{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"cDNA\", experiment.platform = \"BGISEQ\" and tissue_curation = \"Kidney\"", "rows": [[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. 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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", null, "pubmed:35100334", null, "kidney pdx1 heterozygous ko rep3", "GSM5406796", null, "source name:total kidney|genotype:PDX1mut|tissue:kidney", "kidney pdx1 heterozygous ko rep3", "trimmed with trim galore version 0.6.4. 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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", null, "pubmed:35100334", null, "kidney pdx1 heterozygous ko rep2", "GSM5406795", null, "source name:total kidney|genotype:PDX1mut|tissue:kidney", "kidney pdx1 heterozygous ko rep2", "trimmed with trim galore version 0.6.4. 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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", null, "pubmed:35100334", null, "kidney pdx1 heterozygous ko rep1", "GSM5406794", null, "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", null, "Kidneys were removed and stored at  20\u00b0C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer\u2019s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "genotype:PDX1mut|tissue:kidney", "GSM5406794", "GSM5406794: kidney pdx1 heterozygous ko rep1; Danio rerio; RNA Seq", "GSM5406794", null, "1", "Kidneys were removed and stored at  20\u00b0C 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", null, "SRP325966", null, "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, null, null, 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", null, "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", null, "pubmed:35100334", null, "kidney wildtype rep3", "GSM5406793", null, "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", null, "Kidneys were removed and stored at  20\u00b0C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer\u2019s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "genotype:WT|tissue:kidney", "GSM5406793", "GSM5406793: kidney wildtype rep3; Danio rerio; RNA Seq", "GSM5406793", null, "1", "Kidneys were removed and stored at  20\u00b0C 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", null, "SRP325966", null, "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, null, null, 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", null, "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", null, "pubmed:35100334", null, "kidney wildtype rep2", "GSM5406792", null, "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", null, "Kidneys were removed and stored at  20\u00b0C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer\u2019s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "genotype:WT|tissue:kidney", "GSM5406792", "GSM5406792: kidney wildtype rep2; Danio rerio; RNA Seq", "GSM5406792", null, "1", "Kidneys were removed and stored at  20\u00b0C 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", null, "SRP325966", null, "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, null, null, 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", null, "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", null, "pubmed:35100334", null, "kidney wildtype rep1", "GSM5406791", null, "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", null, "Kidneys were removed and stored at  20\u00b0C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer\u2019s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "genotype:WT|tissue:kidney", "GSM5406791", "GSM5406791: kidney wildtype rep1; Danio rerio; RNA Seq", "GSM5406791", null, "1", "Kidneys were removed and stored at  20\u00b0C 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", null, "SRP325966", null, "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, null, null, 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", null, "Germany", "2021-06-29", "Undetermined", "Multi-stage", "Kidney", "Renal System"]], "truncated": false, "filtered_table_rows_count": 12, "expanded_columns": [], "expandable_columns": [], "columns": 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"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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"experiment.library_selection\" = :p0 and \"experiment.platform\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "cDNA", "p1": "BGISEQ", "p2": "Kidney"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=BGISEQ&tissue_curation=Kidney", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=BGISEQ&tissue_curation=Kidney&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": 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"experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=BGISEQ&tissue_curation=Kidney", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=BGISEQ&tissue_curation=Kidney&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=BGISEQ&tissue_curation=Kidney", "results": [{"value": "BGISEQ", "label": "BGISEQ", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&tissue_curation=Kidney", "selected": true}], "truncated": false}, 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