles of adult zebrafish were generated by deep sequencing. Every sample was compose of three adult individuals.   pubmed:38242380   testes GSM7099751   source name:testis|tissue:testis|genotype:WT|geo loc name:missing|collection date:missing testes Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz10 whole genome using HISAT mapped to genes using Bowtie2. fragments per kilo bases per million fragments FPKM were calculated using RSEM. Assembly: GRCz10 Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample. testis   Testes and ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.   tissue:testis|genotype:WT GSM7099751 GSM7099751: testes; Danio rerio; RNA Seq GSM7099751 r1 GSM7099751 1 Testes and ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP427394     WT-testis.fq.gz fastq 1176068400.0 23521368.0 GSM7099751 r1 0:50 A:323799672;C:262049848;G:273563529;T:316045968;N:609383 50       323799672 262049848 273563529 316045968 609383 SRX19680348 SRS17049789 SRA1687194 Wuhan university Wuhan university 1 0.93023   0.11308   0.6462   0.49784   50   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2023-03-15 Undetermined Undetermined Gonad Reproductive System
74614 74614 SRR23868265 SRX19680347 SRS17049788 SRP427394 PRJNA944944 Comparative transcriptome analysis of testes and ovaries reveals sex biased genes and pathways in zebrafish GSE227389 Transcriptome Analysis The goals of this study are to compare the differentially expressed genes between testes and ovaries of zebrafish based on RNA seq data and some of these genes were validated by qRT–PCR.Further the differentially expressed genes were devided into up regulated and down regulated genes for GO and KEGG analysis. Overall design: Testes and ovaries mRNA profiles of adult zebrafish were generated by deep sequencing. Every sample was compose of three adult individuals.   pubmed:38242380   ovaries GSM7099752   source name:ovary|tissue:ovary|genotype:WT|geo loc name:missing|collection date:missing ovaries Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz10 whole genome using HISAT mapped to genes using Bowtie2. fragments per kilo bases per million fragments FPKM were calculated using RSEM. Assembly: GRCz10 Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample. ovary   Testes and ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.   tissue:ovary|genotype:WT GSM7099752 GSM7099752: ovaries; Danio rerio; RNA Seq GSM7099752 r1 GSM7099752 1 Testes and ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE BGISEQ BGISEQ-500   SRP427394     WT-ovary.fq.gz fastq 1176463600.0 23529272.0 GSM7099752 r1 0:50 A:311869864;C:270650722;G:289863261;T:303489229;N:590524 50       311869864 270650722 289863261 303489229 590524 SRX19680347 SRS17049788 SRA1687194 Wuhan university Wuhan university 1 0.93488   0.02755   0.75601   0.46986   50   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2023-03-15 Undetermined Undetermined Gonad Reproductive System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;