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
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,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,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,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,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,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,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,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,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,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,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,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