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33 rows where experiment.platform = "BGISEQ", technology = "unknown" and tissue_curation = "Kidney"

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experiment.library_selection 3

devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

tissue_curation 1

  • Kidney · 33 ✖

technology 1

  • unknown · 33 ✖

experiment.platform 1

  • BGISEQ · 33 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_layout 1

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
63046 63046 SRR13587431 SRX9982126 SRS8153604 SRP303929 PRJNA698005 Danio rerio Raw sequence reads PRJNA698005 Whole Genome Sequencing Danio rerio Raw RNA sequence reads       Model organism or animal sample from Danio rerio The head kidney of Danio rerio   isolate:river|age:adult|sex:not determined|tissue:head kidney|BioSampleModel:Model organism or animal                 9ZHK 9ZHK 9ZHK The head kidney experiment repeat 3 of Gobiocypris rarus     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP303929     9ZHK_1.fq.gz 9ZHK_2.fq.gz fastq fastq 8120179200.0 54134528.0 9ZHK 1.fq.gz 0:150 1:150 A:2233782125;C:1817163304;G:1810150041;T:2259083730;N:0 150 150     2233782125 1817163304 1810150041 2259083730 0 SRX9982126 SRS8153604 SRA1189633 Center for Ecological and Environmental Sciences|Northwestern Polytechnical University Center for Ecological and Environmental Sciences 1 0.92334   0.08214   0.71926   0.53557   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-01-30 Adult Adult Kidney Renal System
63047 63047 SRR13587432 SRX9982125 SRS8153604 SRP303929 PRJNA698005 Danio rerio Raw sequence reads PRJNA698005 Whole Genome Sequencing Danio rerio Raw RNA sequence reads       Model organism or animal sample from Danio rerio The head kidney of Danio rerio   isolate:river|age:adult|sex:not determined|tissue:head kidney|BioSampleModel:Model organism or animal                 24ZHK 24ZHK 24ZHK The head kidney control repeat 3 of Gobiocypris rarus     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP303929     24ZHK_1.fq.gz 24ZHK_2.fq.gz fastq fastq 8285296800.0 55235312.0 24ZHK 1.fq.gz 0:150 1:150 A:2319759918;C:1824087204;G:1797861715;T:2343319625;N:268338 150 150     2319759918 1824087204 1797861715 2343319625 268338 SRX9982125 SRS8153604 SRA1189633 Center for Ecological and Environmental Sciences|Northwestern Polytechnical University Center for Ecological and Environmental Sciences 1 0.93067   0.0988   0.74241   0.55453   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-01-30 Adult Adult Kidney Renal System
63048 63048 SRR13587433 SRX9982124 SRS8153604 SRP303929 PRJNA698005 Danio rerio Raw sequence reads PRJNA698005 Whole Genome Sequencing Danio rerio Raw RNA sequence reads       Model organism or animal sample from Danio rerio The head kidney of Danio rerio   isolate:river|age:adult|sex:not determined|tissue:head kidney|BioSampleModel:Model organism or animal                 8ZHK 8ZHK 8ZHK The head kidney experiment repeat 2 of Gobiocypris rarus     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP303929     8ZHK_1.fq.gz 8ZHK_2.fq.gz fastq fastq 8153939700.0 54359598.0 8ZHK 1.fq.gz 0:150 1:150 A:2258284333;C:1815761334;G:1799498163;T:2279047560;N:1348310 150 150     2258284333 1815761334 1799498163 2279047560 1348310 SRX9982124 SRS8153604 SRA1189633 Center for Ecological and Environmental Sciences|Northwestern Polytechnical University Center for Ecological and Environmental Sciences 1 0.91032   0.08827   0.72673   0.51792   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-01-30 Adult Adult Kidney Renal System
63049 63049 SRR13587434 SRX9982123 SRS8153604 SRP303929 PRJNA698005 Danio rerio Raw sequence reads PRJNA698005 Whole Genome Sequencing Danio rerio Raw RNA sequence reads       Model organism or animal sample from Danio rerio The head kidney of Danio rerio   isolate:river|age:adult|sex:not determined|tissue:head kidney|BioSampleModel:Model organism or animal                 19Z HK 19Z HK 19Z HK The head kidney control repeat 2 of Gobiocypris rarus     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP303929     19Z_HK_1.fq.gz 19Z_HK_2.fq.gz fastq fastq 8406183300.0 56041222.0 19Z HK 1.fq.gz 0:150 1:150 A:2335489974;C:1857072213;G:1842430689;T:2370663226;N:527198 150 150     2335489974 1857072213 1842430689 2370663226 527198 SRX9982123 SRS8153604 SRA1189633 Center for Ecological and Environmental Sciences|Northwestern Polytechnical University Center for Ecological and Environmental Sciences 1 0.90938   0.09376   0.72486   0.55731   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-01-30 Adult Adult Kidney Renal System
63050 63050 SRR13587435 SRX9982122 SRS8153604 SRP303929 PRJNA698005 Danio rerio Raw sequence reads PRJNA698005 Whole Genome Sequencing Danio rerio Raw RNA sequence reads       Model organism or animal sample from Danio rerio The head kidney of Danio rerio   isolate:river|age:adult|sex:not determined|tissue:head kidney|BioSampleModel:Model organism or animal                 10ZHK 10ZHK 10ZHK The head kidney experiment repeat 1 of Gobiocypris rarus     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP303929     10ZHK_1.fq.gz 10ZHK_2.fq.gz fastq fastq 8039735100.0 53598234.0 10ZHK 1.fq.gz 0:150 1:150 A:2243931802;C:1770968625;G:1759940752;T:2264893921;N:0 150 150     2243931802 1770968625 1759940752 2264893921 0 SRX9982122 SRS8153604 SRA1189633 Center for Ecological and Environmental Sciences|Northwestern Polytechnical University Center for Ecological and Environmental Sciences 1 0.9182   0.10087   0.71417   0.54166   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-01-30 Adult Adult Kidney Renal System
63051 63051 SRR13587436 SRX9982121 SRS8153604 SRP303929 PRJNA698005 Danio rerio Raw sequence reads PRJNA698005 Whole Genome Sequencing Danio rerio Raw RNA sequence reads       Model organism or animal sample from Danio rerio The head kidney of Danio rerio   isolate:river|age:adult|sex:not determined|tissue:head kidney|BioSampleModel:Model organism or animal                 10Z HK 10Z HK 10Z HK The head kidney control repeat 1 of Gobiocypris rarus     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP303929     10Z_HK_1.fq.gz 10Z_HK_2.fq.gz fastq fastq 8419659600.0 56131064.0 10Z HK 1.fq.gz 0:150 1:150 A:2310224890;C:1885764527;G:1880790942;T:2342359008;N:520233 150 150     2310224890 1885764527 1880790942 2342359008 520233 SRX9982121 SRS8153604 SRA1189633 Center for Ecological and Environmental Sciences|Northwestern Polytechnical University Center for Ecological and Environmental Sciences 1 0.91616   0.06612   0.76152   0.37751   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-01-30 Adult Adult Kidney Renal System
63058 63058 SRR13587413 SRX9982108 SRS8153601 SRP303929 PRJNA698005 Danio rerio Raw sequence reads PRJNA698005 Whole Genome Sequencing Danio rerio Raw RNA sequence reads       Model organism or animal sample from Danio rerio The kidney of Danio rerio   isolate:river|age:adult|sex:not collected|tissue:kidney|BioSampleModel:Model organism or animal                 9ZK 9ZK 9ZK The kidney experiment repeat 3 of Gobiocypris rarus     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP303929     9ZK_1.fq.gz 9ZK_2.fq.gz fastq fastq 8175736200.0 54504908.0 9ZK 1.fq.gz 0:150 1:150 A:2263839094;C:1817074671;G:1806345887;T:2288476548;N:0 150 150     2263839094 1817074671 1806345887 2288476548 0 SRX9982108 SRS8153601 SRA1189630 Center for Ecological and Environmental Sciences|Northwestern Polytechnical University Center for Ecological and Environmental Sciences 1 0.92014   0.08977   0.72236   0.53162   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-01-30 Adult Adult Kidney Renal System
63059 63059 SRR13587414 SRX9982107 SRS8153601 SRP303929 PRJNA698005 Danio rerio Raw sequence reads PRJNA698005 Whole Genome Sequencing Danio rerio Raw RNA sequence reads       Model organism or animal sample from Danio rerio The kidney of Danio rerio   isolate:river|age:adult|sex:not collected|tissue:kidney|BioSampleModel:Model organism or animal                 24ZK 24ZK 24ZK The kidney control repeat 3 of Gobiocypris rarus     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP303929     24ZK_1.fq.gz 24ZK_2.fq.gz fastq fastq 8238567600.0 54923784.0 24ZK 1.fq.gz 0:150 1:150 A:2258633038;C:1860080137;G:1835508827;T:2284016515;N:329083 150 150     2258633038 1860080137 1835508827 2284016515 329083 SRX9982107 SRS8153601 SRA1189630 Center for Ecological and Environmental Sciences|Northwestern Polytechnical University Center for Ecological and Environmental Sciences 1 0.92468   0.0959   0.70907   0.53327   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-01-30 Adult Adult Kidney Renal System
63060 63060 SRR13587415 SRX9982106 SRS8153601 SRP303929 PRJNA698005 Danio rerio Raw sequence reads PRJNA698005 Whole Genome Sequencing Danio rerio Raw RNA sequence reads       Model organism or animal sample from Danio rerio The kidney of Danio rerio   isolate:river|age:adult|sex:not collected|tissue:kidney|BioSampleModel:Model organism or animal                 8ZK 8ZK 8ZK The kidney experiment repeat 2 of Gobiocypris rarus     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP303929     8ZK_1.fq.gz 8ZK_2.fq.gz fastq fastq 8191887900.0 54612586.0 8ZK 1.fq.gz 0:150 1:150 A:2267646460;C:1825604395;G:1807903598;T:2289958188;N:775259 150 150     2267646460 1825604395 1807903598 2289958188 775259 SRX9982106 SRS8153601 SRA1189630 Center for Ecological and Environmental Sciences|Northwestern Polytechnical University Center for Ecological and Environmental Sciences 1 0.91157   0.09088   0.72723   0.52217   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-01-30 Adult Adult Kidney Renal System
63061 63061 SRR13587416 SRX9982105 SRS8153601 SRP303929 PRJNA698005 Danio rerio Raw sequence reads PRJNA698005 Whole Genome Sequencing Danio rerio Raw RNA sequence reads       Model organism or animal sample from Danio rerio The kidney of Danio rerio   isolate:river|age:adult|sex:not collected|tissue:kidney|BioSampleModel:Model organism or animal                 19Z K 19Z K 19Z K The kidney control repeat 2 of Gobiocypris rarus     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP303929     19Z_K_1.fq.gz 19Z_K_2.fq.gz fastq fastq 8402134200.0 56014228.0 19Z K 1.fq.gz 0:150 1:150 A:2338499372;C:1849973662;G:1840214821;T:2372961719;N:484626 150 150     2338499372 1849973662 1840214821 2372961719 484626 SRX9982105 SRS8153601 SRA1189630 Center for Ecological and Environmental Sciences|Northwestern Polytechnical University Center for Ecological and Environmental Sciences 1 0.90113   0.10231   0.72703   0.56124   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-01-30 Adult Adult Kidney Renal System
63062 63062 SRR13587417 SRX9982104 SRS8153601 SRP303929 PRJNA698005 Danio rerio Raw sequence reads PRJNA698005 Whole Genome Sequencing Danio rerio Raw RNA sequence reads       Model organism or animal sample from Danio rerio The kidney of Danio rerio   isolate:river|age:adult|sex:not collected|tissue:kidney|BioSampleModel:Model organism or animal                 10ZK 10ZK 10ZK The kidney experiment repeat 1 of Gobiocypris rarus     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP303929     10ZK_1.fq.gz 10ZK_2.fq.gz fastq fastq 8208016200.0 54720108.0 10ZK 1.fq.gz 0:150 1:150 A:2303193070;C:1796200671;G:1783288010;T:2325334449;N:0 150 150     2303193070 1796200671 1783288010 2325334449 0 SRX9982104 SRS8153601 SRA1189630 Center for Ecological and Environmental Sciences|Northwestern Polytechnical University Center for Ecological and Environmental Sciences 1 0.9173   0.1039   0.72224   0.541   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-01-30 Adult Adult Kidney Renal System
63063 63063 SRR13587418 SRX9982103 SRS8153601 SRP303929 PRJNA698005 Danio rerio Raw sequence reads PRJNA698005 Whole Genome Sequencing Danio rerio Raw RNA sequence reads       Model organism or animal sample from Danio rerio The kidney of Danio rerio   isolate:river|age:adult|sex:not collected|tissue:kidney|BioSampleModel:Model organism or animal                 10Z K 10Z K 10Z K The kidney control repeat 1 of Gobiocypris rarus     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP303929     10Z_K_1.fq.gz 10Z_K_2.fq.gz fastq fastq 8205024600.0 54700164.0 10Z K 1.fq.gz 0:150 1:150 A:2259032946;C:1833449876;G:1824313852;T:2287704541;N:523385 150 150     2259032946 1833449876 1824313852 2287704541 523385 SRX9982103 SRS8153601 SRA1189630 Center for Ecological and Environmental Sciences|Northwestern Polytechnical University Center for Ecological and Environmental Sciences 1 0.91993   0.0808   0.73308   0.55396   150   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2021-01-30 Adult Adult Kidney Renal System
65128 65128 SRR14935651 SRX11248280 SRS9294818 SRP325966 PRJNA742218 Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing GSE179104 Transcriptome Analysis The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys   pubmed:35100334   kidney pdx1 heterozygous ko rep9 GSM5406802   source name:total kidney|genotype:PDX1mut|tissue:kidney kidney pdx1 heterozygous ko rep9 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. total kidney   Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   genotype:PDX1mut|tissue:kidney GSM5406802 GSM5406802: kidney pdx1 heterozygous ko rep9; Danio rerio; RNA Seq GSM5406802   1 Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5406802 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP325966   loader:fastq load.py 8724R1_18_R1_001.fastq.gz 8724R1_18_R2_001.fastq.gz fastq fastq 11176979232.0 37097872.0 GSM5406802 r1 0:150.64 1:150.65 A:2835225993;C:2589629327;G:2820499304;T:2931557102;N:67506 150 150     2835225993 2589629327 2820499304 2931557102 67506 SRX11248280 SRS9294818 SRA1251952 GEO ZMF, University Heidelberg 2 0.87724 0.87448 0.31729 0.31569 0.73716 0.73933 0.62206 0.62398 151 150 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-06-29 Undetermined Multi-stage Kidney Renal System
65129 65129 SRR14935650 SRX11248279 SRS9294817 SRP325966 PRJNA742218 Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing GSE179104 Transcriptome Analysis The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys   pubmed:35100334   kidney pdx1 heterozygous ko rep8 GSM5406801   source name:total kidney|genotype:PDX1mut|tissue:kidney kidney pdx1 heterozygous ko rep8 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. total kidney   Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   genotype:PDX1mut|tissue:kidney GSM5406801 GSM5406801: kidney pdx1 heterozygous ko rep8; Danio rerio; RNA Seq GSM5406801   1 Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5406801 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP325966   loader:fastq load.py 8724R1_17_R1_001.fastq.gz 8724R1_17_R2_001.fastq.gz fastq fastq 11394814456.0 37822298.0 GSM5406801 r1 0:150.65 1:150.62 A:2870553528;C:2617084802;G:2858252766;T:3048861279;N:62081 150 150     2870553528 2617084802 2858252766 3048861279 62081 SRX11248279 SRS9294817 SRA1251952 GEO ZMF, University Heidelberg 2 0.88351 0.88116 0.29453 0.29339 0.72908 0.73012 0.59959 0.60047 151 151 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-06-29 Undetermined Multi-stage Kidney Renal System
65130 65130 SRR14935649 SRX11248278 SRS9294816 SRP325966 PRJNA742218 Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing GSE179104 Transcriptome Analysis The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys   pubmed:35100334   kidney pdx1 heterozygous ko rep7 GSM5406800   source name:total kidney|genotype:PDX1mut|tissue:kidney kidney pdx1 heterozygous ko rep7 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. total kidney   Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   genotype:PDX1mut|tissue:kidney GSM5406800 GSM5406800: kidney pdx1 heterozygous ko rep7; Danio rerio; RNA Seq GSM5406800   1 Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5406800 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP325966   loader:fastq load.py 8724R1_16_R1_001.fastq.gz 8724R1_16_R2_001.fastq.gz fastq fastq 10795664046.0 35825557.0 GSM5406800 r1 0:150.66 1:150.68 A:2699673063;C:2430598463;G:2795587348;T:2869745840;N:59332 150 150     2699673063 2430598463 2795587348 2869745840 59332 SRX11248278 SRS9294816 SRA1251952 GEO ZMF, University Heidelberg 2 0.87086 0.8686 0.31803 0.31528 0.73517 0.73752 0.60984 0.61136 151 150 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-06-29 Undetermined Multi-stage Kidney Renal System
65131 65131 SRR14935648 SRX11248277 SRS9294815 SRP325966 PRJNA742218 Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing GSE179104 Transcriptome Analysis The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys   pubmed:35100334   kidney pdx1 heterozygous ko rep6 GSM5406799   source name:total kidney|genotype:PDX1mut|tissue:kidney kidney pdx1 heterozygous ko rep6 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. total kidney   Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   genotype:PDX1mut|tissue:kidney GSM5406799 GSM5406799: kidney pdx1 heterozygous ko rep6; Danio rerio; RNA Seq GSM5406799   1 Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5406799 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP325966   loader:fastq load.py 8724R1_15_R1_001.fastq.gz 8724R1_15_R2_001.fastq.gz fastq fastq 10760871119.0 35714100.0 GSM5406799 r1 0:150.66 1:150.65 A:2739382001;C:2429434631;G:2669749643;T:2922244501;N:60343 150 150     2739382001 2429434631 2669749643 2922244501 60343 SRX11248277 SRS9294815 SRA1251952 GEO ZMF, University Heidelberg 2 0.8687 0.86692 0.3287 0.32779 0.73405 0.73486 0.60891 0.61291 151 150 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-06-29 Undetermined Multi-stage Kidney Renal System
65132 65132 SRR14935647 SRX11248276 SRS9294814 SRP325966 PRJNA742218 Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing GSE179104 Transcriptome Analysis The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys   pubmed:35100334   kidney pdx1 heterozygous ko rep5 GSM5406798   source name:total kidney|genotype:PDX1mut|tissue:kidney kidney pdx1 heterozygous ko rep5 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. total kidney   Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   genotype:PDX1mut|tissue:kidney GSM5406798 GSM5406798: kidney pdx1 heterozygous ko rep5; Danio rerio; RNA Seq GSM5406798   1 Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5406798 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP325966   loader:fastq load.py 8724R1_14_R1_001.fastq.gz 8724R1_14_R2_001.fastq.gz fastq fastq 10649537104.0 35349599.0 GSM5406798 r1 0:150.64 1:150.62 A:2731221488;C:2409467117;G:2701711963;T:2807076164;N:60372 150 150     2731221488 2409467117 2701711963 2807076164 60372 SRX11248276 SRS9294814 SRA1251952 GEO ZMF, University Heidelberg 2 0.87441 0.87237 0.29421 0.29338 0.72693 0.72955 0.5953 0.59497 151 151 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-06-29 Undetermined Multi-stage Kidney Renal System
65133 65133 SRR14935646 SRX11248275 SRS9294813 SRP325966 PRJNA742218 Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing GSE179104 Transcriptome Analysis The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys   pubmed:35100334   kidney pdx1 heterozygous ko rep4 GSM5406797   source name:total kidney|genotype:PDX1mut|tissue:kidney kidney pdx1 heterozygous ko rep4 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. total kidney   Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   genotype:PDX1mut|tissue:kidney GSM5406797 GSM5406797: kidney pdx1 heterozygous ko rep4; Danio rerio; RNA Seq GSM5406797   1 Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5406797 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP325966   loader:fastq load.py 8724R1_13_R1_001.fastq.gz 8724R1_13_R2_001.fastq.gz fastq fastq 10694204698.0 35493814.0 GSM5406797 r1 0:150.66 1:150.64 A:2702728213;C:2453895836;G:2650869868;T:2886649326;N:61455 150 150     2702728213 2453895836 2650869868 2886649326 61455 SRX11248275 SRS9294813 SRA1251952 GEO ZMF, University Heidelberg 2 0.87706 0.87455 0.30298 0.30085 0.73492 0.73499 0.60664 0.61545 149 151 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-06-29 Undetermined Multi-stage Kidney Renal System
65134 65134 SRR14935645 SRX11248274 SRS9294812 SRP325966 PRJNA742218 Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing GSE179104 Transcriptome Analysis The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys   pubmed:35100334   kidney pdx1 heterozygous ko rep3 GSM5406796   source name:total kidney|genotype:PDX1mut|tissue:kidney kidney pdx1 heterozygous ko rep3 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. total kidney   Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   genotype:PDX1mut|tissue:kidney GSM5406796 GSM5406796: kidney pdx1 heterozygous ko rep3; Danio rerio; RNA Seq GSM5406796   1 Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5406796 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP325966   loader:fastq load.py 8724R1_12_R1_001.fastq.gz 8724R1_12_R2_001.fastq.gz fastq fastq 10345053183.0 34342254.0 GSM5406796 r1 0:150.63 1:150.60 A:2688355747;C:2362640622;G:2528888231;T:2765108367;N:60216 150 150     2688355747 2362640622 2528888231 2765108367 60216 SRX11248274 SRS9294812 SRA1251952 GEO ZMF, University Heidelberg 2 0.86578 0.86485 0.32858 0.32741 0.74022 0.74192 0.6202 0.62802 150 151 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-06-29 Undetermined Multi-stage Kidney Renal System
65135 65135 SRR14935644 SRX11248273 SRS9294811 SRP325966 PRJNA742218 Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing GSE179104 Transcriptome Analysis The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys   pubmed:35100334   kidney pdx1 heterozygous ko rep2 GSM5406795   source name:total kidney|genotype:PDX1mut|tissue:kidney kidney pdx1 heterozygous ko rep2 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. total kidney   Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   genotype:PDX1mut|tissue:kidney GSM5406795 GSM5406795: kidney pdx1 heterozygous ko rep2; Danio rerio; RNA Seq GSM5406795   1 Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5406795 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP325966   loader:fastq load.py 8724R1_11_R1_001.fastq.gz 8724R1_11_R2_001.fastq.gz fastq fastq 10918902659.0 36232610.0 GSM5406795 r1 0:150.67 1:150.68 A:2720295545;C:2469360250;G:2821457214;T:2907726754;N:62896 150 150     2720295545 2469360250 2821457214 2907726754 62896 SRX11248273 SRS9294811 SRA1251952 GEO ZMF, University Heidelberg 2 0.87461 0.87362 0.33405 0.33405 0.74024 0.73994 0.60898 0.60832 151 151 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-06-29 Undetermined Multi-stage Kidney Renal System
65136 65136 SRR14935643 SRX11248272 SRS9294810 SRP325966 PRJNA742218 Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing GSE179104 Transcriptome Analysis The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys   pubmed:35100334   kidney pdx1 heterozygous ko rep1 GSM5406794   source name:total kidney|genotype:PDX1mut|tissue:kidney kidney pdx1 heterozygous ko rep1 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. total kidney   Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   genotype:PDX1mut|tissue:kidney GSM5406794 GSM5406794: kidney pdx1 heterozygous ko rep1; Danio rerio; RNA Seq GSM5406794   1 Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5406794 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP325966   loader:fastq load.py 8724R1_10_R1_001.fastq.gz 8724R1_10_R2_001.fastq.gz fastq fastq 11557818156.0 38359672.0 GSM5406794 r1 0:150.63 1:150.67 A:2923769735;C:2594538133;G:2968671202;T:3070777088;N:61998 150 150     2923769735 2594538133 2968671202 3070777088 61998 SRX11248272 SRS9294810 SRA1251952 GEO ZMF, University Heidelberg 2 0.8705 0.86891 0.33241 0.3311 0.7363 0.73835 0.61699 0.62373 151 151 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-06-29 Undetermined Multi-stage Kidney Renal System
65137 65137 SRR14935642 SRX11248271 SRS9294809 SRP325966 PRJNA742218 Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing GSE179104 Transcriptome Analysis The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys   pubmed:35100334   kidney wildtype rep3 GSM5406793   source name:total kidney|genotype:WT|tissue:kidney kidney wildtype rep3 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. total kidney   Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   genotype:WT|tissue:kidney GSM5406793 GSM5406793: kidney wildtype rep3; Danio rerio; RNA Seq GSM5406793   1 Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5406793 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP325966   loader:fastq load.py 8724R1_3_R1_001.fastq.gz 8724R1_3_R2_001.fastq.gz fastq fastq 10759333910.0 35709735.0 GSM5406793 r1 0:150.63 1:150.67 A:2742030248;C:2405074908;G:2740896620;T:2871268925;N:63209 150 150     2742030248 2405074908 2740896620 2871268925 63209 SRX11248271 SRS9294809 SRA1251952 GEO ZMF, University Heidelberg 2 0.87736 0.875 0.29165 0.29063 0.73261 0.73361 0.51754 0.51714 150 151 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-06-29 Undetermined Multi-stage Kidney Renal System
65138 65138 SRR14935641 SRX11248270 SRS9294808 SRP325966 PRJNA742218 Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing GSE179104 Transcriptome Analysis The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys   pubmed:35100334   kidney wildtype rep2 GSM5406792   source name:total kidney|genotype:WT|tissue:kidney kidney wildtype rep2 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. total kidney   Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   genotype:WT|tissue:kidney GSM5406792 GSM5406792: kidney wildtype rep2; Danio rerio; RNA Seq GSM5406792   1 Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5406792 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP325966   loader:fastq load.py 8724R1_2_R1_001.fastq.gz 8724R1_2_R2_001.fastq.gz fastq fastq 11014631579.0 36552301.0 GSM5406792 r1 0:150.65 1:150.68 A:2786726244;C:2457413219;G:2801015846;T:2969414816;N:61454 150 150     2786726244 2457413219 2801015846 2969414816 61454 SRX11248270 SRS9294808 SRA1251952 GEO ZMF, University Heidelberg 2 0.87866 0.87699 0.31394 0.31278 0.73588 0.73726 0.61713 0.61801 151 151 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-06-29 Undetermined Multi-stage Kidney Renal System
65139 65139 SRR14935640 SRX11248269 SRS9294807 SRP325966 PRJNA742218 Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing GSE179104 Transcriptome Analysis The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys   pubmed:35100334   kidney wildtype rep1 GSM5406791   source name:total kidney|genotype:WT|tissue:kidney kidney wildtype rep1 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. total kidney   Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols   genotype:WT|tissue:kidney GSM5406791 GSM5406791: kidney wildtype rep1; Danio rerio; RNA Seq GSM5406791   1 Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5406791 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP325966   loader:fastq load.py 8724R1_1_R1_001.fastq.gz 8724R1_1_R2_001.fastq.gz fastq fastq 10413411371.0 34567408.0 GSM5406791 r1 0:150.65 1:150.60 A:2697353558;C:2358512324;G:2568693377;T:2788789911;N:62201 150 150     2697353558 2358512324 2568693377 2788789911 62201 SRX11248269 SRS9294807 SRA1251952 GEO ZMF, University Heidelberg 2 0.86943 0.8664 0.31108 0.30889 0.73815 0.74034 0.56789 0.60471 151 151 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-06-29 Undetermined Multi-stage Kidney Renal System
74167 74167 SRR23576631 SRX19463426 SRS16856050 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.         K9   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:kidney marrow|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:kidneymarrow WT R3|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male kidney marrow K9 K9 RNA Seq of Danio rerio : adult male kidney marrow     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     k9_1.fq.gz k9_2.fq.gz fastq fastq 12170484800.0 121704848.0 k9 1.fq.gz 0:100 1:100 A:3429398396;C:2639165188;G:2664600070;T:3437321146;N:0 100 100     3429398396 2639165188 2664600070 3437321146 0 SRX19463426 SRS16856050 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 0.93913   0.13619   0.76623   0.63929   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Kidney Renal System
74168 74168 SRR23576632 SRX19463425 SRS16856047 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.         K8   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:kidney marrow|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:kidneymarrow WT R2|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male kidney marrow K8 K8 RNA Seq of Danio rerio : adult male kidney marrow     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     k8_1.fq.gz k8_2.fq.gz fastq fastq 12160185000.0 121601850.0 k8 1.fq.gz 0:100 1:100 A:3416677165;C:2642321577;G:2671959016;T:3429227242;N:0 100 100     3416677165 2642321577 2671959016 3429227242 0 SRX19463425 SRS16856047 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 0.94207   0.13408   0.76211   0.63866   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Kidney Renal System
74169 74169 SRR23576633 SRX19463424 SRS16856049 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.         K7   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:kidney marrow|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:kidneymarrow WT R1|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male kidney marrow K7 K7 RNA Seq of Danio rerio : adult male kidney marrow     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     k7_1.fq.gz k7_2.fq.gz fastq fastq 12148090800.0 121480908.0 k7 1.fq.gz 0:100 1:100 A:3393484862;C:2656728106;G:2695881495;T:3401996337;N:0 100 100     3393484862 2656728106 2695881495 3401996337 0 SRX19463424 SRS16856049 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 0.93783   0.12581   0.76205   0.61561   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Kidney Renal System
74170 74170 SRR23576634 SRX19463423 SRS16856046 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.         K6   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:kidney marrow|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:kidneymarrow tert Cre R3|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male kidney marrow K6 K6 RNA Seq of Danio rerio : adult male kidney marrow     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     k6_1.fq.gz k6_2.fq.gz fastq fastq 12173062600.0 121730626.0 k6 1.fq.gz 0:100 1:100 A:3357618903;C:2705746086;G:2734807941;T:3374889670;N:0 100 100     3357618903 2705746086 2734807941 3374889670 0 SRX19463423 SRS16856046 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 0.94651   0.13977   0.76575   0.62959   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Kidney Renal System
74171 74171 SRR23576635 SRX19463422 SRS16856045 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.         K5   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:kidney marrow|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:kidneymarrow tert Cre R2|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male kidney marrow K5 K5 RNA Seq of Danio rerio : adult male kidney marrow     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     k5_1.fq.gz k5_2.fq.gz fastq fastq 12151346800.0 121513468.0 k5 1.fq.gz 0:100 1:100 A:3323730498;C:2725613099;G:2760112468;T:3341890735;N:0 100 100     3323730498 2725613099 2760112468 3341890735 0 SRX19463422 SRS16856045 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 0.94297   0.12142   0.75836   0.6001   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Kidney Renal System
74172 74172 SRR23576636 SRX19463421 SRS16856044 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.         K4   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:kidney marrow|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:kidneymarrow tert Cre R1|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male kidney marrow K4 K4 RNA Seq of Danio rerio : adult male kidney marrow     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     k4_1.fq.gz k4_2.fq.gz fastq fastq 12130512600.0 121305126.0 k4 1.fq.gz 0:100 1:100 A:3347896596;C:2682409134;G:2729255490;T:3370951380;N:0 100 100     3347896596 2682409134 2729255490 3370951380 0 SRX19463421 SRS16856044 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 0.94729   0.12594   0.75684   0.53755   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Kidney Renal System
74173 74173 SRR23576637 SRX19463420 SRS16856043 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.         K3   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:kidney marrow|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:kidneymarrow no Cre R3|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male kidney marrow K3 K3 RNA Seq of Danio rerio : adult male kidney marrow     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     k3_1.fq.gz k3_2.fq.gz fastq fastq 12414982200.0 124149822.0 k3 1.fq.gz 0:100 1:100 A:3396256131;C:2779475706;G:2819830912;T:3419419451;N:0 100 100     3396256131 2779475706 2819830912 3419419451 0 SRX19463420 SRS16856043 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 0.94186   0.13004   0.7613   0.53529   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Kidney Renal System
74175 74175 SRR23576639 SRX19463418 SRS16856041 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.         K2   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:kidney marrow|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:kidneymarrow no Cre R2|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male kidney marrow K2 K2 RNA Seq of Danio rerio : adult male kidney marrow     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     k2_1.fq.gz k2_2.fq.gz fastq fastq 12163413800.0 121634138.0 k2 1.fq.gz 0:100 1:100 A:3349566787;C:2697789330;G:2746344614;T:3369713069;N:0 100 100     3349566787 2697789330 2746344614 3369713069 0 SRX19463418 SRS16856041 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 0.93698   0.12494   0.73933   0.59199   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Kidney Renal System
74176 74176 SRR23576640 SRX19463417 SRS16856042 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.         K1   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:kidney marrow|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:kidneymarrow no Cre R1|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male kidney marrow K1 K1 RNA Seq of Danio rerio : adult male kidney marrow     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     k1_1.fq.gz k1_2.fq.gz fastq fastq 12163054400.0 121630544.0 k1 1.fq.gz 0:100 1:100 A:3337026687;C:2722574700;G:2757511786;T:3345941227;N:0 100 100     3337026687 2722574700 2757511786 3345941227 0 SRX19463417 SRS16856042 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 0.94273   0.11801   0.75258   0.57192   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Kidney Renal 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");;