{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", technology = \"unknown\" and tissue_curation_coarse = \"Renal System\"", "rows": [[8067, "ERR035547", "ERX013537", "ERS017858", "ERP000447", "PRJEB2368", "Sanger zebrafish sequencing", "E-MTAB-460", "Other", null, null, null, "Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.", "Zebrafish adult head kidney", "SAMEA782572", "Wellcome Sanger Institute", "ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782572|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult head kidney|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:head kidney|sample name:E MTAB 460:Zebrafish adult head kidney|sex:mixed", null, null, null, null, null, null, null, null, "Sanger zebrafish sequencing", "E MTAB 460 part2:5625 3", "ZFheadkidney 2 RNA 1523494", "Sanger zebrafish sequencing", "Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was enriched for polyA+ RNA by 2 rounds of polyA pull down with magnetic beads and included a DNase treatment between the 2 rounds. RNA was chemically fragmented  LiCl precipitated  reverse transcribed with random primers  a second strand synthesized and made into a standard Illumina library with a fragment size of 250 to 300 bp.", "Experimental Factor: ORGANISM PART:head kidney", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>2</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>85</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP000447", "Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing", "ENA FIRST PUBLIC:2011 06 14|ENA LAST UPDATE:2018 11 16", "5625_3.srf", "srf", 3610226240.0, 22563914.0, "E MTAB 460 part2:5625 3.srf", "0:76 1:8 2:76", "A:924866194;C:782403420;G:781277214;T:934812782;N:6355318", 76, 8, 76, null, 924866194, 782403420, 781277214, 934812782, 6355318, "ERX013537", "ERS017858", "ERA033503", "SC|Wellcome Trust Sanger Institute", "SC|Wellcome Trust Sanger Institute", 2, 0.8952, 0.89175, 0.09427, 0.09347, 0.70883, 0.71121, 0.3613, 0.35921, 76, 76, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2011-02-03", "Adult", "Adult", "Kidney", "Renal System"], [8072, "ERR023146", "ERX009446", "ERS017858", "ERP000447", "PRJEB2368", "Sanger zebrafish sequencing", "E-MTAB-460", "Other", null, null, null, "Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.", "Zebrafish adult head kidney", "SAMEA782572", "Wellcome Sanger Institute", "ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782572|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult head kidney|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:head kidney|sample name:E MTAB 460:Zebrafish adult head kidney|sex:mixed", null, null, null, null, null, null, null, null, "Sanger zebrafish sequencing", "E MTAB 460:3212 8", "RNA from Zebrafish adult head kidney", "Sanger zebrafish sequencing", "Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.", "Experimental Factor: ORGANISM PART:head kidney", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP000447", "Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing", "ENA FIRST PUBLIC:2011 02 03|ENA LAST UPDATE:2018 11 16", "3212_8.srf", "srf", 1030624600.0, 6780425.0, "E MTAB 460:3212 8.srf", "0:76 1:76", "A:349845451;C:160945226;G:157028856;T:352888853;N:9916214", 76, 76, null, null, 349845451, 160945226, 157028856, 352888853, 9916214, "ERX009446", "ERS017858", "ERA015648", "SC|Wellcome Trust Sanger Institute", "SC|Wellcome Trust Sanger Institute", 2, 0.84103, 0.82642, 0.30085, 0.29526, 0.76094, 0.7652, 0.56228, 0.45561, 76, 76, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2011-02-03", "Adult", "Adult", "Kidney", "Renal System"], [8075, "ERR023149", "ERX009443", "ERS017858", "ERP000447", "PRJEB2368", "Sanger zebrafish sequencing", "E-MTAB-460", "Other", null, null, null, "Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.", "Zebrafish adult head kidney", "SAMEA782572", "Wellcome Sanger Institute", "ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782572|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult head kidney|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:head kidney|sample name:E MTAB 460:Zebrafish adult head kidney|sex:mixed", null, null, null, null, null, null, null, null, "Sanger zebrafish sequencing", "E MTAB 460:4191 6", "RNA from Zebrafish adult head kidney", "Sanger zebrafish sequencing", "Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.", "Experimental Factor: ORGANISM PART:head kidney", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP000447", "Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing", "ENA FIRST PUBLIC:2011 02 03|ENA LAST UPDATE:2018 11 16", "4191_6.srf", "srf", 3888911336.0, 25584943.0, "E MTAB 460:4191 6.srf", "0:76 1:76", "A:1359993097;C:582070992;G:582686161;T:1356976166;N:7184920", 76, 76, null, null, 1359993097, 582070992, 582686161, 1356976166, 7184920, "ERX009443", "ERS017858", "ERA015648", "SC|Wellcome Trust Sanger Institute", "SC|Wellcome Trust Sanger Institute", 2, 0.83678, 0.82953, 0.3327, 0.33041, 0.77045, 0.77104, 0.54977, 0.54422, 76, 76, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2011-02-03", "Adult", "Adult", "Kidney", "Renal System"], [11158, "ERR10047721", "ERX9587609", "ERS12570320", "ERP140136", "PRJEB55250", "Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease", "0ed9a471-a4ab-4ec7-8113-a41cfa1601b4", "Other", "Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency  with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity  the accumulation of glycosphingolipids is used as a marker.  However  recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD  we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition  disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes.", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", null, "RNA seq Mutant Female 4", "MF4", "SAMEA110472297", "Computational Biology Unit", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472297|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29737|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29737|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 10 08 2022 10:54:39:372 85553", "MF4", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140136", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", "EF12_1.fq.gz EF12_2.fq.gz", "fastq fastq", 9295860000.0, 30986200.0, "ena RUN TAB 10 08 2022 10:54:39:372 85554", "0:150 1:150", "A:2456629138;C:2211534829;G:2202795083;T:2424808616;N:92334", 150, 150, null, null, 2456629138, 2211534829, 2202795083, 2424808616, 92334, "ERX9587609", "ERS12570320", "ERA16825549", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 2, 0.94791, 0.94821, 0.05293, 0.05316, 0.71285, 0.71267, 0.5054, 0.50686, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2022-09-15", "Undetermined", "Undetermined", "Kidney", "Renal System"], [11159, "ERR10047720", "ERX9587608", "ERS12570319", "ERP140136", "PRJEB55250", "Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease", "0ed9a471-a4ab-4ec7-8113-a41cfa1601b4", "Other", "Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency  with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity  the accumulation of glycosphingolipids is used as a marker.  However  recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD  we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition  disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes.", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", null, "RNA seq Mutant Female 3", "MF3", "SAMEA110472296", "Computational Biology Unit", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472296|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29736|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29736|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 10 08 2022 10:54:39:372 85551", "MF3", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140136", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", "EF11_1.fq.gz EF11_2.fq.gz", "fastq fastq", 9515997600.0, 31719992.0, "ena RUN TAB 10 08 2022 10:54:39:372 85552", "0:150 1:150", "A:2541032543;C:2239204827;G:2227356932;T:2508310635;N:92663", 150, 150, null, null, 2541032543, 2239204827, 2227356932, 2508310635, 92663, "ERX9587608", "ERS12570319", "ERA16825549", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 2, 0.95512, 0.95547, 0.06023, 0.06014, 0.70721, 0.70658, 0.51615, 0.50766, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2022-09-15", "Undetermined", "Undetermined", "Kidney", "Renal System"], [11160, "ERR10047719", "ERX9587607", "ERS12570318", "ERP140136", "PRJEB55250", "Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease", "0ed9a471-a4ab-4ec7-8113-a41cfa1601b4", "Other", "Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency  with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity  the accumulation of glycosphingolipids is used as a marker.  However  recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD  we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition  disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes.", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", null, "RNA seq Mutant Female 2", "MF2", "SAMEA110472295", "Computational Biology Unit", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472295|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29735|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29735|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 10 08 2022 10:54:39:372 85549", "MF2", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140136", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", "EF10_1.fq.gz EF10_2.fq.gz", "fastq fastq", 10394476500.0, 34648255.0, "ena RUN TAB 10 08 2022 10:54:39:372 85550", "0:150 1:150", "A:2789547305;C:2438564969;G:2423744267;T:2742517499;N:102460", 150, 150, null, null, 2789547305, 2438564969, 2423744267, 2742517499, 102460, "ERX9587607", "ERS12570318", "ERA16825549", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 2, 0.95582, 0.95591, 0.06231, 0.06252, 0.70565, 0.70715, 0.51407, 0.51477, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2022-09-15", "Undetermined", "Undetermined", "Kidney", "Renal System"], [11161, "ERR10047718", "ERX9587606", "ERS12570317", "ERP140136", "PRJEB55250", "Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease", "0ed9a471-a4ab-4ec7-8113-a41cfa1601b4", "Other", "Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency  with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity  the accumulation of glycosphingolipids is used as a marker.  However  recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD  we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition  disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes.", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", null, "RNA seq Mutant Female 1", "MF1", "SAMEA110472294", "Computational Biology Unit", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472294|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29734|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29734|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 10 08 2022 10:54:39:372 85547", "MF1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140136", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", "EF9_1.fq.gz EF9_2.fq.gz", "fastq fastq", 9531565200.0, 31771884.0, "ena RUN TAB 10 08 2022 10:54:39:372 85548", "0:150 1:150", "A:2534403521;C:2257857645;G:2242329348;T:2496889068;N:85618", 150, 150, null, null, 2534403521, 2257857645, 2242329348, 2496889068, 85618, "ERX9587606", "ERS12570317", "ERA16825549", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 2, 0.95744, 0.95773, 0.05406, 0.054, 0.70703, 0.70627, 0.49691, 0.49886, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2022-09-15", "Undetermined", "Undetermined", "Kidney", "Renal System"], [11162, "ERR10047717", "ERX9587605", "ERS12570316", "ERP140136", "PRJEB55250", "Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease", "0ed9a471-a4ab-4ec7-8113-a41cfa1601b4", "Other", "Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency  with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity  the accumulation of glycosphingolipids is used as a marker.  However  recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD  we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition  disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes.", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", null, "RNA seq Mutant Male 4", "MM4", "SAMEA110472293", "Computational Biology Unit", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472293|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29733|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29733|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 10 08 2022 10:54:39:371 85545", "MM4", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140136", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", "EM16_1.fq.gz EM16_2.fq.gz", "fastq fastq", 9801781200.0, 32672604.0, "ena RUN TAB 10 08 2022 10:54:39:371 85546", "0:150 1:150", "A:2617469644;C:2307347982;G:2294965646;T:2581792895;N:205033", 150, 150, null, null, 2617469644, 2307347982, 2294965646, 2581792895, 205033, "ERX9587605", "ERS12570316", "ERA16825549", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 2, 0.95755, 0.95764, 0.0539, 0.05338, 0.71587, 0.71484, 0.51048, 0.52067, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2022-09-15", "Undetermined", "Undetermined", "Kidney", "Renal System"], [11163, "ERR10047716", "ERX9587604", "ERS12570315", "ERP140136", "PRJEB55250", "Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease", "0ed9a471-a4ab-4ec7-8113-a41cfa1601b4", "Other", "Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency  with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity  the accumulation of glycosphingolipids is used as a marker.  However  recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD  we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition  disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes.", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", null, "RNA seq Mutant Male 3", "MM3", "SAMEA110472292", "Computational Biology Unit", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472292|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29732|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29732|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 10 08 2022 10:54:39:371 85543", "MM3", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140136", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", "EM15_1.fq.gz EM15_2.fq.gz", "fastq fastq", 9922431900.0, 33074773.0, "ena RUN TAB 10 08 2022 10:54:39:371 85544", "0:150 1:150", "A:2640289295;C:2345938205;G:2336699617;T:2599294368;N:210415", 150, 150, null, null, 2640289295, 2345938205, 2336699617, 2599294368, 210415, "ERX9587604", "ERS12570315", "ERA16825549", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 2, 0.95894, 0.95898, 0.04903, 0.04914, 0.71346, 0.71388, 0.51462, 0.51356, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2022-09-15", "Undetermined", "Undetermined", "Kidney", "Renal System"], [11164, "ERR10047715", "ERX9587603", "ERS12570314", "ERP140136", "PRJEB55250", "Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease", "0ed9a471-a4ab-4ec7-8113-a41cfa1601b4", "Other", "Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency  with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity  the accumulation of glycosphingolipids is used as a marker.  However  recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD  we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition  disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes.", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", null, "RNA seq Mutant Male 2", "MM2", "SAMEA110472291", "Computational Biology Unit", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472291|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29731|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29731|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 10 08 2022 10:54:39:371 85541", "MM2", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140136", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", "EM14_1.fq.gz EM14_2.fq.gz", "fastq fastq", 9470081700.0, 31566939.0, "ena RUN TAB 10 08 2022 10:54:39:371 85542", "0:150 1:150", "A:2518757590;C:2239498890;G:2227790286;T:2483847148;N:187786", 150, 150, null, null, 2518757590, 2239498890, 2227790286, 2483847148, 187786, "ERX9587603", "ERS12570314", "ERA16825549", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 2, 0.95826, 0.95753, 0.05166, 0.05151, 0.71827, 0.71725, 0.50776, 0.50874, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2022-09-15", "Undetermined", "Undetermined", "Kidney", "Renal System"], [11165, "ERR10047714", "ERX9587602", "ERS12570313", "ERP140136", "PRJEB55250", "Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease", "0ed9a471-a4ab-4ec7-8113-a41cfa1601b4", "Other", "Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency  with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity  the accumulation of glycosphingolipids is used as a marker.  However  recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD  we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition  disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes.", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", null, "RNA seq Mutant Male 1", "MM1", "SAMEA110472290", "Computational Biology Unit", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472290|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29730|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29730|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 10 08 2022 10:54:39:371 85539", "MM1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140136", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", "EM13_1.fq.gz EM13_2.fq.gz", "fastq fastq", 9896066100.0, 32986887.0, "ena RUN TAB 10 08 2022 10:54:39:371 85540", "0:150 1:150", "A:2615586694;C:2355549418;G:2345987621;T:2578734637;N:207730", 150, 150, null, null, 2615586694, 2355549418, 2345987621, 2578734637, 207730, "ERX9587602", "ERS12570313", "ERA16825549", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 2, 0.96075, 0.9607, 0.04898, 0.04814, 0.71914, 0.71762, 0.50604, 0.51092, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2022-09-15", "Undetermined", "Undetermined", "Kidney", "Renal System"], [11166, "ERR10047713", "ERX9587601", "ERS12570312", "ERP140136", "PRJEB55250", "Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease", "0ed9a471-a4ab-4ec7-8113-a41cfa1601b4", "Other", "Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency  with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity  the accumulation of glycosphingolipids is used as a marker.  However  recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD  we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition  disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes.", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", null, "RNA seq Wild type Female 4", "WF4", "SAMEA110472289", "Computational Biology Unit", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472289|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29729|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29729|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 10 08 2022 10:54:39:370 85537", "WF4", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140136", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", "WF4_1.fq.gz WF4_2.fq.gz", "fastq fastq", 8902470600.0, 29674902.0, "ena RUN TAB 10 08 2022 10:54:39:370 85538", "0:150 1:150", "A:2387064218;C:2088721835;G:2083589487;T:2343005357;N:89703", 150, 150, null, null, 2387064218, 2088721835, 2083589487, 2343005357, 89703, "ERX9587601", "ERS12570312", "ERA16825549", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 2, 0.95676, 0.95666, 0.0593, 0.05927, 0.70092, 0.70337, 0.49608, 0.49899, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2022-09-15", "Undetermined", "Undetermined", "Kidney", "Renal System"], [11167, "ERR10047712", "ERX9587600", "ERS12570311", "ERP140136", "PRJEB55250", "Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease", "0ed9a471-a4ab-4ec7-8113-a41cfa1601b4", "Other", "Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency  with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity  the accumulation of glycosphingolipids is used as a marker.  However  recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD  we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition  disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes.", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", null, "RNA seq Wild type Female 3", "WF3", "SAMEA110472288", "Computational Biology Unit", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472288|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29728|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29728|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 10 08 2022 10:54:39:370 85535", "WF3", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140136", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", "WF3_1.fq.gz WF3_2.fq.gz", "fastq fastq", 9063103800.0, 30210346.0, "ena RUN TAB 10 08 2022 10:54:39:370 85536", "0:150 1:150", "A:2432312114;C:2123240631;G:2111227574;T:2396247669;N:75812", 150, 150, null, null, 2432312114, 2123240631, 2111227574, 2396247669, 75812, "ERX9587600", "ERS12570311", "ERA16825549", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 2, 0.95482, 0.95494, 0.06998, 0.07003, 0.70122, 0.70228, 0.50936, 0.50507, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2022-09-15", "Undetermined", "Undetermined", "Kidney", "Renal System"], [11168, "ERR10047711", "ERX9587599", "ERS12570310", "ERP140136", "PRJEB55250", "Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease", "0ed9a471-a4ab-4ec7-8113-a41cfa1601b4", "Other", "Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency  with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity  the accumulation of glycosphingolipids is used as a marker.  However  recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD  we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition  disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes.", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", null, "RNA seq Wild type Female 2", "WF2", "SAMEA110472287", "Computational Biology Unit", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472287|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29727|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29727|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 10 08 2022 10:54:39:370 85533", "WF2", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140136", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", "WF2_1.fq.gz WF2_2.fq.gz", "fastq fastq", 11904985800.0, 39683286.0, "ena RUN TAB 10 08 2022 10:54:39:370 85534", "0:150 1:150", "A:3185302826;C:2804829029;G:2783464897;T:3131272515;N:116533", 150, 150, null, null, 3185302826, 2804829029, 2783464897, 3131272515, 116533, "ERX9587599", "ERS12570310", "ERA16825549", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 2, 0.95589, 0.95646, 0.058, 0.05797, 0.70457, 0.70492, 0.51464, 0.5143, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2022-09-15", "Undetermined", "Undetermined", "Kidney", "Renal System"], [11169, "ERR10047710", "ERX9587598", "ERS12570309", "ERP140136", "PRJEB55250", "Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease", "0ed9a471-a4ab-4ec7-8113-a41cfa1601b4", "Other", "Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency  with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity  the accumulation of glycosphingolipids is used as a marker.  However  recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD  we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition  disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes.", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", null, "RNA seq Wild type Female 1", "WF1", "SAMEA110472286", "Computational Biology Unit", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472286|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29726|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29726|sequencing method:Illumina NovaSeq 6000|sex:female|tissue type:Kidney", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 10 08 2022 10:54:39:370 85531", "WF1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140136", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", "WF1_1.fq.gz WF1_2.fq.gz", "fastq fastq", 9491977800.0, 31639926.0, "ena RUN TAB 10 08 2022 10:54:39:370 85532", "0:150 1:150", "A:2540140444;C:2236702404;G:2215435797;T:2499606420;N:92735", 150, 150, null, null, 2540140444, 2236702404, 2215435797, 2499606420, 92735, "ERX9587598", "ERS12570309", "ERA16825549", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 2, 0.95868, 0.95935, 0.05681, 0.05651, 0.70487, 0.70538, 0.50749, 0.50617, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2022-09-15", "Undetermined", "Undetermined", "Kidney", "Renal System"], [11170, "ERR10047709", "ERX9587597", "ERS12570308", "ERP140136", "PRJEB55250", "Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease", "0ed9a471-a4ab-4ec7-8113-a41cfa1601b4", "Other", "Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency  with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity  the accumulation of glycosphingolipids is used as a marker.  However  recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD  we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition  disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes.", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", null, "RNA seq Wild type Male 4", "WM4", "SAMEA110472285", "Computational Biology Unit", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472285|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29725|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29725|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 10 08 2022 10:54:39:369 85529", "WM4", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140136", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", "WM8_1.fq.gz WM8_2.fq.gz", "fastq fastq", 9911994300.0, 33039981.0, "ena RUN TAB 10 08 2022 10:54:39:369 85530", "0:150 1:150", "A:2647417182;C:2332033790;G:2324021308;T:2608423782;N:98238", 150, 150, null, null, 2647417182, 2332033790, 2324021308, 2608423782, 98238, "ERX9587597", "ERS12570308", "ERA16825549", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 2, 0.95754, 0.95758, 0.05322, 0.05309, 0.71936, 0.71898, 0.52558, 0.52697, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2022-09-15", "Undetermined", "Undetermined", "Kidney", "Renal System"], [11171, "ERR10047708", "ERX9587596", "ERS12570307", "ERP140136", "PRJEB55250", "Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease", "0ed9a471-a4ab-4ec7-8113-a41cfa1601b4", "Other", "Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency  with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity  the accumulation of glycosphingolipids is used as a marker.  However  recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD  we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition  disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes.", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", null, "RNA seq Wild type Male 3", "WM3", "SAMEA110472284", "Computational Biology Unit", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472284|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29724|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29724|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 10 08 2022 10:54:39:369 85527", "WM3", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140136", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", "WM7_1.fq.gz WM7_2.fq.gz", "fastq fastq", 10756015500.0, 35853385.0, "ena RUN TAB 10 08 2022 10:54:39:369 85528", "0:150 1:150", "A:2882486379;C:2526051573;G:2510570253;T:2836803943;N:103352", 150, 150, null, null, 2882486379, 2526051573, 2510570253, 2836803943, 103352, "ERX9587596", "ERS12570307", "ERA16825549", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 2, 0.95343, 0.9538, 0.055, 0.05491, 0.71784, 0.71883, 0.53419, 0.52955, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2022-09-15", "Undetermined", "Undetermined", "Kidney", "Renal System"], [11172, "ERR10047707", "ERX9587595", "ERS12570306", "ERP140136", "PRJEB55250", "Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease", "0ed9a471-a4ab-4ec7-8113-a41cfa1601b4", "Other", "Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency  with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity  the accumulation of glycosphingolipids is used as a marker.  However  recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD  we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition  disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes.", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", null, "RNA seq Wild type Male 2", "WM2", "SAMEA110472283", "Computational Biology Unit", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472283|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29723|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29723|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 10 08 2022 10:54:39:369 85525", "WM2", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140136", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", "WM6_1.fq.gz WM6_2.fq.gz", "fastq fastq", 8944434000.0, 29814780.0, "ena RUN TAB 10 08 2022 10:54:39:369 85526", "0:150 1:150", "A:2384550098;C:2112886362;G:2095147407;T:2351765069;N:85064", 150, 150, null, null, 2384550098, 2112886362, 2095147407, 2351765069, 85064, "ERX9587595", "ERS12570306", "ERA16825549", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 2, 0.95717, 0.95759, 0.05527, 0.05526, 0.72009, 0.72011, 0.52634, 0.52832, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2022-09-15", "Undetermined", "Undetermined", "Kidney", "Renal System"], [11173, "ERR10047706", "ERX9587594", "ERS12570305", "ERP140136", "PRJEB55250", "Gene expression analysis in GLA mutant zebrafish revealed enhanced Ca2+ signaling similar to Fabry disease", "0ed9a471-a4ab-4ec7-8113-a41cfa1601b4", "Other", "Fabry disease is an X linked inborn metabolic disorder due to partial or complete deficiency of lysosomal a galactosidase A activity. The disease is characterized by progressive renal insufficiency  with cardio and cerebrovascular involvement. The lack of experimental models of Fabry disease has limited the understanding of the disease and consequently has delayed the development of new therapies. Due to partial or complete deficiency of the lysosomal a galactosidase A activity  the accumulation of glycosphingolipids is used as a marker.  However  recent studies suggested that they are not an ideal marker for treatment monitoring or treatment response. Here we use our GLA knockout zebrafish to investigate the possible biomarkers in an A4GALT free condition. We describe here an RNA sequencing analysis aiming to determine underlying transcriptomics signatures that could discriminate GLA mutant fish from the wild type fish in Gb3 free conditions. As in the FD  we found an upregulated Ca2+ signaling pathway accompanied by downregulated cardiac muscle contraction pathway. In addition  disrupted mitochondrial and lysosome related pathways in the mutant were observed and tested using immunohistochemistry. Our results point out that our model can mimic the effects of GLA mutations independently of the Gb 3 accumulation and potentially can be used to find new targets that improve FD outcomes.", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", null, "RNA seq Wild type Male 1", "WM1", "SAMEA110472282", "Computational Biology Unit", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15|External Id:SAMEA110472282|INSDC center alias:Computational Biology Unit|INSDC center name:Computational Biology Unit|INSDC first public:2022 09 15T00:19:05Z|INSDC last update:2022 09 15T00:19:05Z|INSDC status:public|Submitter Id:ena SAMPLE TAB 08 08 2022 11:55:36:722 29722|collection date:2021 07|common name:zebrafish|sample name:ena SAMPLE TAB 08 08 2022 11:55:36:722 29722|sequencing method:Illumina NovaSeq 6000|sex:male|tissue type:Kidney", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing", "ena EXPERIMENT TAB 10 08 2022 10:54:39:368 85523", "WM1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP140136", "Illumina NovaSeq 6000 paired end sequencing", "ENA FIRST PUBLIC:2022 09 15|ENA LAST UPDATE:2022 09 15", "WM5_1.fq.gz WM5_2.fq.gz", "fastq fastq", 9558564300.0, 31861881.0, "ena RUN TAB 10 08 2022 10:54:39:369 85524", "0:150 1:150", "A:2556941509;C:2249230277;G:2236855770;T:2515442411;N:94333", 150, 150, null, null, 2556941509, 2249230277, 2236855770, 2515442411, 94333, "ERX9587594", "ERS12570305", "ERA16825549", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 2, 0.95505, 0.95484, 0.05372, 0.05318, 0.71798, 0.71898, 0.52584, 0.52042, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2022-09-15", "Undetermined", "Undetermined", "Kidney", "Renal System"], [32162, "SRR29095835", "SRX24619914", "SRS21357066", "SRP508906", "PRJNA1113956", "A zebrafish model of diabetic nephropathy", "PRJNA1113956", "Other", "We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines  named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria  which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics  such as glomerular basement membrane thickening  foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably  the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated  a phenomenon observed in the early phase of human DN.", null, null, null, "6 month zebrafish kidney 1", "DN zebrafish", null, "strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "6 month zebrafish with proteinuria kidney 4", "OF 4", "OF 4", "6 month zebrafish with proteinuria kidney 4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP508906", null, null, "OF_4_1.fq OF_4_2.fq", "fastq fastq", 4377669000.0, 14592230.0, "OF 4 1.fq", "0:150 1:150", "A:1194166573;C:999239529;G:1001594280;T:1182651631;N:16987", 150, 150, null, null, 1194166573, 999239529, 1001594280, 1182651631, 16987, "SRX24619914", "SRS21357066", "SRA1872692", "Mie Univeristy|School of Medicine", "Mie Univeristy", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2024-05-21", "Adult", "Adult", "Kidney", "Renal System"], [32163, "SRR29095836", "SRX24619913", "SRS21357066", "SRP508906", "PRJNA1113956", "A zebrafish model of diabetic nephropathy", "PRJNA1113956", "Other", "We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines  named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria  which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics  such as glomerular basement membrane thickening  foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably  the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated  a phenomenon observed in the early phase of human DN.", null, null, null, "6 month zebrafish kidney 1", "DN zebrafish", null, "strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "6 month zebrafish with proteinuria kidney 3", "OF 3", "OF 3", "6 month zebrafish with proteinuria kidney 3", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP508906", null, null, "OF_3_1.fq OF_3_2.fq", "fastq fastq", 4798165200.0, 15993884.0, "OF 3 1.fq", "0:150 1:150", "A:1290466714;C:1114007506;G:1115137813;T:1278535708;N:17459", 150, 150, null, null, 1290466714, 1114007506, 1115137813, 1278535708, 17459, "SRX24619913", "SRS21357066", "SRA1872692", "Mie Univeristy|School of Medicine", "Mie Univeristy", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2024-05-21", "Adult", "Adult", "Kidney", "Renal System"], [32164, "SRR29095837", "SRX24619912", "SRS21357066", "SRP508906", "PRJNA1113956", "A zebrafish model of diabetic nephropathy", "PRJNA1113956", "Other", "We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines  named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria  which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics  such as glomerular basement membrane thickening  foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably  the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated  a phenomenon observed in the early phase of human DN.", null, null, null, "6 month zebrafish kidney 1", "DN zebrafish", null, "strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "6 month zebrafish with proteinuria kidney 2", "OF 2", "OF 2", "6 month zebrafish with proteinuria kidney 2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP508906", null, null, "OF_2_1.fq OF_2_2.fq", "fastq fastq", 5661202800.0, 18870676.0, "OF 2 1.fq", "0:150 1:150", "A:1549085619;C:1287400217;G:1288853902;T:1535841249;N:21813", 150, 150, null, null, 1549085619, 1287400217, 1288853902, 1535841249, 21813, "SRX24619912", "SRS21357066", "SRA1872692", "Mie Univeristy|School of Medicine", "Mie Univeristy", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2024-05-21", "Adult", "Adult", "Kidney", "Renal System"], [32165, "SRR29095838", "SRX24619911", "SRS21357066", "SRP508906", "PRJNA1113956", "A zebrafish model of diabetic nephropathy", "PRJNA1113956", "Other", "We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines  named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria  which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics  such as glomerular basement membrane thickening  foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably  the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated  a phenomenon observed in the early phase of human DN.", null, null, null, "6 month zebrafish kidney 1", "DN zebrafish", null, "strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "6 month zebrafish with proteinuria kidney 1", "OF 1", "OF 1", "6 month zebrafish with proteinuria kidney 1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP508906", null, null, "OF_1_1.fq OF_1_2.fq", "fastq fastq", 5957895600.0, 19859652.0, "OF 1 1.fq", "0:150 1:150", "A:1627320757;C:1359602784;G:1360982917;T:1609967331;N:21811", 150, 150, null, null, 1627320757, 1359602784, 1360982917, 1609967331, 21811, "SRX24619911", "SRS21357066", "SRA1872692", "Mie Univeristy|School of Medicine", "Mie Univeristy", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2024-05-21", "Adult", "Adult", "Kidney", "Renal System"], [32166, "SRR29095839", "SRX24619910", "SRS21357066", "SRP508906", "PRJNA1113956", "A zebrafish model of diabetic nephropathy", "PRJNA1113956", "Other", "We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines  named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria  which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics  such as glomerular basement membrane thickening  foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably  the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated  a phenomenon observed in the early phase of human DN.", null, null, null, "6 month zebrafish kidney 1", "DN zebrafish", null, "strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "6 month zebrafish kidney 4", "NF 6", "NF 6", "6 month zebrafish kidney 4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP508906", null, null, "NF_6_1.fq NF_6_2.fq", "fastq fastq", 5469504900.0, 18231683.0, "NF 6 1.fq", "0:150 1:150", "A:1480833386;C:1260945093;G:1261275041;T:1466430429;N:20951", 150, 150, null, null, 1480833386, 1260945093, 1261275041, 1466430429, 20951, "SRX24619910", "SRS21357066", "SRA1872692", "Mie Univeristy|School of Medicine", "Mie Univeristy", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2024-05-21", "Adult", "Adult", "Kidney", "Renal System"], [32167, "SRR29095840", "SRX24619909", "SRS21357066", "SRP508906", "PRJNA1113956", "A zebrafish model of diabetic nephropathy", "PRJNA1113956", "Other", "We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines  named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria  which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics  such as glomerular basement membrane thickening  foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably  the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated  a phenomenon observed in the early phase of human DN.", null, null, null, "6 month zebrafish kidney 1", "DN zebrafish", null, "strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "6 month zebrafish kidney 3", "NF 5", "NF 5", "6 month zebrafish kidney 3", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP508906", null, null, "NF_5_1.fq NF_5_2.fq", "fastq fastq", 6386781900.0, 21289273.0, "NF 5 1.fq", "0:150 1:150", "A:1743273279;C:1458330156;G:1460747658;T:1724406616;N:24191", 150, 150, null, null, 1743273279, 1458330156, 1460747658, 1724406616, 24191, "SRX24619909", "SRS21357066", "SRA1872692", "Mie Univeristy|School of Medicine", "Mie Univeristy", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2024-05-21", "Adult", "Adult", "Kidney", "Renal System"], [32168, "SRR29095841", "SRX24619908", "SRS21357066", "SRP508906", "PRJNA1113956", "A zebrafish model of diabetic nephropathy", "PRJNA1113956", "Other", "We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines  named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria  which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics  such as glomerular basement membrane thickening  foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably  the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated  a phenomenon observed in the early phase of human DN.", null, null, null, "6 month zebrafish kidney 1", "DN zebrafish", null, "strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "6 month zebrafish kidney 2", "NF 2", "NF 2", "6 month zebrafish kidney 2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP508906", null, null, "NF_2_1.fq NF_2_2.fq", "fastq fastq", 5747851800.0, 19159506.0, "NF 2 1.fq", "0:150 1:150", "A:1564796254;C:1316015979;G:1317516650;T:1549501774;N:21143", 150, 150, null, null, 1564796254, 1316015979, 1317516650, 1549501774, 21143, "SRX24619908", "SRS21357066", "SRA1872692", "Mie Univeristy|School of Medicine", "Mie Univeristy", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2024-05-21", "Adult", "Adult", "Kidney", "Renal System"], [32169, "SRR29095842", "SRX24619907", "SRS21357066", "SRP508906", "PRJNA1113956", "A zebrafish model of diabetic nephropathy", "PRJNA1113956", "Other", "We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines  named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria  which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics  such as glomerular basement membrane thickening  foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably  the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated  a phenomenon observed in the early phase of human DN.", null, null, null, "6 month zebrafish kidney 1", "DN zebrafish", null, "strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "6 month zebrafish kidney 1", "NF 1", "NF 1", "6 month zebrafish kidney 1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP508906", null, null, "NF_1_1.fq NF_1_2.fq", "fastq fastq", 5369089800.0, 17896966.0, "NF 1 1.fq", "0:150 1:150", "A:1413369042;C:1273865602;G:1277141372;T:1404694133;N:19651", 150, 150, null, null, 1413369042, 1273865602, 1277141372, 1404694133, 19651, "SRX24619907", "SRS21357066", "SRA1872692", "Mie Univeristy|School of Medicine", "Mie Univeristy", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2024-05-21", "Adult", "Adult", "Kidney", "Renal System"], [32611, "SRR29356860", "SRX24871764", "SRS21581236", "SRP513122", "PRJNA1122499", "An mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE269547", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune protective mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from zebrafish immunized with the mRNA vaccine and the LPP control.  For mRNA vaccination  mRNA candidate vaccines were injected with 1\u00b5g LPP mRNA in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL  negative control zebrafish were immunized with LPP GFP mRNA  immunized twice with two week intervals week 0 and 2.post 12 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group.", null, "pubmed:39759874", null, "kidneys  LPP immunized sample3", "GSM8321946", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Vector control immunized group|treatment:2 dose of LPP GFP mRNA immunized|geo loc name:missing|collection date:missing", "kidneys  LPP immunized sample3", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes FPKM counts for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine immunization  adult zebrafish AB strain  3 to 4\u2009mpf  15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 \u03bcL for intramuscular i.m immunization. 1\u03bcg L3T mRNA vaccine or LPP GFP mRNA were injected in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL. post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction.", "post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:Vector control immunized group|treatment:2 dose of LPP GFP mRNA immunized", "GSM8321946", "GSM8321946: kidneys  LPP immunized sample3; Danio rerio; RNA Seq", "GSM8321946 r1", "GSM8321946", "1", "post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP513122", null, null, "LPP3.R1.fq.gz LPP3.R2.fq.gz", "fastq fastq", 6930388402.0, 24028386.0, "GSM8321946 r1", "0:144.22 1:144.21", "A:1741896633;C:1718081658;G:1728245814;T:1742156412;N:7885", 144, 144, null, null, 1741896633, 1718081658, 1728245814, 1742156412, 7885, "SRX24871764", "SRS21581236", "SRA1896369", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.95561, 0.95769, 0.04873, 0.04831, 0.70556, 0.705, 0.50774, 0.50807, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-11", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [32612, "SRR29356861", "SRX24871763", "SRS21581235", "SRP513122", "PRJNA1122499", "An mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE269547", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune protective mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from zebrafish immunized with the mRNA vaccine and the LPP control.  For mRNA vaccination  mRNA candidate vaccines were injected with 1\u00b5g LPP mRNA in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL  negative control zebrafish were immunized with LPP GFP mRNA  immunized twice with two week intervals week 0 and 2.post 12 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group.", null, "pubmed:39759874", null, "kidneys  LPP immunized sample2", "GSM8321945", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Vector control immunized group|treatment:2 dose of LPP GFP mRNA immunized|geo loc name:missing|collection date:missing", "kidneys  LPP immunized sample2", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes FPKM counts for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine immunization  adult zebrafish AB strain  3 to 4\u2009mpf  15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 \u03bcL for intramuscular i.m immunization. 1\u03bcg L3T mRNA vaccine or LPP GFP mRNA were injected in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL. post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction.", "post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:Vector control immunized group|treatment:2 dose of LPP GFP mRNA immunized", "GSM8321945", "GSM8321945: kidneys  LPP immunized sample2; Danio rerio; RNA Seq", "GSM8321945 r1", "GSM8321945", "1", "post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP513122", null, null, "LPP2.R1.fq.gz LPP2.R2.fq.gz", "fastq fastq", 6970934950.0, 24067775.0, "GSM8321945 r1", "0:144.82 1:144.82", "A:1750927361;C:1729272618;G:1740379247;T:1750348140;N:7584", 144, 144, null, null, 1750927361, 1729272618, 1740379247, 1750348140, 7584, "SRX24871763", "SRS21581235", "SRA1896369", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.95562, 0.95799, 0.04685, 0.04619, 0.7067, 0.7051, 0.50198, 0.49861, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-11", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [32613, "SRR29356862", "SRX24871762", "SRS21581234", "SRP513122", "PRJNA1122499", "An mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE269547", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune protective mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from zebrafish immunized with the mRNA vaccine and the LPP control.  For mRNA vaccination  mRNA candidate vaccines were injected with 1\u00b5g LPP mRNA in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL  negative control zebrafish were immunized with LPP GFP mRNA  immunized twice with two week intervals week 0 and 2.post 12 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group.", null, "pubmed:39759874", null, "kidneys  LPP immunized sample1", "GSM8321944", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Vector control immunized group|treatment:2 dose of LPP GFP mRNA immunized|geo loc name:missing|collection date:missing", "kidneys  LPP immunized sample1", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes FPKM counts for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine immunization  adult zebrafish AB strain  3 to 4\u2009mpf  15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 \u03bcL for intramuscular i.m immunization. 1\u03bcg L3T mRNA vaccine or LPP GFP mRNA were injected in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL. post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction.", "post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:Vector control immunized group|treatment:2 dose of LPP GFP mRNA immunized", "GSM8321944", "GSM8321944: kidneys  LPP immunized sample1; Danio rerio; RNA Seq", "GSM8321944 r1", "GSM8321944", "1", "post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP513122", null, null, "LPP1.R1.fq.gz LPP1.R2.fq.gz", "fastq fastq", 6946964789.0, 24016865.0, "GSM8321944 r1", "0:144.63 1:144.62", "A:1753009524;C:1714194993;G:1724914785;T:1754837582;N:7905", 144, 144, null, null, 1753009524, 1714194993, 1724914785, 1754837582, 7905, "SRX24871762", "SRS21581234", "SRA1896369", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.94958, 0.95243, 0.05857, 0.05785, 0.70181, 0.70074, 0.5058, 0.50491, 150, 145, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-11", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [32614, "SRR29356863", "SRX24871761", "SRS21581233", "SRP513122", "PRJNA1122499", "An mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE269547", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune protective mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from zebrafish immunized with the mRNA vaccine and the LPP control.  For mRNA vaccination  mRNA candidate vaccines were injected with 1\u00b5g LPP mRNA in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL  negative control zebrafish were immunized with LPP GFP mRNA  immunized twice with two week intervals week 0 and 2.post 12 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group.", null, "pubmed:39759874", null, "kidneys  L3T immunized sample3", "GSM8321943", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:L3T immunized group|treatment:2 dose of L3T mRNA immunized|geo loc name:missing|collection date:missing", "kidneys  L3T immunized sample3", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes FPKM counts for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine immunization  adult zebrafish AB strain  3 to 4\u2009mpf  15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 \u03bcL for intramuscular i.m immunization. 1\u03bcg L3T mRNA vaccine or LPP GFP mRNA were injected in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL. post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction.", "post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:L3T immunized group|treatment:2 dose of L3T mRNA immunized", "GSM8321943", "GSM8321943: kidneys  L3T immunized sample3; Danio rerio; RNA Seq", "GSM8321943 r1", "GSM8321943", "1", "post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP513122", null, null, "L3T3.R1.fq.gz L3T3.R2.fq.gz", "fastq fastq", 7056672882.0, 24530821.0, "GSM8321943 r1", "0:143.84 1:143.83", "A:1768243408;C:1755016636;G:1763993995;T:1769411088;N:7755", 143, 143, null, null, 1768243408, 1755016636, 1763993995, 1769411088, 7755, "SRX24871761", "SRS21581233", "SRA1896369", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.95045, 0.95387, 0.04717, 0.04638, 0.712, 0.71125, 0.52106, 0.51883, 106, 106, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-11", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [32615, "SRR29356864", "SRX24871760", "SRS21581232", "SRP513122", "PRJNA1122499", "An mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE269547", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune protective mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from zebrafish immunized with the mRNA vaccine and the LPP control.  For mRNA vaccination  mRNA candidate vaccines were injected with 1\u00b5g LPP mRNA in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL  negative control zebrafish were immunized with LPP GFP mRNA  immunized twice with two week intervals week 0 and 2.post 12 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group.", null, "pubmed:39759874", null, "kidneys  L3T immunized sample2", "GSM8321942", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:L3T immunized group|treatment:2 dose of L3T mRNA immunized|geo loc name:missing|collection date:missing", "kidneys  L3T immunized sample2", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes FPKM counts for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine immunization  adult zebrafish AB strain  3 to 4\u2009mpf  15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 \u03bcL for intramuscular i.m immunization. 1\u03bcg L3T mRNA vaccine or LPP GFP mRNA were injected in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL. post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction.", "post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:L3T immunized group|treatment:2 dose of L3T mRNA immunized", "GSM8321942", "GSM8321942: kidneys  L3T immunized sample2; Danio rerio; RNA Seq", "GSM8321942 r1", "GSM8321942", "1", "post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP513122", null, null, "L3T2.R1.fq.gz L3T2.R2.fq.gz", "fastq fastq", 7021833716.0, 24281953.0, "GSM8321942 r1", "0:144.59 1:144.59", "A:1777129692;C:1728181109;G:1738562098;T:1777953935;N:6882", 144, 144, null, null, 1777129692, 1728181109, 1738562098, 1777953935, 6882, "SRX24871760", "SRS21581232", "SRA1896369", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.9484, 0.9523, 0.0532, 0.05294, 0.7052, 0.70362, 0.51282, 0.50716, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-11", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [32616, "SRR29356865", "SRX24871759", "SRS21581231", "SRP513122", "PRJNA1122499", "An mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE269547", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune protective mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from zebrafish immunized with the mRNA vaccine and the LPP control.  For mRNA vaccination  mRNA candidate vaccines were injected with 1\u00b5g LPP mRNA in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL  negative control zebrafish were immunized with LPP GFP mRNA  immunized twice with two week intervals week 0 and 2.post 12 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group.", null, "pubmed:39759874", null, "kidneys  L3T immunized sample1", "GSM8321941", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:L3T immunized group|treatment:2 dose of L3T mRNA immunized|geo loc name:missing|collection date:missing", "kidneys  L3T immunized sample1", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes FPKM counts for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine immunization  adult zebrafish AB strain  3 to 4\u2009mpf  15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 \u03bcL for intramuscular i.m immunization. 1\u03bcg L3T mRNA vaccine or LPP GFP mRNA were injected in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL. post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction.", "post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:L3T immunized group|treatment:2 dose of L3T mRNA immunized", "GSM8321941", "GSM8321941: kidneys  L3T immunized sample1; Danio rerio; RNA Seq", "GSM8321941 r1", "GSM8321941", "1", "post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP513122", null, null, "L3T1.R1.fq.gz L3T1.R2.fq.gz", "fastq fastq", 6941829152.0, 24117590.0, "GSM8321941 r1", "0:143.92 1:143.91", "A:1756734172;C:1708781793;G:1718505186;T:1757800293;N:7708", 143, 143, null, null, 1756734172, 1708781793, 1718505186, 1757800293, 7708, "SRX24871759", "SRS21581231", "SRA1896369", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.95019, 0.95324, 0.05797, 0.05755, 0.70013, 0.69934, 0.5137, 0.5148, 147, 147, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-11", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [32785, "SRR29441653", "SRX24954080", "SRS21657738", "SRP514436", "PRJNA1125004", "A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE270105", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control  PBS control   and untreatment control infection 14 days  as well as healthy control.  Adult zebrafish AB strain  3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u00b5g at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group  Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group or PBS immunized group.", null, "pubmed:39759874", null, "M.m infection sample3", "GSM8334559", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:14 days of M.m infection group|treatment:without xxx|geo loc name:missing|collection date:missing", "M.m infection sample3", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine therapeutic   adult zebrafish AB strain  3 to 4\u2009mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u03bcg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis.  post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group.", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:14 days of M.m infection  group|treatment:without xxx", "GSM8334559", "GSM8334559: M.m infection sample3; Danio rerio; RNA Seq", "GSM8334559 r1", "GSM8334559", "1", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514436", null, null, "M_m_infection_3.R2.fq.gz M_m_infection_3.R1.fq.gz", "fastq fastq", 6356874134.0, 21531449.0, "GSM8334559 r1", "0:147.62 1:147.62", "A:1629631082;C:1541934257;G:1557877748;T:1627277838;N:153209", 147, 147, null, null, 1629631082, 1541934257, 1557877748, 1627277838, 153209, "SRX24954080", "SRS21657738", "SRA1905347", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.95052, 0.95088, 0.05066, 0.0508, 0.69716, 0.6969, 0.51335, 0.50048, 143, 143, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-17", "Adult", "Adult", "Kidney", "Renal System"], [32786, "SRR29441654", "SRX24954079", "SRS21657737", "SRP514436", "PRJNA1125004", "A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE270105", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control  PBS control   and untreatment control infection 14 days  as well as healthy control.  Adult zebrafish AB strain  3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u00b5g at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group  Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group or PBS immunized group.", null, "pubmed:39759874", null, "M.m infection sample2", "GSM8334558", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:14 days of M.m infection group|treatment:without xxx|geo loc name:missing|collection date:missing", "M.m infection sample2", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine therapeutic   adult zebrafish AB strain  3 to 4\u2009mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u03bcg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis.  post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group.", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:14 days of M.m infection  group|treatment:without xxx", "GSM8334558", "GSM8334558: M.m infection sample2; Danio rerio; RNA Seq", "GSM8334558 r1", "GSM8334558", "1", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514436", null, null, "M_m_infection_2.R2.fq.gz M_m_infection_2.R1.fq.gz", "fastq fastq", 7054524333.0, 23848504.0, "GSM8334558 r1", "0:147.90 1:147.91", "A:1815742764;C:1704164760;G:1721079421;T:1813355137;N:182251", 147, 147, null, null, 1815742764, 1704164760, 1721079421, 1813355137, 182251, "SRX24954079", "SRS21657737", "SRA1905347", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.94873, 0.9497, 0.05329, 0.05319, 0.70021, 0.69897, 0.51348, 0.51487, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-17", "Adult", "Adult", "Kidney", "Renal System"], [32787, "SRR29441655", "SRX24954078", "SRS21657736", "SRP514436", "PRJNA1125004", "A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE270105", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control  PBS control   and untreatment control infection 14 days  as well as healthy control.  Adult zebrafish AB strain  3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u00b5g at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group  Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group or PBS immunized group.", null, "pubmed:39759874", null, "M.m infection sample1", "GSM8334557", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:14 days of M.m infection group|treatment:without xxx|geo loc name:missing|collection date:missing", "M.m infection sample1", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine therapeutic   adult zebrafish AB strain  3 to 4\u2009mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u03bcg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis.  post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group.", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:14 days of M.m infection  group|treatment:without xxx", "GSM8334557", "GSM8334557: M.m infection sample1; Danio rerio; RNA Seq", "GSM8334557 r1", "GSM8334557", "1", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514436", null, null, "M_m_infection_1.R2.fq.gz M_m_infection_1.R1.fq.gz", "fastq fastq", 6946198558.0, 23547133.0, "GSM8334557 r1", "0:147.49 1:147.50", "A:1790987034;C:1672981012;G:1691024254;T:1791031433;N:174825", 147, 147, null, null, 1790987034, 1672981012, 1691024254, 1791031433, 174825, "SRX24954078", "SRS21657736", "SRA1905347", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.94915, 0.94881, 0.05429, 0.05404, 0.69682, 0.69678, 0.50968, 0.51363, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-17", "Adult", "Adult", "Kidney", "Renal System"], [32788, "SRR29441656", "SRX24954077", "SRS21657735", "SRP514436", "PRJNA1125004", "A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE270105", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control  PBS control   and untreatment control infection 14 days  as well as healthy control.  Adult zebrafish AB strain  3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u00b5g at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group  Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group or PBS immunized group.", null, "pubmed:39759874", null, "Blank sample3", "GSM8334556", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Healthy group|treatment:without xxx|geo loc name:missing|collection date:missing", "Blank sample3", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine therapeutic   adult zebrafish AB strain  3 to 4\u2009mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u03bcg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis.  post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group.", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:Healthy group|treatment:without xxx", "GSM8334556", "GSM8334556: Blank sample3; Danio rerio; RNA Seq", "GSM8334556 r1", "GSM8334556", "1", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514436", null, null, "Blank3.R2.fq.gz Blank3.R1.fq.gz", "fastq fastq", 6932407082.0, 23420695.0, "GSM8334556 r1", "0:147.99 1:148.00", "A:1790632840;C:1666849105;G:1684978083;T:1789775995;N:171059", 147, 148, null, null, 1790632840, 1666849105, 1684978083, 1789775995, 171059, "SRX24954077", "SRS21657735", "SRA1905347", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.94957, 0.94988, 0.05378, 0.05336, 0.70715, 0.70705, 0.52195, 0.51293, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-17", "Adult", "Adult", "Kidney", "Renal System"], [32789, "SRR29441657", "SRX24954076", "SRS21657734", "SRP514436", "PRJNA1125004", "A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE270105", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control  PBS control   and untreatment control infection 14 days  as well as healthy control.  Adult zebrafish AB strain  3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u00b5g at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group  Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group or PBS immunized group.", null, "pubmed:39759874", null, "Blank sample2", "GSM8334555", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Healthy group|treatment:without xxx|geo loc name:missing|collection date:missing", "Blank sample2", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine therapeutic   adult zebrafish AB strain  3 to 4\u2009mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u03bcg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis.  post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group.", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:Healthy group|treatment:without xxx", "GSM8334555", "GSM8334555: Blank sample2; Danio rerio; RNA Seq", "GSM8334555 r1", "GSM8334555", "1", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514436", null, null, "Blank2.R2.fq.gz Blank2.R1.fq.gz", "fastq fastq", 6589805773.0, 22282641.0, "GSM8334555 r1", "0:147.86 1:147.87", "A:1700645441;C:1585546539;G:1603218609;T:1700235278;N:159906", 147, 147, null, null, 1700645441, 1585546539, 1603218609, 1700235278, 159906, "SRX24954076", "SRS21657734", "SRA1905347", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.94982, 0.94956, 0.05437, 0.05385, 0.69986, 0.70003, 0.51649, 0.51715, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-17", "Adult", "Adult", "Kidney", "Renal System"], [32790, "SRR29441658", "SRX24954075", "SRS21657732", "SRP514436", "PRJNA1125004", "A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE270105", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control  PBS control   and untreatment control infection 14 days  as well as healthy control.  Adult zebrafish AB strain  3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u00b5g at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group  Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group or PBS immunized group.", null, "pubmed:39759874", null, "Blank sample1", "GSM8334554", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Healthy group|treatment:without xxx|geo loc name:missing|collection date:missing", "Blank sample1", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine therapeutic   adult zebrafish AB strain  3 to 4\u2009mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u03bcg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis.  post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group.", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:Healthy group|treatment:without xxx", "GSM8334554", "GSM8334554: Blank sample1; Danio rerio; RNA Seq", "GSM8334554 r1", "GSM8334554", "1", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514436", null, null, "Blank1.R2.fq.gz Blank1.R1.fq.gz", "fastq fastq", 6988209016.0, 23723555.0, "GSM8334554 r1", "0:147.28 1:147.29", "A:1793934528;C:1692773043;G:1711063141;T:1790264470;N:173834", 147, 147, null, null, 1793934528, 1692773043, 1711063141, 1790264470, 173834, "SRX24954075", "SRS21657732", "SRA1905347", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.95053, 0.9509, 0.04981, 0.04955, 0.7008, 0.7008, 0.51262, 0.51791, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-17", "Adult", "Adult", "Kidney", "Renal System"], [32791, "SRR29441659", "SRX24954074", "SRS21657733", "SRP514436", "PRJNA1125004", "A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE270105", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control  PBS control   and untreatment control infection 14 days  as well as healthy control.  Adult zebrafish AB strain  3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u00b5g at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group  Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group or PBS immunized group.", null, "pubmed:39759874", null, "PBS treated sample3", "GSM8334553", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:PBS treated group|treatment:2 dose of PBS immunized|geo loc name:missing|collection date:missing", "PBS treated sample3", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine therapeutic   adult zebrafish AB strain  3 to 4\u2009mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u03bcg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis.  post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group.", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:PBS treated group|treatment:2 dose of PBS immunized", "GSM8334553", "GSM8334553: PBS treated sample3; Danio rerio; RNA Seq", "GSM8334553 r1", "GSM8334553", "1", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514436", null, null, "PBS3.R1.fq.gz PBS3.R2.fq.gz", "fastq fastq", 6902483407.0, 23381761.0, "GSM8334553 r1", "0:147.60 1:147.61", "A:1789006509;C:1653537037;G:1669979967;T:1789782638;N:177256", 147, 147, null, null, 1789006509, 1653537037, 1669979967, 1789782638, 177256, "SRX24954074", "SRS21657733", "SRA1905347", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.94782, 0.94837, 0.05863, 0.05874, 0.70025, 0.69899, 0.51852, 0.51943, 91, 91, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-17", "Adult", "Adult", "Kidney", "Renal System"], [32792, "SRR29441660", "SRX24954073", "SRS21657731", "SRP514436", "PRJNA1125004", "A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE270105", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control  PBS control   and untreatment control infection 14 days  as well as healthy control.  Adult zebrafish AB strain  3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u00b5g at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group  Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group or PBS immunized group.", null, "pubmed:39759874", null, "PBS treated sample2", "GSM8334552", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:PBS treated group|treatment:2 dose of PBS immunized|geo loc name:missing|collection date:missing", "PBS treated sample2", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine therapeutic   adult zebrafish AB strain  3 to 4\u2009mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u03bcg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis.  post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group.", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:PBS treated group|treatment:2 dose of PBS immunized", "GSM8334552", "GSM8334552: PBS treated sample2; Danio rerio; RNA Seq", "GSM8334552 r1", "GSM8334552", "1", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514436", null, null, "PBS2.R2.fq.gz PBS2.R1.fq.gz", "fastq fastq", 6919699470.0, 23450956.0, "GSM8334552 r1", "0:147.53 1:147.54", "A:1796088883;C:1654995114;G:1672062487;T:1796386928;N:166058", 147, 147, null, null, 1796088883, 1654995114, 1672062487, 1796386928, 166058, "SRX24954073", "SRS21657731", "SRA1905347", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.9461, 0.94623, 0.06022, 0.06009, 0.70029, 0.70017, 0.51507, 0.50298, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-17", "Adult", "Adult", "Kidney", "Renal System"], [32793, "SRR29441661", "SRX24954072", "SRS21657730", "SRP514436", "PRJNA1125004", "A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE270105", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control  PBS control   and untreatment control infection 14 days  as well as healthy control.  Adult zebrafish AB strain  3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u00b5g at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group  Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group or PBS immunized group.", null, "pubmed:39759874", null, "PBS treated sample1", "GSM8334551", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:PBS treated group|treatment:2 dose of PBS immunized|geo loc name:missing|collection date:missing", "PBS treated sample1", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine therapeutic   adult zebrafish AB strain  3 to 4\u2009mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u03bcg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis.  post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group.", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:PBS treated group|treatment:2 dose of PBS immunized", "GSM8334551", "GSM8334551: PBS treated sample1; Danio rerio; RNA Seq", "GSM8334551 r1", "GSM8334551", "1", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514436", null, null, "PBS1.R1.fq.gz PBS1.R2.fq.gz", "fastq fastq", 6655764529.0, 22519009.0, "GSM8334551 r1", "0:147.78 1:147.78", "A:1714166803;C:1603814821;G:1622004265;T:1715617121;N:161519", 147, 147, null, null, 1714166803, 1603814821, 1622004265, 1715617121, 161519, "SRX24954072", "SRS21657730", "SRA1905347", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.946, 0.94657, 0.06234, 0.06258, 0.69558, 0.69548, 0.51124, 0.51042, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-17", "Adult", "Adult", "Kidney", "Renal System"], [32794, "SRR29441662", "SRX24954071", "SRS21657729", "SRP514436", "PRJNA1125004", "A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE270105", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control  PBS control   and untreatment control infection 14 days  as well as healthy control.  Adult zebrafish AB strain  3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u00b5g at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group  Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group or PBS immunized group.", null, "pubmed:39759874", null, "LPP treated sample3", "GSM8334550", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Vector control treated group|treatment:2 dose of LPP GFP mRNA immunized|geo loc name:missing|collection date:missing", "LPP treated sample3", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine therapeutic   adult zebrafish AB strain  3 to 4\u2009mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u03bcg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis.  post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group.", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:Vector control treated group|treatment:2 dose of LPP GFP mRNA immunized", "GSM8334550", "GSM8334550: LPP treated sample3; Danio rerio; RNA Seq", "GSM8334550 r1", "GSM8334550", "1", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514436", null, null, "LPP3.R2.fq.gz LPP3.R1.fq.gz", "fastq fastq", 6960795416.0, 23521350.0, "GSM8334550 r1", "0:147.96 1:147.97", "A:1794863170;C:1675740682;G:1695061647;T:1794948614;N:181303", 147, 147, null, null, 1794863170, 1675740682, 1695061647, 1794948614, 181303, "SRX24954071", "SRS21657729", "SRA1905347", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.94576, 0.94611, 0.05967, 0.05967, 0.71116, 0.71068, 0.51094, 0.50281, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-17", "Adult", "Adult", "Kidney", "Renal System"], [32795, "SRR29441663", "SRX24954070", "SRS21657728", "SRP514436", "PRJNA1125004", "A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE270105", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control  PBS control   and untreatment control infection 14 days  as well as healthy control.  Adult zebrafish AB strain  3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u00b5g at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group  Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group or PBS immunized group.", null, "pubmed:39759874", null, "LPP treated sample2", "GSM8334549", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Vector control treated group|treatment:2 dose of LPP GFP mRNA immunized|geo loc name:missing|collection date:missing", "LPP treated sample2", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine therapeutic   adult zebrafish AB strain  3 to 4\u2009mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u03bcg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis.  post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group.", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:Vector control treated group|treatment:2 dose of LPP GFP mRNA immunized", "GSM8334549", "GSM8334549: LPP treated sample2; Danio rerio; RNA Seq", "GSM8334549 r1", "GSM8334549", "1", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514436", null, null, "LPP2.R1.fq.gz LPP2.R2.fq.gz", "fastq fastq", 6995236493.0, 23852541.0, "GSM8334549 r1", "0:146.63 1:146.64", "A:1801247979;C:1688505572;G:1704475825;T:1800830679;N:176438", 146, 146, null, null, 1801247979, 1688505572, 1704475825, 1800830679, 176438, "SRX24954070", "SRS21657728", "SRA1905347", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.946, 0.94652, 0.0561, 0.05623, 0.70358, 0.70366, 0.52017, 0.51073, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-17", "Adult", "Adult", "Kidney", "Renal System"], [32796, "SRR29441664", "SRX24954069", "SRS21657726", "SRP514436", "PRJNA1125004", "A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE270105", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control  PBS control   and untreatment control infection 14 days  as well as healthy control.  Adult zebrafish AB strain  3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u00b5g at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group  Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group or PBS immunized group.", null, "pubmed:39759874", null, "LPP treated sample1", "GSM8334548", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Vector control treated group|treatment:2 dose of LPP GFP mRNA immunized|geo loc name:missing|collection date:missing", "LPP treated sample1", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine therapeutic   adult zebrafish AB strain  3 to 4\u2009mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u03bcg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis.  post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group.", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:Vector control treated group|treatment:2 dose of LPP GFP mRNA immunized", "GSM8334548", "GSM8334548: LPP treated sample1; Danio rerio; RNA Seq", "GSM8334548 r1", "GSM8334548", "1", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514436", null, null, "LPP1.R2.fq.gz LPP1.R1.fq.gz", "fastq fastq", 6929011698.0, 23415693.0, "GSM8334548 r1", "0:147.95 1:147.96", "A:1800504335;C:1654697874;G:1672501459;T:1801139766;N:168264", 147, 147, null, null, 1800504335, 1654697874, 1672501459, 1801139766, 168264, "SRX24954069", "SRS21657726", "SRA1905347", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.94635, 0.9465, 0.05964, 0.05918, 0.71151, 0.71121, 0.51212, 0.51768, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-17", "Adult", "Adult", "Kidney", "Renal System"], [32797, "SRR29441665", "SRX24954068", "SRS21657724", "SRP514436", "PRJNA1125004", "A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE270105", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control  PBS control   and untreatment control infection 14 days  as well as healthy control.  Adult zebrafish AB strain  3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u00b5g at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group  Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group or PBS immunized group.", null, "pubmed:39759874", null, "L3T treated sample3", "GSM8334547", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:L3T treated group|treatment:2 dose of L3T mRNA immunized|geo loc name:missing|collection date:missing", "L3T treated sample3", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine therapeutic   adult zebrafish AB strain  3 to 4\u2009mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u03bcg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis.  post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group.", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:L3T treated group|treatment:2 dose of L3T mRNA immunized", "GSM8334547", "GSM8334547: L3T treated sample3; Danio rerio; RNA Seq", "GSM8334547 r1", "GSM8334547", "1", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514436", null, null, "L3T3.R2.fq.gz L3T3.R1.fq.gz", "fastq fastq", 7001083805.0, 23754500.0, "GSM8334547 r1", "0:147.36 1:147.37", "A:1812658982;C:1679795926;G:1696938100;T:1811517827;N:172970", 147, 147, null, null, 1812658982, 1679795926, 1696938100, 1811517827, 172970, "SRX24954068", "SRS21657724", "SRA1905347", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.94456, 0.94488, 0.05931, 0.05871, 0.70112, 0.70035, 0.49966, 0.50266, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-17", "Adult", "Adult", "Kidney", "Renal System"], [32798, "SRR29441666", "SRX24954067", "SRS21657727", "SRP514436", "PRJNA1125004", "A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE270105", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control  PBS control   and untreatment control infection 14 days  as well as healthy control.  Adult zebrafish AB strain  3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u00b5g at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group  Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group or PBS immunized group.", null, "pubmed:39759874", null, "L3T treated sample2", "GSM8334546", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:L3T treated group|treatment:2 dose of L3T mRNA immunized|geo loc name:missing|collection date:missing", "L3T treated sample2", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine therapeutic   adult zebrafish AB strain  3 to 4\u2009mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u03bcg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis.  post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group.", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:L3T treated group|treatment:2 dose of L3T mRNA immunized", "GSM8334546", "GSM8334546: L3T treated sample2; Danio rerio; RNA Seq", "GSM8334546 r1", "GSM8334546", "1", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514436", null, null, "L3T2.R2.fq.gz L3T2.R1.fq.gz", "fastq fastq", 7045440387.0, 23900950.0, "GSM8334546 r1", "0:147.38 1:147.39", "A:1809443747;C:1705557966;G:1721919646;T:1808345574;N:173454", 147, 147, null, null, 1809443747, 1705557966, 1721919646, 1808345574, 173454, "SRX24954067", "SRS21657727", "SRA1905347", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.94629, 0.94712, 0.05505, 0.05485, 0.69753, 0.69654, 0.50587, 0.50695, 131, 131, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-17", "Adult", "Adult", "Kidney", "Renal System"], [32799, "SRR29441667", "SRX24954066", "SRS21657725", "SRP514436", "PRJNA1125004", "A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy", "GSE270105", "Transcriptome Analysis", "Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control  PBS control   and untreatment control infection 14 days  as well as healthy control.  Adult zebrafish AB strain  3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u00b5g at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group  Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group or PBS immunized group.", null, "pubmed:39759874", null, "L3T treated sample1", "GSM8334545", null, "source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:L3T treated group|treatment:2 dose of L3T mRNA immunized|geo loc name:missing|collection date:missing", "L3T treated sample1", "The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample", "kidneys", "For determination of the host immune response induced by mRNA vaccine therapeutic   adult zebrafish AB strain  3 to 4\u2009mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5\u03bcg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector  and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis.  post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment  to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group.", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer\u2019s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer\u2019s instructions.", "The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature \u223c28\u00b0C  pH \u223c7.4  and conductivity \u223c1500\u03bcS.", "tissue:kidneys|cell type:whole cell immune cell|group:L3T treated group|treatment:2 dose of L3T mRNA immunized", "GSM8334545", "GSM8334545: L3T treated sample1; Danio rerio; RNA Seq", "GSM8334545 r1", "GSM8334545", "1", "post 7 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514436", null, null, "L3T1.R1.fq.gz L3T1.R2.fq.gz", "fastq fastq", 7005817977.0, 23717988.0, "GSM8334545 r1", "0:147.68 1:147.70", "A:1802621490;C:1692580332;G:1709393477;T:1801045146;N:177532", 147, 147, null, null, 1802621490, 1692580332, 1709393477, 1801045146, 177532, "SRX24954066", "SRS21657725", "SRA1905347", "Zhang Lab, Department of Microbiology, Fudan University", "Zhang Lab, Department of Microbiology, Fudan University", 2, 0.94218, 0.94275, 0.05735, 0.05684, 0.69436, 0.69325, 0.5057, 0.50501, 134, 134, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-17", "Adult", "Adult", "Kidney", "Renal System"], [32800, "SRR29453136", "SRX24965357", "SRS21668889", "SRP514613", "PRJNA1125316", "RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection", "GSE270136", "Transcriptome Analysis", "Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish line. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu4 mutation revealed differentially expressed genes compared to WT controls. Differentially expressed genes were associated with neutrophil degranulation  haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. Six samples were analyzed  three biological replicates in two groups  fish homozygous for pycardtpu4 mutation and wild type WT control.", null, "pubmed:39916610", null, "kidney derived neutrophils  homozygous  Mm infected  rep3", "GSM8335407", null, "source name:kidney|tissue:kidney|cell type:neutrophils|genotype:homozygous for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB|infection:M. marinum|geo loc name:missing|collection date:missing", "kidney derived neutrophils  homozygous  Mm infected  rep3", "Reads were aligned to the reference genome GRz11 grcz11 gca 000002035 4 with HISAT2. Raw expression estimates raw read counts for genes grcz11 gca 000002035 4 were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.", "kidney", "Adult zebrafish were infected with 69 118 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", "Fish homozygous for pycardtpu4 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.", "tissue:kidney|cell type:neutrophils|genotype:homozygous for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB|infection:M. marinum", "GSM8335407", "GSM8335407: kidney derived neutrophils  homozygous  Mm infected  rep3; Danio rerio; RNA Seq", "GSM8335407 r1", "GSM8335407", "1", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514613", null, null, "R18_H_MM_1.fq.gz R18_H_MM_2.fq.gz", "fastq fastq", 6901009500.0, 23003365.0, "GSM8335407 r1", "0:150 1:150", "A:1920522839;C:1515700169;G:1537191557;T:1927497878;N:97057", 150, 150, null, null, 1920522839, 1515700169, 1537191557, 1927497878, 97057, "SRX24965357", "SRS21668889", "SRA1902200", "University of Tampere", "University of Tampere", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2024-06-18", "Larval", "Larval", "Kidney", "Renal System"], [32801, "SRR29453137", "SRX24965356", "SRS21668888", "SRP514613", "PRJNA1125316", "RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection", "GSE270136", "Transcriptome Analysis", "Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish line. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu4 mutation revealed differentially expressed genes compared to WT controls. Differentially expressed genes were associated with neutrophil degranulation  haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. Six samples were analyzed  three biological replicates in two groups  fish homozygous for pycardtpu4 mutation and wild type WT control.", null, "pubmed:39916610", null, "kidney derived neutrophils  homozygous  Mm infected  rep2", "GSM8335406", null, "source name:kidney|tissue:kidney|cell type:neutrophils|genotype:homozygous for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB|infection:M. marinum|geo loc name:missing|collection date:missing", "kidney derived neutrophils  homozygous  Mm infected  rep2", "Reads were aligned to the reference genome GRz11 grcz11 gca 000002035 4 with HISAT2. Raw expression estimates raw read counts for genes grcz11 gca 000002035 4 were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.", "kidney", "Adult zebrafish were infected with 69 118 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", "Fish homozygous for pycardtpu4 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.", "tissue:kidney|cell type:neutrophils|genotype:homozygous for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB|infection:M. marinum", "GSM8335406", "GSM8335406: kidney derived neutrophils  homozygous  Mm infected  rep2; Danio rerio; RNA Seq", "GSM8335406 r1", "GSM8335406", "1", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514613", null, null, "R10_H_MM_1.fq.gz R10_H_MM_2.fq.gz", "fastq fastq", 6877413600.0, 22924712.0, "GSM8335406 r1", "0:150 1:150", "A:1901340557;C:1516911325;G:1537883236;T:1921186807;N:91675", 150, 150, null, null, 1901340557, 1516911325, 1537883236, 1921186807, 91675, "SRX24965356", "SRS21668888", "SRA1902200", "University of Tampere", "University of Tampere", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2024-06-18", "Larval", "Larval", "Kidney", "Renal System"], [32802, "SRR29453138", "SRX24965355", "SRS21668887", "SRP514613", "PRJNA1125316", "RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection", "GSE270136", "Transcriptome Analysis", "Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish line. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu4 mutation revealed differentially expressed genes compared to WT controls. Differentially expressed genes were associated with neutrophil degranulation  haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. Six samples were analyzed  three biological replicates in two groups  fish homozygous for pycardtpu4 mutation and wild type WT control.", null, "pubmed:39916610", null, "kidney derived neutrophils  homozygous  Mm infected  rep1", "GSM8335405", null, "source name:kidney|tissue:kidney|cell type:neutrophils|genotype:homozygous for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB|infection:M. marinum|geo loc name:missing|collection date:missing", "kidney derived neutrophils  homozygous  Mm infected  rep1", "Reads were aligned to the reference genome GRz11 grcz11 gca 000002035 4 with HISAT2. Raw expression estimates raw read counts for genes grcz11 gca 000002035 4 were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.", "kidney", "Adult zebrafish were infected with 69 118 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", "Fish homozygous for pycardtpu4 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.", "tissue:kidney|cell type:neutrophils|genotype:homozygous for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB|infection:M. marinum", "GSM8335405", "GSM8335405: kidney derived neutrophils  homozygous  Mm infected  rep1; Danio rerio; RNA Seq", "GSM8335405 r1", "GSM8335405", "1", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514613", null, null, "R8_2_H_MM_1.fq.gz R8_2_H_MM_2.fq.gz", "fastq fastq", 6921242700.0, 23070809.0, "GSM8335405 r1", "0:150 1:150", "A:1923648919;C:1520702661;G:1540739284;T:1936060582;N:91254", 150, 150, null, null, 1923648919, 1520702661, 1540739284, 1936060582, 91254, "SRX24965355", "SRS21668887", "SRA1902200", "University of Tampere", "University of Tampere", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2024-06-18", "Larval", "Larval", "Kidney", "Renal System"], [32803, "SRR29453139", "SRX24965354", "SRS21668886", "SRP514613", "PRJNA1125316", "RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection", "GSE270136", "Transcriptome Analysis", "Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish line. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu4 mutation revealed differentially expressed genes compared to WT controls. Differentially expressed genes were associated with neutrophil degranulation  haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. Six samples were analyzed  three biological replicates in two groups  fish homozygous for pycardtpu4 mutation and wild type WT control.", null, "pubmed:39916610", null, "kidney derived neutrophils  wt  Mm infected  rep3", "GSM8335404", null, "source name:kidney|tissue:kidney|cell type:neutrophils|genotype:wild type for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB|infection:M. marinum|geo loc name:missing|collection date:missing", "kidney derived neutrophils  wt  Mm infected  rep3", "Reads were aligned to the reference genome GRz11 grcz11 gca 000002035 4 with HISAT2. Raw expression estimates raw read counts for genes grcz11 gca 000002035 4 were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.", "kidney", "Adult zebrafish were infected with 69 118 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", "Fish homozygous for pycardtpu4 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.", "tissue:kidney|cell type:neutrophils|genotype:wild type for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB|infection:M. marinum", "GSM8335404", "GSM8335404: kidney derived neutrophils  wt  Mm infected  rep3; Danio rerio; RNA Seq", "GSM8335404 r1", "GSM8335404", "1", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514613", null, null, "R16_WT_MM_1.fq.gz R16_WT_MM_2.fq.gz", "fastq fastq", 6755682900.0, 22518943.0, "GSM8335404 r1", "0:150 1:150", "A:1866248606;C:1494647864;G:1513464764;T:1881229301;N:92365", 150, 150, null, null, 1866248606, 1494647864, 1513464764, 1881229301, 92365, "SRX24965354", "SRS21668886", "SRA1902200", "University of Tampere", "University of Tampere", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2024-06-18", "Larval", "Larval", "Kidney", "Renal System"], [32804, "SRR29453140", "SRX24965353", "SRS21668885", "SRP514613", "PRJNA1125316", "RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection", "GSE270136", "Transcriptome Analysis", "Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish line. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu4 mutation revealed differentially expressed genes compared to WT controls. Differentially expressed genes were associated with neutrophil degranulation  haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. Six samples were analyzed  three biological replicates in two groups  fish homozygous for pycardtpu4 mutation and wild type WT control.", null, "pubmed:39916610", null, "kidney derived neutrophils  wt  Mm infected  rep2", "GSM8335403", null, "source name:kidney|tissue:kidney|cell type:neutrophils|genotype:wild type for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB|infection:M. marinum|geo loc name:missing|collection date:missing", "kidney derived neutrophils  wt  Mm infected  rep2", "Reads were aligned to the reference genome GRz11 grcz11 gca 000002035 4 with HISAT2. Raw expression estimates raw read counts for genes grcz11 gca 000002035 4 were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.", "kidney", "Adult zebrafish were infected with 69 118 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", "Fish homozygous for pycardtpu4 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.", "tissue:kidney|cell type:neutrophils|genotype:wild type for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB|infection:M. marinum", "GSM8335403", "GSM8335403: kidney derived neutrophils  wt  Mm infected  rep2; Danio rerio; RNA Seq", "GSM8335403 r1", "GSM8335403", "1", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514613", null, null, "R7_WT_MM_1.fq.gz R7_WT_MM_2.fq.gz", "fastq fastq", 6801886200.0, 22672954.0, "GSM8335403 r1", "0:150 1:150", "A:1897407228;C:1488944523;G:1508394915;T:1907051254;N:88280", 150, 150, null, null, 1897407228, 1488944523, 1508394915, 1907051254, 88280, "SRX24965353", "SRS21668885", "SRA1902200", "University of Tampere", "University of Tampere", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2024-06-18", "Larval", "Larval", "Kidney", "Renal System"], [32805, "SRR29453141", "SRX24965352", "SRS21668884", "SRP514613", "PRJNA1125316", "RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection", "GSE270136", "Transcriptome Analysis", "Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish line. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu4 mutation revealed differentially expressed genes compared to WT controls. Differentially expressed genes were associated with neutrophil degranulation  haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. Six samples were analyzed  three biological replicates in two groups  fish homozygous for pycardtpu4 mutation and wild type WT control.", null, "pubmed:39916610", null, "kidney derived neutrophils  wt  Mm infected  rep1", "GSM8335402", null, "source name:kidney|tissue:kidney|cell type:neutrophils|genotype:wild type for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB|infection:M. marinum|geo loc name:missing|collection date:missing", "kidney derived neutrophils  wt  Mm infected  rep1", "Reads were aligned to the reference genome GRz11 grcz11 gca 000002035 4 with HISAT2. Raw expression estimates raw read counts for genes grcz11 gca 000002035 4 were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.", "kidney", "Adult zebrafish were infected with 69 118 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", "Fish homozygous for pycardtpu4 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.", "tissue:kidney|cell type:neutrophils|genotype:wild type for pycard pycardtpu4 crossed to transgenic Tgmpx:GFPi114 AB|infection:M. marinum", "GSM8335402", "GSM8335402: kidney derived neutrophils  wt  Mm infected  rep1; Danio rerio; RNA Seq", "GSM8335402 r1", "GSM8335402", "1", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP514613", null, null, "R5_WT_MM_1.fq.gz R5_WT_MM_2.fq.gz", "fastq fastq", 6760544400.0, 22535148.0, "GSM8335402 r1", "0:150 1:150", "A:1863279045;C:1498858984;G:1519081612;T:1879233731;N:91028", 150, 150, null, null, 1863279045, 1498858984, 1519081612, 1879233731, 91028, "SRX24965352", "SRS21668884", "SRA1902200", "University of Tampere", "University of Tampere", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2024-06-18", "Larval", "Larval", "Kidney", "Renal System"], [34535, "SRR32064717", "SRX27413530", "SRS23843189", "SRP558767", "PRJNA1213790", "RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection", "GSE287594", "Transcriptome Analysis", "Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation  haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed  six biological replicates in two groups  fish homozygous for pycardtpu5 mutation and wild type WT control.", null, "pubmed:39916610", null, "kidney derived neutrophils  homozygous  Mm infected  rep6", "GSM8748663", null, "source name:kidney|tissue:kidney|cell type:neutrophils|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected|geo loc name:missing|collection date:missing", "kidney derived neutrophils  homozygous  Mm infected  rep6", "Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.", "kidney", "Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", "Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.", "tissue:kidney|cell type:neutrophils|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected", "GSM8748663", "GSM8748663: kidney derived neutrophils  homozygous  Mm infected  rep6; Danio rerio; RNA Seq", "GSM8748663 r1", "GSM8748663", "1", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP558767", null, null, "RNA35_H_MM_R_1.fq.gz RNA35_H_MM_R_2.fq.gz", "fastq fastq", 6950452200.0, 23168174.0, "GSM8748663 r1", "0:150 1:150", "A:1920598119;C:1565819640;G:1566891465;T:1896911503;N:231473", 150, 150, null, null, 1920598119, 1565819640, 1566891465, 1896911503, 231473, "SRX27413530", "SRS23843189", "SRA2056436", "University of Tampere", "University of Tampere", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2025-01-21", "Larval", "Larval", "Kidney", "Renal System"], [34536, "SRR32064718", "SRX27413529", "SRS23843188", "SRP558767", "PRJNA1213790", "RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection", "GSE287594", "Transcriptome Analysis", "Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation  haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed  six biological replicates in two groups  fish homozygous for pycardtpu5 mutation and wild type WT control.", null, "pubmed:39916610", null, "kidney derived neutrophils  homozygous  Mm infected  rep5", "GSM8748662", null, "source name:kidney|tissue:kidney|cell type:neutrophils|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected|geo loc name:missing|collection date:missing", "kidney derived neutrophils  homozygous  Mm infected  rep5", "Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.", "kidney", "Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", "Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.", "tissue:kidney|cell type:neutrophils|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected", "GSM8748662", "GSM8748662: kidney derived neutrophils  homozygous  Mm infected  rep5; Danio rerio; RNA Seq", "GSM8748662 r1", "GSM8748662", "1", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP558767", null, null, "RNA31_H_MM_R_1.fq.gz RNA31_H_MM_R_2.fq.gz", "fastq fastq", 6663708000.0, 22212360.0, "GSM8748662 r1", "0:150 1:150", "A:1831236930;C:1510631608;G:1510442962;T:1810728281;N:668219", 150, 150, null, null, 1831236930, 1510631608, 1510442962, 1810728281, 668219, "SRX27413529", "SRS23843188", "SRA2056436", "University of Tampere", "University of Tampere", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2025-01-21", "Larval", "Larval", "Kidney", "Renal System"], [34537, "SRR32064719", "SRX27413528", "SRS23843187", "SRP558767", "PRJNA1213790", "RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection", "GSE287594", "Transcriptome Analysis", "Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation  haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed  six biological replicates in two groups  fish homozygous for pycardtpu5 mutation and wild type WT control.", null, "pubmed:39916610", null, "kidney derived neutrophils  homozygous  Mm infected  rep4", "GSM8748661", null, "source name:kidney|tissue:kidney|cell type:neutrophils|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected|geo loc name:missing|collection date:missing", "kidney derived neutrophils  homozygous  Mm infected  rep4", "Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.", "kidney", "Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", "Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.", "tissue:kidney|cell type:neutrophils|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected", "GSM8748661", "GSM8748661: kidney derived neutrophils  homozygous  Mm infected  rep4; Danio rerio; RNA Seq", "GSM8748661 r1", "GSM8748661", "1", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP558767", null, null, "RNA17_H_MM_R_1.fq.gz RNA17_H_MM_R_2.fq.gz", "fastq fastq", 6328866900.0, 21096223.0, "GSM8748661 r1", "0:150 1:150", "A:1736278764;C:1437925823;G:1439447440;T:1714587759;N:627114", 150, 150, null, null, 1736278764, 1437925823, 1439447440, 1714587759, 627114, "SRX27413528", "SRS23843187", "SRA2056436", "University of Tampere", "University of Tampere", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2025-01-21", "Larval", "Larval", "Kidney", "Renal System"], [34538, "SRR32064720", "SRX27413527", "SRS23843186", "SRP558767", "PRJNA1213790", "RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection", "GSE287594", "Transcriptome Analysis", "Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation  haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed  six biological replicates in two groups  fish homozygous for pycardtpu5 mutation and wild type WT control.", null, "pubmed:39916610", null, "kidney derived neutrophils  homozygous  Mm infected  rep3", "GSM8748660", null, "source name:kidney|tissue:kidney|cell type:neutrophils|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected|geo loc name:missing|collection date:missing", "kidney derived neutrophils  homozygous  Mm infected  rep3", "Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.", "kidney", "Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", "Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.", "tissue:kidney|cell type:neutrophils|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected", "GSM8748660", "GSM8748660: kidney derived neutrophils  homozygous  Mm infected  rep3; Danio rerio; RNA Seq", "GSM8748660 r1", "GSM8748660", "1", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP558767", null, null, "RNA16_H_MM_R_1.fq.gz RNA16_H_MM_R_2.fq.gz", "fastq fastq", 5994609000.0, 19982030.0, "GSM8748660 r1", "0:150 1:150", "A:1647964217;C:1357673528;G:1357262640;T:1631490903;N:217712", 150, 150, null, null, 1647964217, 1357673528, 1357262640, 1631490903, 217712, "SRX27413527", "SRS23843186", "SRA2056436", "University of Tampere", "University of Tampere", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2025-01-21", "Larval", "Larval", "Kidney", "Renal System"], [34539, "SRR32064721", "SRX27413526", "SRS23843185", "SRP558767", "PRJNA1213790", "RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection", "GSE287594", "Transcriptome Analysis", "Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation  haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed  six biological replicates in two groups  fish homozygous for pycardtpu5 mutation and wild type WT control.", null, "pubmed:39916610", null, "kidney derived neutrophils  homozygous  Mm infected  rep2", "GSM8748659", null, "source name:kidney|tissue:kidney|cell type:neutrophils|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected|geo loc name:missing|collection date:missing", "kidney derived neutrophils  homozygous  Mm infected  rep2", "Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.", "kidney", "Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", "Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.", "tissue:kidney|cell type:neutrophils|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected", "GSM8748659", "GSM8748659: kidney derived neutrophils  homozygous  Mm infected  rep2; Danio rerio; RNA Seq", "GSM8748659 r1", "GSM8748659", "1", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP558767", null, null, "RNA15_H_MM_R_1.fq.gz RNA15_H_MM_R_2.fq.gz", "fastq fastq", 5973435300.0, 19911451.0, "GSM8748659 r1", "0:150 1:150", "A:1650140619;C:1346802182;G:1348552488;T:1627259927;N:680084", 150, 150, null, null, 1650140619, 1346802182, 1348552488, 1627259927, 680084, "SRX27413526", "SRS23843185", "SRA2056436", "University of Tampere", "University of Tampere", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2025-01-21", "Larval", "Larval", "Kidney", "Renal System"], [34540, "SRR32064722", "SRX27413525", "SRS23843184", "SRP558767", "PRJNA1213790", "RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection", "GSE287594", "Transcriptome Analysis", "Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation  haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed  six biological replicates in two groups  fish homozygous for pycardtpu5 mutation and wild type WT control.", null, "pubmed:39916610", null, "kidney derived neutrophils  homozygous  Mm infected  rep1", "GSM8748658", null, "source name:kidney|tissue:kidney|cell type:neutrophils|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected|geo loc name:missing|collection date:missing", "kidney derived neutrophils  homozygous  Mm infected  rep1", "Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.", "kidney", "Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", "Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.", "tissue:kidney|cell type:neutrophils|genotype:homozygous for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected", "GSM8748658", "GSM8748658: kidney derived neutrophils  homozygous  Mm infected  rep1; Danio rerio; RNA Seq", "GSM8748658 r1", "GSM8748658", "1", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP558767", null, null, "RNA14_H_MM_R_1.fq.gz RNA14_H_MM_R_2.fq.gz", "fastq fastq", 6516002400.0, 21720008.0, "GSM8748658 r1", "0:150 1:150", "A:1798422932;C:1471942244;G:1470322290;T:1774672386;N:642548", 150, 150, null, null, 1798422932, 1471942244, 1470322290, 1774672386, 642548, "SRX27413525", "SRS23843184", "SRA2056436", "University of Tampere", "University of Tampere", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2025-01-21", "Larval", "Larval", "Kidney", "Renal System"], [34541, "SRR32064723", "SRX27413524", "SRS23843183", "SRP558767", "PRJNA1213790", "RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection", "GSE287594", "Transcriptome Analysis", "Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation  haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed  six biological replicates in two groups  fish homozygous for pycardtpu5 mutation and wild type WT control.", null, "pubmed:39916610", null, "kidney derived neutrophils  wt  Mm infected  rep6", "GSM8748657", null, "source name:kidney|tissue:kidney|cell type:neutrophils|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected|geo loc name:missing|collection date:missing", "kidney derived neutrophils  wt  Mm infected  rep6", "Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.", "kidney", "Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", "Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.", "tissue:kidney|cell type:neutrophils|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected", "GSM8748657", "GSM8748657: kidney derived neutrophils  wt  Mm infected  rep6; Danio rerio; RNA Seq", "GSM8748657 r1", "GSM8748657", "1", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP558767", null, null, "RNA32_W_MM_R_1.fq.gz RNA32_W_MM_R_2.fq.gz", "fastq fastq", 6440025300.0, 21466751.0, "GSM8748657 r1", "0:150 1:150", "A:1785469029;C:1447831778;G:1441059581;T:1765446885;N:218027", 150, 150, null, null, 1785469029, 1447831778, 1441059581, 1765446885, 218027, "SRX27413524", "SRS23843183", "SRA2056436", "University of Tampere", "University of Tampere", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2025-01-21", "Larval", "Larval", "Kidney", "Renal System"], [34542, "SRR32064724", "SRX27413523", "SRS23843182", "SRP558767", "PRJNA1213790", "RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection", "GSE287594", "Transcriptome Analysis", "Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation  haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed  six biological replicates in two groups  fish homozygous for pycardtpu5 mutation and wild type WT control.", null, "pubmed:39916610", null, "kidney derived neutrophils  wt  Mm infected  rep5", "GSM8748656", null, "source name:kidney|tissue:kidney|cell type:neutrophils|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected|geo loc name:missing|collection date:missing", "kidney derived neutrophils  wt  Mm infected  rep5", "Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.", "kidney", "Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", "Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.", "tissue:kidney|cell type:neutrophils|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected", "GSM8748656", "GSM8748656: kidney derived neutrophils  wt  Mm infected  rep5; Danio rerio; RNA Seq", "GSM8748656 r1", "GSM8748656", "1", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP558767", null, null, "RNA29_W_MM_R_1.fq.gz RNA29_W_MM_R_2.fq.gz", "fastq fastq", 6450517200.0, 21501724.0, "GSM8748656 r1", "0:150 1:150", "A:1786241571;C:1451411588;G:1447987838;T:1764221339;N:654864", 150, 150, null, null, 1786241571, 1451411588, 1447987838, 1764221339, 654864, "SRX27413523", "SRS23843182", "SRA2056436", "University of Tampere", "University of Tampere", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2025-01-21", "Larval", "Larval", "Kidney", "Renal System"], [34543, "SRR32064725", "SRX27413522", "SRS23843181", "SRP558767", "PRJNA1213790", "RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection", "GSE287594", "Transcriptome Analysis", "Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation  haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed  six biological replicates in two groups  fish homozygous for pycardtpu5 mutation and wild type WT control.", null, "pubmed:39916610", null, "kidney derived neutrophils  wt  Mm infected  rep4", "GSM8748655", null, "source name:kidney|tissue:kidney|cell type:neutrophils|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected|geo loc name:missing|collection date:missing", "kidney derived neutrophils  wt  Mm infected  rep4", "Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.", "kidney", "Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", "Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.", "tissue:kidney|cell type:neutrophils|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected", "GSM8748655", "GSM8748655: kidney derived neutrophils  wt  Mm infected  rep4; Danio rerio; RNA Seq", "GSM8748655 r1", "GSM8748655", "1", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP558767", null, null, "RNA28_W_MM_R_1.fq.gz RNA28_W_MM_R_2.fq.gz", "fastq fastq", 6306771900.0, 21022573.0, "GSM8748655 r1", "0:150 1:150", "A:1748779929;C:1415200694;G:1412343882;T:1729784544;N:662851", 150, 150, null, null, 1748779929, 1415200694, 1412343882, 1729784544, 662851, "SRX27413522", "SRS23843181", "SRA2056436", "University of Tampere", "University of Tampere", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2025-01-21", "Larval", "Larval", "Kidney", "Renal System"], [34544, "SRR32064726", "SRX27413521", "SRS23843180", "SRP558767", "PRJNA1213790", "RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection", "GSE287594", "Transcriptome Analysis", "Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation  haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed  six biological replicates in two groups  fish homozygous for pycardtpu5 mutation and wild type WT control.", null, "pubmed:39916610", null, "kidney derived neutrophils  wt  Mm infected  rep3", "GSM8748654", null, "source name:kidney|tissue:kidney|cell type:neutrophils|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected|geo loc name:missing|collection date:missing", "kidney derived neutrophils  wt  Mm infected  rep3", "Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.", "kidney", "Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", "Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.", "tissue:kidney|cell type:neutrophils|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected", "GSM8748654", "GSM8748654: kidney derived neutrophils  wt  Mm infected  rep3; Danio rerio; RNA Seq", "GSM8748654 r1", "GSM8748654", "1", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP558767", null, null, "RNA11_W_MM_R_1.fq.gz RNA11_W_MM_R_2.fq.gz", "fastq fastq", 6880056600.0, 22933522.0, "GSM8748654 r1", "0:150 1:150", "A:1907309824;C:1546968275;G:1546306637;T:1879237297;N:234567", 150, 150, null, null, 1907309824, 1546968275, 1546306637, 1879237297, 234567, "SRX27413521", "SRS23843180", "SRA2056436", "University of Tampere", "University of Tampere", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2025-01-21", "Larval", "Larval", "Kidney", "Renal System"], [34545, "SRR32064727", "SRX27413520", "SRS23843179", "SRP558767", "PRJNA1213790", "RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection", "GSE287594", "Transcriptome Analysis", "Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation  haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed  six biological replicates in two groups  fish homozygous for pycardtpu5 mutation and wild type WT control.", null, "pubmed:39916610", null, "kidney derived neutrophils  wt  Mm infected  rep2", "GSM8748653", null, "source name:kidney|tissue:kidney|cell type:neutrophils|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected|geo loc name:missing|collection date:missing", "kidney derived neutrophils  wt  Mm infected  rep2", "Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.", "kidney", "Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", "Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.", "tissue:kidney|cell type:neutrophils|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected", "GSM8748653", "GSM8748653: kidney derived neutrophils  wt  Mm infected  rep2; Danio rerio; RNA Seq", "GSM8748653 r1", "GSM8748653", "1", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP558767", null, null, "RNA10_W_MM_R_1.fq.gz RNA10_W_MM_R_2.fq.gz", "fastq fastq", 6391782300.0, 21305941.0, "GSM8748653 r1", "0:150 1:150", "A:1768453408;C:1440642021;G:1438187733;T:1744118899;N:380239", 150, 150, null, null, 1768453408, 1440642021, 1438187733, 1744118899, 380239, "SRX27413520", "SRS23843179", "SRA2056436", "University of Tampere", "University of Tampere", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2025-01-21", "Larval", "Larval", "Kidney", "Renal System"], [34546, "SRR32064728", "SRX27413519", "SRS23843178", "SRP558767", "PRJNA1213790", "RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection", "GSE287594", "Transcriptome Analysis", "Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish Danio rerio has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation  haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls. Overall design: Identification of differentially expressed genes in Mycobacterium marinum infection in kidney derived neutrophils of zebrafish devoid of inflammasome adaptor pycard at four weeks post infection. 12 samples were analyzed  six biological replicates in two groups  fish homozygous for pycardtpu5 mutation and wild type WT control.", null, "pubmed:39916610", null, "kidney derived neutrophils  wt  Mm infected  rep1", "GSM8748652", null, "source name:kidney|tissue:kidney|cell type:neutrophils|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected|geo loc name:missing|collection date:missing", "kidney derived neutrophils  wt  Mm infected  rep1", "Reads were aligned to the reference genome GRz11 ensembl 109 danio rerio grcz11 primary with HISAT2. Raw expression estimates raw read counts for genes ensembl 109 danio rerio grcz11 primary were counted using FeatureCounts. Analysis of differentially expressed genes was performed with DESeq2 Assembly: GRz11 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its ENSDARG id. The remaining columns indicate the read counts such that each column represents a sample.", "kidney", "Adult zebrafish were infected with 4 8 CFU of ATCC 927 strain Mycobacterium marinum. 4 weeks post infection fish were euthanized and neutrophils were sorted with FACS based on GFP from dissected and suspended kidneys.", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", "Fish homozygous for pycardtpu5 mutation and WT controls originally crossed to transgenic Tgmpx:GFPi114 AB to gain fluorescence in neutrophils fish were maintained according to the standard protocol. The mutant zebrafish line was generated with CRISPR/Cas9 method.", "tissue:kidney|cell type:neutrophils|genotype:wild type for pycard pycardtpu5 crossed to transgenic Tgmpx:GFPi114 AB|treatment:M. marinum infected", "GSM8748652", "GSM8748652: kidney derived neutrophils  wt  Mm infected  rep1; Danio rerio; RNA Seq", "GSM8748652 r1", "GSM8748652", "1", "RNA was extracted and genomic DNA removed from kidney derived neutrophils with QIAGEN RNeasy Micro Plus Kit according to a kit protocol. Library construction was performed on the Illumina platform paired end sequencing  150 bp read length yielding > 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP558767", null, null, "RNA9_W_MM_R_1.fq.gz RNA9_W_MM_R_2.fq.gz", "fastq fastq", 6637369200.0, 22124564.0, "GSM8748652 r1", "0:150 1:150", "A:1824710129;C:1507871608;G:1512676495;T:1791435639;N:675329", 150, 150, null, null, 1824710129, 1507871608, 1512676495, 1791435639, 675329, "SRX27413519", "SRS23843178", "SRA2056436", "University of Tampere", "University of Tampere", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2025-01-21", "Larval", "Larval", "Kidney", "Renal System"], [34960, "SRR32588717", "SRX27895234", "SRS24266236", "SRP568323", "PRJNA1232602", "Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains", "PRJNA1232602", "Other", "In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from Danio rerio", "C2 F2 F K", null, "strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:kidney|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Iso Seq RNA from kidney", "C2 F2 F K", "C2 F2 F K", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "m84270_240904_132604_s1.skera.flnc.fastq.gz", "fastq", 109258150145.0, 61126158.0, "m84270 240904 132604 s1.skera.flnc.fastq.gz", "0:1787.42", "A:32153042096;C:22604112467;G:23394852841;T:31106142741;N:0", 1787, null, null, null, 32153042096, 22604112467, 23394852841, 31106142741, 0, "SRX27895234", "SRS24266236", "SRA2089085", "National Human Genome Research Institute|Translational and Functional Genomics Branch", "National Human Genome Research Institute National Human Genome Research Institute", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-03-06", "Adult", "Adult", "Kidney", "Renal System"], [34970, "SRR32588727", "SRX27895224", "SRS24266224", "SRP568323", "PRJNA1232602", "Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains", "PRJNA1232602", "Other", "In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from Danio rerio", "C2 F2 M K22", null, "strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:kidney|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Iso Seq RNA from kidney", "C2 F2 M K22", "C2 F2 M K22", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "m64467e_240829_144745.hifi_reads.flnc.fastq.gz", "fastq", 14838539048.0, 3383142.0, "m64467e 240829 144745.hifi reads.flnc.fastq.gz", "0:4386.02", "A:4211191682;C:3185079857;G:3320422646;T:4121844863;N:0", 4386, null, null, null, 4211191682, 3185079857, 3320422646, 4121844863, 0, "SRX27895224", "SRS24266224", "SRA2089085", "National Human Genome Research Institute|Translational and Functional Genomics Branch", "National Human Genome Research Institute National Human Genome Research Institute", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-03-06", "Adult", "Adult", "Kidney", "Renal System"], [34971, "SRR32588728", "SRX27895223", "SRS24266234", "SRP568323", "PRJNA1232602", "Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains", "PRJNA1232602", "Other", "In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from Danio rerio", "C2 F2 M K21", null, "strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:Kidney|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Iso Seq RNA from kidney", "C2 F2 M K21", "C2 F2 M K21", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "m84270_240913_170640_s3.skera.flnc.fastq.gz", "fastq", 100849133955.0, 51593887.0, "m84270 240913 170640 s3.skera.flnc.fastq.gz", "0:1954.67", "A:28887816631;C:21568633305;G:22323254809;T:28069429210;N:0", 1954, null, null, null, 28887816631, 21568633305, 22323254809, 28069429210, 0, "SRX27895223", "SRS24266234", "SRA2089085", "National Human Genome Research Institute|Translational and Functional Genomics Branch", "National Human Genome Research Institute National Human Genome Research Institute", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-03-06", "Adult", "Adult", "Kidney", "Renal System"], [38061, "SRR1524243", "SRX661008", "SRS665983", "SRP044781", "PRJNA255848", "Danio rerio Transcriptome", "PRJNA255848", "Transcriptome Analysis", "Transcriptome analysis of 12 zebrafish tissues", "parent bioproject:PRJNA255979", "pubmed:27189481", "Zebrafish Kidney", "Zebrafish Kidney", "F Dr 7", null, "strain:AB|age:5 month|biomaterial provider:INRA|sex:male and female|tissue:Kidney|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish Kidney", "F Dr 7", "F Dr 7", "Total RNA was qualified using an Agilent BioAnalyzer and 1 \u00b5g was used for polyA selection and library construction with Illumina's TruSeq stranded total RNA sample preparation kit according to the manufacturer's instructions TruSeq stranded total RNA SamplePrep Guide RevC", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP044781", null, null, "F_Dr_7_TGACCA_L003_R2.fastq.gz F_Dr_7_TGACCA_L003_R1.fastq.gz", "fastq fastq", 9274322800.0, 46371614.0, "F Dr 7 files", "0:100 1:100", "A:2454755033;C:2186725747;G:2191996485;T:2432936369;N:7909166", 100, 100, null, null, 2454755033, 2186725747, 2191996485, 2432936369, 7909166, "SRX661008", "SRS665983", "SRA176464", "INRA|Fish Physiology and Genomics", "INRA PhyloFish", 2, 0.93261, 0.92609, 0.06804, 0.06819, 0.69757, 0.69771, 0.48358, 0.49333, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "France", "2015-07-24", "Adult", "Adult", "Kidney", "Renal System"], [38266, "SRR1609749", "SRX730402", "SRS719623", "SRP048807", "PRJNA263496", "Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish", "GSE62221", "Transcriptome Analysis", "The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes  the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures  ranging from normal 28\u00b0C to mild 18\u00b0C and severe 10\u00b0C cold  using RNA seq. The tissues varied in the number of cold responsive genes  of which the kidney appeared to be most sensitive  whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns  demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes  such as RNA splicing and proton transport  as well tissue specific processes  such as \u2018negative regulation of endopeptidase activity\u2019 in the kidney. To identify the cis regulatory elements governing the concerted cold responses  the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program  DREME. Eleven motifs  6 known and 5 novel  were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs  such as the AP 1 and STAT1 binding sites  are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool  we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures", null, "pubmed:26227973", null, "kidney10", "GSM1523044", null, "source name:kidney|tissue:kidney|temperature:10\u00b0C|strain:Tubingen|age:6 mpf", "kidney10", "Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html  which is a python based script  was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "kidney", "fish were maintained 12h to adapt low temperatures and then killed by pithing", "Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:kidney|temperature:10\u00b0C|strain:Tubingen|age:6 mpf", "GSM1523044", "GSM1523044: kidney10; Danio rerio; RNA Seq", "GSM1523044", null, "1", "Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1523044", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP048807", null, null, "kidney10_1.fq.gz kidney10_2.fq.gz", "fastq fastq", 4315071200.0, 21575356.0, "GSM1523044 r1", "0:100 1:100", "A:1152823680;C:1012018705;G:1003451232;T:1146696176;N:81407", 100, 100, null, null, 1152823680, 1012018705, 1003451232, 1146696176, 81407, "SRX730402", "SRS719623", "SRA189240", "GEO", "Shanghai Ocean University", 2, 0.95345, 0.94751, 0.05494, 0.05445, 0.7455, 0.74856, 0.53555, 0.52518, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-10-09", "Adult", "Adult", "Kidney", "Renal System"], [38267, "SRR1609748", "SRX730401", "SRS719622", "SRP048807", "PRJNA263496", "Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish", "GSE62221", "Transcriptome Analysis", "The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes  the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures  ranging from normal 28\u00b0C to mild 18\u00b0C and severe 10\u00b0C cold  using RNA seq. The tissues varied in the number of cold responsive genes  of which the kidney appeared to be most sensitive  whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns  demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes  such as RNA splicing and proton transport  as well tissue specific processes  such as \u2018negative regulation of endopeptidase activity\u2019 in the kidney. To identify the cis regulatory elements governing the concerted cold responses  the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program  DREME. Eleven motifs  6 known and 5 novel  were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs  such as the AP 1 and STAT1 binding sites  are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool  we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures", null, "pubmed:26227973", null, "kidney18", "GSM1523043", null, "source name:kidney|tissue:kidney|temperature:18\u00b0C|strain:Tubingen|age:6 mpf", "kidney18", "Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html  which is a python based script  was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "kidney", "fish were maintained 12h to adapt low temperatures and then killed by pithing", "Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:kidney|temperature:18\u00b0C|strain:Tubingen|age:6 mpf", "GSM1523043", "GSM1523043: kidney18; Danio rerio; RNA Seq", "GSM1523043", null, "1", "Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1523043", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP048807", null, null, "kidney18_1.fq.gz kidney18_2.fq.gz", "fastq fastq", 3876913200.0, 19384566.0, "GSM1523043 r1", "0:100 1:100", "A:1015185474;C:927880228;G:918980502;T:1014805063;N:61933", 100, 100, null, null, 1015185474, 927880228, 918980502, 1014805063, 61933, "SRX730401", "SRS719622", "SRA189240", "GEO", "Shanghai Ocean University", 2, 0.94462, 0.93747, 0.03424, 0.03391, 0.72243, 0.7262, 0.49704, 0.4967, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-10-09", "Adult", "Adult", "Kidney", "Renal System"], [38268, "SRR1609747", "SRX730400", "SRS719621", "SRP048807", "PRJNA263496", "Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish", "GSE62221", "Transcriptome Analysis", "The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes  the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures  ranging from normal 28\u00b0C to mild 18\u00b0C and severe 10\u00b0C cold  using RNA seq. The tissues varied in the number of cold responsive genes  of which the kidney appeared to be most sensitive  whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns  demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes  such as RNA splicing and proton transport  as well tissue specific processes  such as \u2018negative regulation of endopeptidase activity\u2019 in the kidney. To identify the cis regulatory elements governing the concerted cold responses  the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program  DREME. Eleven motifs  6 known and 5 novel  were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs  such as the AP 1 and STAT1 binding sites  are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool  we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures", null, "pubmed:26227973", null, "kidney28", "GSM1523042", null, "source name:kidney|tissue:kidney|temperature:28\u00b0C|strain:Tubingen|age:6 mpf", "kidney28", "Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html  which is a python based script  was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "kidney", "fish were maintained 12h to adapt low temperatures and then killed by pithing", "Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:kidney|temperature:28\u00b0C|strain:Tubingen|age:6 mpf", "GSM1523042", "GSM1523042: kidney28; Danio rerio; RNA Seq", "GSM1523042", null, "1", "Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1523042", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP048807", null, null, "kidney28_1.fq.gz kidney28_2.fq.gz", "fastq fastq", 4590135400.0, 22950677.0, "GSM1523042 r1", "0:100 1:100", "A:1216408799;C:1078601401;G:1076605621;T:1218430409;N:89170", 100, 100, null, null, 1216408799, 1078601401, 1076605621, 1218430409, 89170, "SRX730400", "SRS719621", "SRA189240", "GEO", "Shanghai Ocean University", 2, 0.96555, 0.9628, 0.03027, 0.03021, 0.79015, 0.79269, 0.26504, 0.27074, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-10-09", "Adult", "Adult", "Kidney", "Renal System"], [38296, "SRR1647681", "SRX756916", "SRS742120", "SRP049663", "PRJNA266803", "Spring Varaemia of Carp Virus SVCV infection of adult zebrafish", "GSE63133", "Transcriptome Analysis", "During viral infection  a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here  we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection  i.e. 6h and 24h post infection. For 12 zebrafish IRFs  we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues  but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7  which together with DrIRF3  was highly induced by SVCV infection. For type I IFNs  zebrafish has four IFN genes  three of which  IFN1/2/3  particularly IFN 1 and IFN 3  were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately  50 \u00b5L SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection  and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.", null, "pubmed:25535281", null, "24K", "GSM1541905", null, "source name:head kidney|tissue:head kidney|disease state:24h post SVCV infection", "24K", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "head kidney", null, "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:head kidney|disease state:24h post SVCV infection", "GSM1541905", "GSM1541905: 24K; Danio rerio; RNA Seq", "GSM1541905", null, "1", "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1541905", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP049663", null, null, "24K_GTGAAA_L003_R1.fastq", "fastq", 1020487560.0, 20009560.0, "GSM1541905 r1", "0:51", "A:266117014;C:246797067;G:240014464;T:267491299;N:67716", 51, null, null, null, 266117014, 246797067, 240014464, 267491299, 67716, "SRX756916", "SRS742120", "SRA200717", "GEO", "Institute of Hydrobiology, Chinese Academy of Sciences", 1, 0.92411, null, 0.07686, null, 0.68647, null, 0.4627, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-11-10", "Undetermined", "Adult", "Kidney", "Renal System"], [38297, "SRR1647680", "SRX756915", "SRS742117", "SRP049663", "PRJNA266803", "Spring Varaemia of Carp Virus SVCV infection of adult zebrafish", "GSE63133", "Transcriptome Analysis", "During viral infection  a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here  we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection  i.e. 6h and 24h post infection. For 12 zebrafish IRFs  we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues  but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7  which together with DrIRF3  was highly induced by SVCV infection. For type I IFNs  zebrafish has four IFN genes  three of which  IFN1/2/3  particularly IFN 1 and IFN 3  were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately  50 \u00b5L SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection  and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.", null, "pubmed:25535281", null, "6K", "GSM1541904", null, "source name:head kidney|tissue:head kidney|disease state:6h post SVCV infection", "6K", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "head kidney", null, "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:head kidney|disease state:6h post SVCV infection", "GSM1541904", "GSM1541904: 6K; Danio rerio; RNA Seq", "GSM1541904", null, "1", "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1541904", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP049663", null, null, "6K_GTCCGC_L003_R1.fastq", "fastq", 929436036.0, 18224236.0, "GSM1541904 r1", "0:51", "A:242005719;C:225485975;G:219890494;T:241993975;N:59873", 51, null, null, null, 242005719, 225485975, 219890494, 241993975, 59873, "SRX756915", "SRS742117", "SRA200717", "GEO", "Institute of Hydrobiology, Chinese Academy of Sciences", 1, 0.92547, null, 0.09105, null, 0.69264, null, 0.49166, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-11-10", "Undetermined", "Adult", "Kidney", "Renal System"], [38298, "SRR1647679", "SRX756914", "SRS742116", "SRP049663", "PRJNA266803", "Spring Varaemia of Carp Virus SVCV infection of adult zebrafish", "GSE63133", "Transcriptome Analysis", "During viral infection  a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here  we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection  i.e. 6h and 24h post infection. For 12 zebrafish IRFs  we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues  but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7  which together with DrIRF3  was highly induced by SVCV infection. For type I IFNs  zebrafish has four IFN genes  three of which  IFN1/2/3  particularly IFN 1 and IFN 3  were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately  50 \u00b5L SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection  and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.", null, "pubmed:25535281", null, "0K", "GSM1541903", null, "source name:head kidney|tissue:head kidney|disease state:un infected", "0K", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "head kidney", null, "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:head kidney|disease state:un infected", "GSM1541903", "GSM1541903: 0K; Danio rerio; RNA Seq", "GSM1541903", null, "1", "Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1541903", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP049663", null, null, "0K_CCGTCC_L003_R1.fastq", "fastq", 1077979095.0, 21136845.0, "GSM1541903 r1", "0:51", "A:280277150;C:261348733;G:255721013;T:280562071;N:70128", 51, null, null, null, 280277150, 261348733, 255721013, 280562071, 70128, "SRX756914", "SRS742116", "SRA200717", "GEO", "Institute of Hydrobiology, Chinese Academy of Sciences", 1, 0.92545, null, 0.08181, null, 0.68373, null, 0.49408, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2014-11-10", "Undetermined", "Adult", "Kidney", "Renal System"], [41473, "SRR5457065", "SRX2745133", "SRS1761840", "SRP092128", "PRJNA350712", "Phylogenetic analysis of intron retention in vertebrates", "PRJNA350712", "Other", "Our study is detailing new evidence for transcriptomic complexity realized by a mechanism of orchestrated intron retention.", null, null, null, "zebrafish granulocytes", "dre granulocytes", null, "strain: |age:3 month 6 month|sex:male|tissue:kidney marrow|biomaterial provider:Graham Lieschke|cell type:granulocyte|health state:healthy|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish granulocytes", "dre gran TruSeq RNA paired Ill HiSeq2000", "dre gran TruSeq RNA paired Ill HiSeq2000", "RNA seq libraries were prepared from >1  g of total RNA using TruSeq RNA sample prep kit Illumina according to the manufacturers\u00cd instructions", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP092128", null, null, "Zebrafish-1_ZF1_1.fastq.gz Zebrafish-1_ZF1_2.fastq.gz Zebrafish-1_ZF3_1.fastq.gz Zebrafish-1_ZF3_2.fastq.gz", "fastq fastq fastq fastq", 27103033264.0, 134173432.0, "Zebrafish 1 ZF3 2.fastq.gz", "0:101 1:101", "A:7205178092;C:6377884075;G:6326441274;T:7192445241;N:1084582", 101, 101, null, null, 7205178092, 6377884075, 6326441274, 7192445241, 1084582, "SRX2745133", "SRS1761840", "SRA555068", "Centenary Institute|Gene &amp; Stem Cell Therapy Program", "Centenary Institute", 2, 0.97153, 0.98059, 0.09216, 0.09282, 0.72679, 0.7234, 0.46875, 0.47002, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Australia", "2017-04-19", "Adult", "Adult", "Kidney", "Renal System"], [41873, "SRR5320505", "SRX2619910", "SRS2029873", "SRP101556", "PRJNA378487", "Transcriptional profiling of the zebrafish proximal tubule", "GSE95808", "Transcriptome Analysis", "The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney  the pronephros  represents a simplified form of the mammalian organ  yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here  we establish a high resolution expression profile of isolated  GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation  proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue", null, "pubmed:31188030", null, "Morpholino 7", "GSM2526320", null, "tissue:larval kidney|line:tgPT::EGFP|genotype/variation:Hnf1b depleted", "Morpholino 7", "Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts.", "larval kidney", null, "Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols", null, "line:tgPT::EGFP|genotype/variation:Hnf1b depleted", "GSM2526320", "GSM2526320: Morpholino 7; Danio rerio; RNA Seq", "GSM2526320", null, "1", "Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols", "GEO Accession:GSM2526320", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP101556", null, null, "C6H9AANXX-1531-06-1-1_CTTGTAAT_L001_R1_001.fastq.gz C6H9AANXX-1531-06-1-1_CTTGTAAT_L001_R2_001.fastq.gz", "fastq fastq", 8670821250.0, 34683285.0, "GSM2526320 r1", "0:125 1:125", "A:2285357364;C:2049868144;G:2107192972;T:2225558024;N:2844746", 125, 125, null, null, 2285357364, 2049868144, 2107192972, 2225558024, 2844746, "SRX2619910", "SRS2029873", "SRA543390", "GEO", "Molecular Medicine and Pathology, University of Auckland", 2, 0.96682, 0.96763, 0.08369, 0.08426, 0.69296, 0.69493, 0.47739, 0.47931, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "New Zealand", "2017-03-08", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [41874, "SRR5320504", "SRX2619909", "SRS2029872", "SRP101556", "PRJNA378487", "Transcriptional profiling of the zebrafish proximal tubule", "GSE95808", "Transcriptome Analysis", "The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney  the pronephros  represents a simplified form of the mammalian organ  yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here  we establish a high resolution expression profile of isolated  GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation  proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue", null, "pubmed:31188030", null, "Morpholino 5", "GSM2526319", null, "tissue:larval kidney|line:tgPT::EGFP|genotype/variation:Hnf1b depleted", "Morpholino 5", "Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts.", "larval kidney", null, "Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols", null, "line:tgPT::EGFP|genotype/variation:Hnf1b depleted", "GSM2526319", "GSM2526319: Morpholino 5; Danio rerio; RNA Seq", "GSM2526319", null, "1", "Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols", "GEO Accession:GSM2526319", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP101556", null, null, "C6H9AANXX-1531-05-1-1_CAGATCAT_L001_R1_001.fastq.gz C6H9AANXX-1531-05-1-1_CAGATCAT_L001_R2_001.fastq.gz", "fastq fastq", 9864273500.0, 39457094.0, "GSM2526319 r1", "0:125 1:125", "A:2628741477;C:2304848464;G:2364915536;T:2562525014;N:3243009", 125, 125, null, null, 2628741477, 2304848464, 2364915536, 2562525014, 3243009, "SRX2619909", "SRS2029872", "SRA543390", "GEO", "Molecular Medicine and Pathology, University of Auckland", 2, 0.96115, 0.96161, 0.10876, 0.10854, 0.67495, 0.67616, 0.45304, 0.45767, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "New Zealand", "2017-03-08", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [41875, "SRR5320503", "SRX2619908", "SRS2029871", "SRP101556", "PRJNA378487", "Transcriptional profiling of the zebrafish proximal tubule", "GSE95808", "Transcriptome Analysis", "The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney  the pronephros  represents a simplified form of the mammalian organ  yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here  we establish a high resolution expression profile of isolated  GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation  proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue", null, "pubmed:31188030", null, "Morpholino 4", "GSM2526318", null, "tissue:larval kidney|line:tgPT::EGFP|genotype/variation:Hnf1b depleted", "Morpholino 4", "Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts.", "larval kidney", null, "Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols", null, "line:tgPT::EGFP|genotype/variation:Hnf1b depleted", "GSM2526318", "GSM2526318: Morpholino 4; Danio rerio; RNA Seq", "GSM2526318", null, "1", "Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols", "GEO Accession:GSM2526318", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP101556", null, null, "C6H9AANXX-1531-04-1-1_GCCAATAT_L001_R1_001.fastq.gz C6H9AANXX-1531-04-1-1_GCCAATAT_L001_R2_001.fastq.gz", "fastq fastq", 8503939500.0, 34015758.0, "GSM2526318 r1", "0:125 1:125", "A:2251120561;C:2002327793;G:2052310864;T:2195401798;N:2778484", 125, 125, null, null, 2251120561, 2002327793, 2052310864, 2195401798, 2778484, "SRX2619908", "SRS2029871", "SRA543390", "GEO", "Molecular Medicine and Pathology, University of Auckland", 2, 0.96344, 0.96379, 0.09973, 0.09974, 0.68043, 0.68264, 0.46613, 0.46851, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "New Zealand", "2017-03-08", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [41876, "SRR5320502", "SRX2619907", "SRS2029870", "SRP101556", "PRJNA378487", "Transcriptional profiling of the zebrafish proximal tubule", "GSE95808", "Transcriptome Analysis", "The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney  the pronephros  represents a simplified form of the mammalian organ  yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here  we establish a high resolution expression profile of isolated  GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation  proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue", null, "pubmed:31188030", null, "Control 3", "GSM2526317", null, "tissue:larval kidney|line:tgPT::EGFP|genotype/variation:wild type", "Control 3", "Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts.", "larval kidney", null, "Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols", null, "line:tgPT::EGFP|genotype/variation:wild type", "GSM2526317", "GSM2526317: Control 3; Danio rerio; RNA Seq", "GSM2526317", null, "1", "Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols", "GEO Accession:GSM2526317", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP101556", null, null, "C6H9AANXX-1531-03-1-1_ACAGTGAT_L001_R1_001.fastq.gz C6H9AANXX-1531-03-1-1_ACAGTGAT_L001_R2_001.fastq.gz", "fastq fastq", 9619758500.0, 38479034.0, "GSM2526317 r1", "0:125 1:125", "A:2561625595;C:2249183851;G:2312313710;T:2493482524;N:3152820", 125, 125, null, null, 2561625595, 2249183851, 2312313710, 2493482524, 3152820, "SRX2619907", "SRS2029870", "SRA543390", "GEO", "Molecular Medicine and Pathology, University of Auckland", 2, 0.96067, 0.96218, 0.10832, 0.10898, 0.66675, 0.66866, 0.47609, 0.47441, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "New Zealand", "2017-03-08", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [41877, "SRR5320501", "SRX2619906", "SRS2029869", "SRP101556", "PRJNA378487", "Transcriptional profiling of the zebrafish proximal tubule", "GSE95808", "Transcriptome Analysis", "The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney  the pronephros  represents a simplified form of the mammalian organ  yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here  we establish a high resolution expression profile of isolated  GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation  proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue", null, "pubmed:31188030", null, "Control 2", "GSM2526316", null, "tissue:larval kidney|line:tgPT::EGFP|genotype/variation:wild type", "Control 2", "Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts.", "larval kidney", null, "Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols", null, "line:tgPT::EGFP|genotype/variation:wild type", "GSM2526316", "GSM2526316: Control 2; Danio rerio; RNA Seq", "GSM2526316", null, "1", "Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols", "GEO Accession:GSM2526316", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP101556", null, null, "C6H9AANXX-1531-02-1-1_TGACCAAT_L001_R1_001.fastq.gz C6H9AANXX-1531-02-1-1_TGACCAAT_L001_R2_001.fastq.gz", "fastq fastq", 8939151000.0, 35756604.0, "GSM2526316 r1", "0:125 1:125", "A:2379909844;C:2090182914;G:2143061952;T:2323063658;N:2932632", 125, 125, null, null, 2379909844, 2090182914, 2143061952, 2323063658, 2932632, "SRX2619906", "SRS2029869", "SRA543390", "GEO", "Molecular Medicine and Pathology, University of Auckland", 2, 0.96176, 0.96203, 0.10658, 0.10717, 0.67087, 0.67194, 0.45961, 0.46137, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "New Zealand", "2017-03-08", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [41878, "SRR5320500", "SRX2619905", "SRS2029868", "SRP101556", "PRJNA378487", "Transcriptional profiling of the zebrafish proximal tubule", "GSE95808", "Transcriptome Analysis", "The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney  the pronephros  represents a simplified form of the mammalian organ  yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here  we establish a high resolution expression profile of isolated  GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation  proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue", null, "pubmed:31188030", null, "Control 1", "GSM2526315", null, "tissue:larval kidney|line:tgPT::EGFP|genotype/variation:wild type", "Control 1", "Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts.", "larval kidney", null, "Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols", null, "line:tgPT::EGFP|genotype/variation:wild type", "GSM2526315", "GSM2526315: Control 1; Danio rerio; RNA Seq", "GSM2526315", null, "1", "Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols", "GEO Accession:GSM2526315", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP101556", null, null, "C6H9AANXX-1531-01-1-1_CGATGTAT_L001_R1_001.fastq.gz C6H9AANXX-1531-01-1-1_CGATGTAT_L001_R2_001.fastq.gz", "fastq fastq", 9579790250.0, 38319161.0, "GSM2526315 r1", "0:125 1:125", "A:2520690618;C:2269535412;G:2326632146;T:2459796830;N:3135244", 125, 125, null, null, 2520690618, 2269535412, 2326632146, 2459796830, 3135244, "SRX2619905", "SRS2029868", "SRA543390", "GEO", "Molecular Medicine and Pathology, University of Auckland", 2, 0.96456, 0.96615, 0.08928, 0.09003, 0.68373, 0.6856, 0.46544, 0.46416, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "New Zealand", "2017-03-08", "Multi-stage", "Multi-stage", "Kidney", "Renal System"], [47595, "SRR6661145", "SRX3638241", "SRS2904492", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "KidWTPHZ 3", "GSM2975189", null, "source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type", "KidWTPHZ 3", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type", "GSM2975189", "GSM2975189: KidWTPHZ 3; Danio rerio; RNA Seq", "GSM2975189", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975189", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "KidWTPHZ_3.fastq.gz", "fastq", 858099990.0, 16825490.0, "GSM2975189 r1", "0:51", "A:231903062;C:197865548;G:200825484;T:227491985;N:13911", 51, null, null, null, 231903062, 197865548, 200825484, 227491985, 13911, "SRX3638241", "SRS2904492", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.9605, null, 0.10316, null, 0.70721, null, 0.51089, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Kidney", "Renal System"], [47596, "SRR6661144", "SRX3638240", "SRS2904491", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "KidWTPHZ 2", "GSM2975188", null, "source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type", "KidWTPHZ 2", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type", "GSM2975188", "GSM2975188: KidWTPHZ 2; Danio rerio; RNA Seq", "GSM2975188", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975188", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "KidWTPHZ_2.fastq.gz", "fastq", 799571013.0, 15677863.0, "GSM2975188 r1", "0:51", "A:217401512;C:183178629;G:185275617;T:213702318;N:12937", 51, null, null, null, 217401512, 183178629, 185275617, 213702318, 12937, "SRX3638240", "SRS2904491", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.96209, null, 0.10882, null, 0.70861, null, 0.5149, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Kidney", "Renal System"], [47597, "SRR6661143", "SRX3638239", "SRS2904490", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "KidWTPHZ 1", "GSM2975187", null, "source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type", "KidWTPHZ 1", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type", "GSM2975187", "GSM2975187: KidWTPHZ 1; Danio rerio; RNA Seq", "GSM2975187", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975187", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "KidWTPHZ_1.fastq.gz", "fastq", 816038505.0, 16000755.0, "GSM2975187 r1", "0:51", "A:218420574;C:190260181;G:192288409;T:215056318;N:13023", 51, null, null, null, 218420574, 190260181, 192288409, 215056318, 13023, "SRX3638239", "SRS2904490", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.96264, null, 0.09527, null, 0.70834, null, 0.51477, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Kidney", "Renal System"], [47598, "SRR6661142", "SRX3638238", "SRS2904489", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "KidWT 3", "GSM2975186", null, "source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type", "KidWT 3", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type", "GSM2975186", "GSM2975186: KidWT 3; Danio rerio; RNA Seq", "GSM2975186", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975186", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "KidWT_3.fastq.gz", "fastq", 852094026.0, 16707726.0, "GSM2975186 r1", "0:51", "A:234167802;C:192807979;G:194651214;T:230453461;N:13570", 51, null, null, null, 234167802, 192807979, 194651214, 230453461, 13570, "SRX3638238", "SRS2904489", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.95788, null, 0.12336, null, 0.70258, null, 0.48964, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Kidney", "Renal System"], [47599, "SRR6661141", "SRX3638237", "SRS2904488", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "KidWT 2", "GSM2975185", null, "source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type", "KidWT 2", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type", "GSM2975185", "GSM2975185: KidWT 2; Danio rerio; RNA Seq", "GSM2975185", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975185", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "KidWT_2.fastq.gz", "fastq", 969772038.0, 19015138.0, "GSM2975185 r1", "0:51", "A:265582126;C:219526888;G:222468938;T:262178447;N:15639", 51, null, null, null, 265582126, 219526888, 222468938, 262178447, 15639, "SRX3638237", "SRS2904488", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.95803, null, 0.12522, null, 0.69794, null, 0.50805, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Kidney", "Renal System"], [47600, "SRR6661140", "SRX3638236", "SRS2904487", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "KidWT 1", "GSM2975184", null, "source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type", "KidWT 1", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type", "GSM2975184", "GSM2975184: KidWT 1; Danio rerio; RNA Seq", "GSM2975184", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975184", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "KidWT_1.fastq.gz", "fastq", 815590011.0, 15991961.0, "GSM2975184 r1", "0:51", "A:224190865;C:184406547;G:186159880;T:220819162;N:13557", 51, null, null, null, 224190865, 184406547, 186159880, 220819162, 13557, "SRX3638236", "SRS2904487", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.95883, null, 0.13181, null, 0.7023, null, 0.49523, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Kidney", "Renal System"], [47601, "SRR6661139", "SRX3638235", "SRS2904486", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "KidDKOPHZ 3", "GSM2975183", null, "source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "KidDKOPHZ 3", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "GSM2975183", "GSM2975183: KidDKOPHZ 3; Danio rerio; RNA Seq", "GSM2975183", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975183", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "KidDKOPHZ_3.fastq.gz", "fastq", 789588885.0, 15482135.0, "GSM2975183 r1", "0:51", "A:215354577;C:180286176;G:181162894;T:212772248;N:12990", 51, null, null, null, 215354577, 180286176, 181162894, 212772248, 12990, "SRX3638235", "SRS2904486", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.92385, null, 0.10405, null, 0.70471, null, 0.50985, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Kidney", "Renal System"], [47602, "SRR6661138", "SRX3638234", "SRS2904485", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "KidDKOPHZ 2", "GSM2975182", null, "source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "KidDKOPHZ 2", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "GSM2975182", "GSM2975182: KidDKOPHZ 2; Danio rerio; RNA Seq", "GSM2975182", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975182", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "KidDKOPHZ_2.fastq.gz", "fastq", 866844552.0, 16996952.0, "GSM2975182 r1", "0:51", "A:235445628;C:198901971;G:200334068;T:232148841;N:14044", 51, null, null, null, 235445628, 198901971, 200334068, 232148841, 14044, "SRX3638234", "SRS2904485", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.92657, null, 0.10886, null, 0.71112, null, 0.52093, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Kidney", "Renal System"], [47603, "SRR6661137", "SRX3638233", "SRS2904484", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "KidDKOPHZ 1", "GSM2975181", null, "source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "KidDKOPHZ 1", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "GSM2975181", "GSM2975181: KidDKOPHZ 1; Danio rerio; RNA Seq", "GSM2975181", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975181", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "KidDKOPHZ_1.fastq.gz", "fastq", 795526560.0, 15598560.0, "GSM2975181 r1", "0:51", "A:216666052;C:181785239;G:183159054;T:213903089;N:13126", 51, null, null, null, 216666052, 181785239, 183159054, 213903089, 13126, "SRX3638233", "SRS2904484", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.92522, null, 0.10277, null, 0.7121, null, 0.51721, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Kidney", "Renal System"], [47604, "SRR6661136", "SRX3638232", "SRS2904483", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "KidDKO 3", "GSM2975180", null, "source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "KidDKO 3", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "GSM2975180", "GSM2975180: KidDKO 3; Danio rerio; RNA Seq", "GSM2975180", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975180", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "KidDKO_3.fastq.gz", "fastq", 699170577.0, 13709227.0, "GSM2975180 r1", "0:51", "A:191094810;C:157413925;G:158857752;T:191792628;N:11462", 51, null, null, null, 191094810, 157413925, 158857752, 191792628, 11462, "SRX3638232", "SRS2904483", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.9183, null, 0.12207, null, 0.7083, null, 0.52994, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Kidney", "Renal System"], [47605, "SRR6661135", "SRX3638231", "SRS2904482", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "KidDKO 2", "GSM2975179", null, "source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "KidDKO 2", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "GSM2975179", "GSM2975179: KidDKO 2; Danio rerio; RNA Seq", "GSM2975179", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975179", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "KidDKO_2.fastq.gz", "fastq", 720757194.0, 14132494.0, "GSM2975179 r1", "0:51", "A:198433339;C:163064446;G:163967236;T:195280391;N:11782", 51, null, null, null, 198433339, 163064446, 163967236, 195280391, 11782, "SRX3638231", "SRS2904482", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.92921, null, 0.11261, null, 0.7063, null, 0.52644, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Kidney", "Renal System"], [47606, "SRR6661134", "SRX3638230", "SRS2904481", "SRP131956", "PRJNA432507", "Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne", "GSE109978", "Transcriptome Analysis", "RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on T\u00fc wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish T\u00fc  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.", null, "pubmed:30248094", null, "KidDKO 1", "GSM2975178", null, "source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "KidDKO 1", "Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.", "whole animal", "Adult zebrafish are treated in Phenylhydrazine containg 2.5 \u00b5g/ml fish water", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "Normal zebrafish husbandary", "tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO", "GSM2975178", "GSM2975178: KidDKO 1; Danio rerio; RNA Seq", "GSM2975178", null, "1", "TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation", "GEO Accession:GSM2975178", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131956", null, null, "KidDKO_1.fastq.gz", "fastq", 835548606.0, 16383306.0, "GSM2975178 r1", "0:51", "A:227900020;C:191118125;G:192603640;T:223913065;N:13756", 51, null, null, null, 227900020, 191118125, 192603640, 223913065, 13756, "SRX3638230", "SRS2904481", "SRA654641", "GEO", "Laboratory of Molecular Biology, NIH/NIDDK", 1, 0.93166, null, 0.10926, null, 0.7063, null, 0.50705, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2018-02-01", "Adult", "Adult", "Kidney", "Renal System"], [48074, "SRR7008287", "SRX3940775", "SRS3171576", "SRP140471", "PRJNA450343", "A Zebrafish Acromegaly Model Elevates DNA Damage and Impairs DNA Repair Pathways", "GSE113169", "Transcriptome Analysis", "Acromegaly is a pathological condition due to excess growth hormone GH secretion. Acromegaly patients exhibit a deterioration of health and many associated complications  such as cardiovascular issues  arthritis  kidney diseases  muscular weakness  and colon cancer. Since these complications are generalized throughout the body  we investigated the effect of GH excess on cellular integrity. Here  we established stable acromegaly model zebrafish lines that overexpress tilapia GH and the red fluorescence protein RFP reporter gene for tracking GH gene expression throughout generations  and performed RNA Seq data analysis from different organs. Intriguingly  heatmap and Expression2Kinases X2K analysis revealed the enrichment of DNA damage markers in various organs. Moreover  H2A.X immunostaining analysis in acromegaly zebrafish larvae and the adult acromegaly model brain and muscle showed a robust increase in the number of DNA damaged cells. Using Gene Set Enrichment Analysis GSEA  we found that the acromegaly zebrafish model had impaired DNA repair pathways in the liver  such as double strand break DSB  homologous recombination repair HRR  non homologous end joining NHEJ  nucleotide excision repair NER  and translesion synthesis TLS. Interestingly  the impairment of DNA repair was even more prominent in acromegaly model than in aged zebrafish three years old. Thus  our study demonstrates that affection of cellular integrity is characteristic of acromegaly Overall design: Total mRNA obtained from 1 years old acromegaly zebrafish model muscle  brain  kidney  liver and 3 dpf larvae compared to wild type WT zebrafish were generated by deep sequencing using Illumina.", null, "pubmed:30336646;pubmed:32517323;pubmed:33849304", null, "Kidney WT rep2", "GSM3098423", null, "source name:Kidney|genotype:wild type|tissue:Kidney|age:1 year old", "Kidney WT rep2", "Illumina Casava1.7 software used for basecalling. HISAT2 software was used according to the instructions from the program designers to map the raw reads of acromegaly and WT samples to zebrafish genome reference GRCz10 retrieved from Ensembl database together with the annotation file. The Cufflinks pipeline was used to assign reads to known transcripts and test for differential expression between acromegaly model and the WT samples. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads FPKM. Genome build: GRCz10 Supplementary files format and content: One tab delimited text file containing all FPKM values for all Samples.", "Kidney", null, "tissues were removed  and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.", null, "genotype:wild type|tissue:Kidney|age:1 year old", "GSM3098423", "GSM3098423: Kidney WT rep2; Danio rerio; RNA Seq", "GSM3098423", null, "1", "tissues were removed  and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.", "GEO Accession:GSM3098423", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP140471", null, null, "WT_K6_Kidney_21_1.fq.gz WT_K6_Kidney_21_2.fq.gz", "fastq fastq", 452219400.0, 2261097.0, "GSM3098423 r1", "0:100 1:100", "A:119997841;C:105588197;G:105552577;T:121010097;N:70688", 100, 100, null, null, 119997841, 105588197, 105552577, 121010097, 70688, "SRX3940775", "SRS3171576", "SRA690975", "GEO", "Aquatic Molecular Biology and Biotechnology, Aquatic Bioscience, The University of Tokyo", 2, 0.93414, 0.93513, 0.07437, 0.07244, 0.71622, 0.71593, 0.5221, 0.52872, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-04-16", "Adult", "Adult", "Kidney", "Renal System"], [48075, "SRR7008286", "SRX3940774", "SRS3171575", "SRP140471", "PRJNA450343", "A Zebrafish Acromegaly Model Elevates DNA Damage and Impairs DNA Repair Pathways", "GSE113169", "Transcriptome Analysis", "Acromegaly is a pathological condition due to excess growth hormone GH secretion. Acromegaly patients exhibit a deterioration of health and many associated complications  such as cardiovascular issues  arthritis  kidney diseases  muscular weakness  and colon cancer. Since these complications are generalized throughout the body  we investigated the effect of GH excess on cellular integrity. Here  we established stable acromegaly model zebrafish lines that overexpress tilapia GH and the red fluorescence protein RFP reporter gene for tracking GH gene expression throughout generations  and performed RNA Seq data analysis from different organs. Intriguingly  heatmap and Expression2Kinases X2K analysis revealed the enrichment of DNA damage markers in various organs. Moreover  H2A.X immunostaining analysis in acromegaly zebrafish larvae and the adult acromegaly model brain and muscle showed a robust increase in the number of DNA damaged cells. Using Gene Set Enrichment Analysis GSEA  we found that the acromegaly zebrafish model had impaired DNA repair pathways in the liver  such as double strand break DSB  homologous recombination repair HRR  non homologous end joining NHEJ  nucleotide excision repair NER  and translesion synthesis TLS. Interestingly  the impairment of DNA repair was even more prominent in acromegaly model than in aged zebrafish three years old. Thus  our study demonstrates that affection of cellular integrity is characteristic of acromegaly Overall design: Total mRNA obtained from 1 years old acromegaly zebrafish model muscle  brain  kidney  liver and 3 dpf larvae compared to wild type WT zebrafish were generated by deep sequencing using Illumina.", null, "pubmed:30336646;pubmed:32517323;pubmed:33849304", null, "Kidney WT rep1", "GSM3098422", null, "source name:Kidney|genotype:wild type|tissue:Kidney|age:1 year old", "Kidney WT rep1", "Illumina Casava1.7 software used for basecalling. HISAT2 software was used according to the instructions from the program designers to map the raw reads of acromegaly and WT samples to zebrafish genome reference GRCz10 retrieved from Ensembl database together with the annotation file. The Cufflinks pipeline was used to assign reads to known transcripts and test for differential expression between acromegaly model and the WT samples. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads FPKM. Genome build: GRCz10 Supplementary files format and content: One tab delimited text file containing all FPKM values for all Samples.", "Kidney", null, "tissues were removed  and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.", null, "genotype:wild type|tissue:Kidney|age:1 year old", "GSM3098422", "GSM3098422: Kidney WT rep1; Danio rerio; RNA Seq", "GSM3098422", null, "1", "tissues were removed  and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.", "GEO Accession:GSM3098422", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP140471", null, null, "WT_K4_Kidney_20_1.fq.gz WT_K4_Kidney_20_2.fq.gz", "fastq fastq", 468105400.0, 2340527.0, "GSM3098422 r1", "0:100 1:100", "A:125918771;C:107695952;G:107289472;T:127127892;N:73313", 100, 100, null, null, 125918771, 107695952, 107289472, 127127892, 73313, "SRX3940774", "SRS3171575", "SRA690975", "GEO", "Aquatic Molecular Biology and Biotechnology, Aquatic Bioscience, The University of Tokyo", 2, 0.93618, 0.93627, 0.08989, 0.08801, 0.73026, 0.72971, 0.54855, 0.55327, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-04-16", "Adult", "Adult", "Kidney", "Renal System"], [48076, "SRR7008285", "SRX3940773", "SRS3171574", "SRP140471", "PRJNA450343", "A Zebrafish Acromegaly Model Elevates DNA Damage and Impairs DNA Repair Pathways", "GSE113169", "Transcriptome Analysis", "Acromegaly is a pathological condition due to excess growth hormone GH secretion. Acromegaly patients exhibit a deterioration of health and many associated complications  such as cardiovascular issues  arthritis  kidney diseases  muscular weakness  and colon cancer. Since these complications are generalized throughout the body  we investigated the effect of GH excess on cellular integrity. Here  we established stable acromegaly model zebrafish lines that overexpress tilapia GH and the red fluorescence protein RFP reporter gene for tracking GH gene expression throughout generations  and performed RNA Seq data analysis from different organs. Intriguingly  heatmap and Expression2Kinases X2K analysis revealed the enrichment of DNA damage markers in various organs. Moreover  H2A.X immunostaining analysis in acromegaly zebrafish larvae and the adult acromegaly model brain and muscle showed a robust increase in the number of DNA damaged cells. Using Gene Set Enrichment Analysis GSEA  we found that the acromegaly zebrafish model had impaired DNA repair pathways in the liver  such as double strand break DSB  homologous recombination repair HRR  non homologous end joining NHEJ  nucleotide excision repair NER  and translesion synthesis TLS. Interestingly  the impairment of DNA repair was even more prominent in acromegaly model than in aged zebrafish three years old. Thus  our study demonstrates that affection of cellular integrity is characteristic of acromegaly Overall design: Total mRNA obtained from 1 years old acromegaly zebrafish model muscle  brain  kidney  liver and 3 dpf larvae compared to wild type WT zebrafish were generated by deep sequencing using Illumina.", null, "pubmed:30336646;pubmed:32517323;pubmed:33849304", null, "Kidney ACRO rep3", "GSM3098421", null, "source name:Kidney|genotype:Acromegaly zebrafish model|tissue:Kidney|age:1 year old", "Kidney ACRO rep3", "Illumina Casava1.7 software used for basecalling. HISAT2 software was used according to the instructions from the program designers to map the raw reads of acromegaly and WT samples to zebrafish genome reference GRCz10 retrieved from Ensembl database together with the annotation file. The Cufflinks pipeline was used to assign reads to known transcripts and test for differential expression between acromegaly model and the WT samples. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads FPKM. Genome build: GRCz10 Supplementary files format and content: One tab delimited text file containing all FPKM values for all Samples.", "Kidney", null, "tissues were removed  and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.", null, "genotype:Acromegaly zebrafish model|tissue:Kidney|age:1 year old", "GSM3098421", "GSM3098421: Kidney ACRO rep3; Danio rerio; RNA Seq", "GSM3098421", null, "1", "tissues were removed  and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.", "GEO Accession:GSM3098421", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP140471", null, null, "GH_K3_Kidney_19_1.fq.gz GH_K3_Kidney_19_2.fq.gz", "fastq fastq", 516366800.0, 2581834.0, "GSM3098421 r1", "0:100 1:100", "A:139000034;C:118629581;G:117673967;T:140984276;N:78942", 100, 100, null, null, 139000034, 118629581, 117673967, 140984276, 78942, "SRX3940773", "SRS3171574", "SRA690975", "GEO", "Aquatic Molecular Biology and Biotechnology, Aquatic Bioscience, The University of Tokyo", 2, 0.93368, 0.93424, 0.08046, 0.07881, 0.73032, 0.73125, 0.52305, 0.51853, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-04-16", "Adult", "Adult", "Kidney", "Renal System"], [48077, "SRR7008284", "SRX3940772", "SRS3171573", "SRP140471", "PRJNA450343", "A Zebrafish Acromegaly Model Elevates DNA Damage and Impairs DNA Repair Pathways", "GSE113169", "Transcriptome Analysis", "Acromegaly is a pathological condition due to excess growth hormone GH secretion. Acromegaly patients exhibit a deterioration of health and many associated complications  such as cardiovascular issues  arthritis  kidney diseases  muscular weakness  and colon cancer. Since these complications are generalized throughout the body  we investigated the effect of GH excess on cellular integrity. Here  we established stable acromegaly model zebrafish lines that overexpress tilapia GH and the red fluorescence protein RFP reporter gene for tracking GH gene expression throughout generations  and performed RNA Seq data analysis from different organs. Intriguingly  heatmap and Expression2Kinases X2K analysis revealed the enrichment of DNA damage markers in various organs. Moreover  H2A.X immunostaining analysis in acromegaly zebrafish larvae and the adult acromegaly model brain and muscle showed a robust increase in the number of DNA damaged cells. Using Gene Set Enrichment Analysis GSEA  we found that the acromegaly zebrafish model had impaired DNA repair pathways in the liver  such as double strand break DSB  homologous recombination repair HRR  non homologous end joining NHEJ  nucleotide excision repair NER  and translesion synthesis TLS. Interestingly  the impairment of DNA repair was even more prominent in acromegaly model than in aged zebrafish three years old. Thus  our study demonstrates that affection of cellular integrity is characteristic of acromegaly Overall design: Total mRNA obtained from 1 years old acromegaly zebrafish model muscle  brain  kidney  liver and 3 dpf larvae compared to wild type WT zebrafish were generated by deep sequencing using Illumina.", null, "pubmed:30336646;pubmed:32517323;pubmed:33849304", null, "Kidney ACRO rep2", "GSM3098420", null, "source name:Kidney|genotype:Acromegaly zebrafish model|tissue:Kidney|age:1 year old", "Kidney ACRO rep2", "Illumina Casava1.7 software used for basecalling. HISAT2 software was used according to the instructions from the program designers to map the raw reads of acromegaly and WT samples to zebrafish genome reference GRCz10 retrieved from Ensembl database together with the annotation file. The Cufflinks pipeline was used to assign reads to known transcripts and test for differential expression between acromegaly model and the WT samples. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads FPKM. Genome build: GRCz10 Supplementary files format and content: One tab delimited text file containing all FPKM values for all Samples.", "Kidney", null, "tissues were removed  and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.", null, "genotype:Acromegaly zebrafish model|tissue:Kidney|age:1 year old", "GSM3098420", "GSM3098420: Kidney ACRO rep2; Danio rerio; RNA Seq", "GSM3098420", null, "1", "tissues were removed  and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.", "GEO Accession:GSM3098420", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP140471", null, null, "GH_K2_Kidney_18_1.fq.gz GH_K2_Kidney_18_2.fq.gz", "fastq fastq", 554022000.0, 2770110.0, "GSM3098420 r1", "0:100 1:100", "A:145695233;C:130810207;G:130333919;T:147099701;N:82940", 100, 100, null, null, 145695233, 130810207, 130333919, 147099701, 82940, "SRX3940772", "SRS3171573", "SRA690975", "GEO", "Aquatic Molecular Biology and Biotechnology, Aquatic Bioscience, The University of Tokyo", 2, 0.94063, 0.94251, 0.08052, 0.07972, 0.72316, 0.72372, 0.51706, 0.53029, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-04-16", "Adult", "Adult", "Kidney", "Renal System"], [48078, "SRR7008283", "SRX3940771", "SRS3171572", "SRP140471", "PRJNA450343", "A Zebrafish Acromegaly Model Elevates DNA Damage and Impairs DNA Repair Pathways", "GSE113169", "Transcriptome Analysis", "Acromegaly is a pathological condition due to excess growth hormone GH secretion. Acromegaly patients exhibit a deterioration of health and many associated complications  such as cardiovascular issues  arthritis  kidney diseases  muscular weakness  and colon cancer. Since these complications are generalized throughout the body  we investigated the effect of GH excess on cellular integrity. Here  we established stable acromegaly model zebrafish lines that overexpress tilapia GH and the red fluorescence protein RFP reporter gene for tracking GH gene expression throughout generations  and performed RNA Seq data analysis from different organs. Intriguingly  heatmap and Expression2Kinases X2K analysis revealed the enrichment of DNA damage markers in various organs. Moreover  H2A.X immunostaining analysis in acromegaly zebrafish larvae and the adult acromegaly model brain and muscle showed a robust increase in the number of DNA damaged cells. Using Gene Set Enrichment Analysis GSEA  we found that the acromegaly zebrafish model had impaired DNA repair pathways in the liver  such as double strand break DSB  homologous recombination repair HRR  non homologous end joining NHEJ  nucleotide excision repair NER  and translesion synthesis TLS. Interestingly  the impairment of DNA repair was even more prominent in acromegaly model than in aged zebrafish three years old. Thus  our study demonstrates that affection of cellular integrity is characteristic of acromegaly Overall design: Total mRNA obtained from 1 years old acromegaly zebrafish model muscle  brain  kidney  liver and 3 dpf larvae compared to wild type WT zebrafish were generated by deep sequencing using Illumina.", null, "pubmed:30336646;pubmed:32517323;pubmed:33849304", null, "Kidney ACRO rep1", "GSM3098419", null, "source name:Kidney|genotype:Acromegaly zebrafish model|tissue:Kidney|age:1 year old", "Kidney ACRO rep1", "Illumina Casava1.7 software used for basecalling. HISAT2 software was used according to the instructions from the program designers to map the raw reads of acromegaly and WT samples to zebrafish genome reference GRCz10 retrieved from Ensembl database together with the annotation file. The Cufflinks pipeline was used to assign reads to known transcripts and test for differential expression between acromegaly model and the WT samples. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads FPKM. Genome build: GRCz10 Supplementary files format and content: One tab delimited text file containing all FPKM values for all Samples.", "Kidney", null, "tissues were removed  and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.", null, "genotype:Acromegaly zebrafish model|tissue:Kidney|age:1 year old", "GSM3098419", "GSM3098419: Kidney ACRO rep1; Danio rerio; RNA Seq", "GSM3098419", null, "1", "tissues were removed  and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.", "GEO Accession:GSM3098419", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP140471", null, null, "GH_K1_Kidney_17_1.fq.gz GH_K1_Kidney_17_2.fq.gz", "fastq fastq", 421518000.0, 2107590.0, "GSM3098419 r1", "0:100 1:100", "A:108267615;C:102016623;G:102089011;T:109080343;N:64408", 100, 100, null, null, 108267615, 102016623, 102089011, 109080343, 64408, "SRX3940771", "SRS3171572", "SRA690975", "GEO", "Aquatic Molecular Biology and Biotechnology, Aquatic Bioscience, The University of Tokyo", 2, 0.93823, 0.94043, 0.08003, 0.07811, 0.72508, 0.72502, 0.49632, 0.50453, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2018-04-16", "Adult", "Adult", "Kidney", "Renal System"]], "truncated": false, "filtered_table_rows_count": 402, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "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_source\" = :p0 and \"technology\" = :p1 and \"tissue_curation_coarse\" = :p2 order by rowid limit 101", "params": {"p0": "TRANSCRIPTOMIC", "p1": "unknown", "p2": "Renal System"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 400, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&experiment.library_strategy=miRNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 402, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=unknown&tissue_curation_coarse=Renal+System", "selected": true}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System", "results": [{"value": "cDNA", "label": "cDNA", "count": 244, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&experiment.library_selection=cDNA", "selected": false}, {"value": "PolyA", "label": "PolyA", "count": 66, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&experiment.library_selection=PolyA", "selected": false}, {"value": "other", "label": "other", "count": 49, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&experiment.library_selection=other", "selected": false}, {"value": "unspecified", "label": "unspecified", "count": 20, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&experiment.library_selection=unspecified", "selected": false}, {"value": "RANDOM", "label": "RANDOM", "count": 14, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&experiment.library_selection=RANDOM", "selected": false}, {"value": "Oligo-dT", "label": "Oligo-dT", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&experiment.library_selection=Oligo-dT", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 320, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&experiment.library_layout=PAIRED", "selected": false}, {"value": "SINGLE", "label": "SINGLE", "count": 82, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&experiment.library_layout=SINGLE", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 354, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&experiment.platform=ILLUMINA", "selected": false}, {"value": "BGISEQ", "label": "BGISEQ", "count": 33, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&experiment.platform=BGISEQ", "selected": false}, {"value": "DNBSEQ", "label": "DNBSEQ", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&experiment.platform=DNBSEQ", "selected": false}, {"value": "PACBIO_SMRT", "label": "PACBIO_SMRT", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&experiment.platform=PACBIO_SMRT", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System", "results": [{"value": "Adult", "label": "Adult", "count": 243, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&devstage_curation_coarse=Adult", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 60, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&devstage_curation_coarse=Multi-stage", "selected": false}, {"value": "Larval", "label": "Larval", "count": 49, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&devstage_curation_coarse=Larval", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 48, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&devstage_curation_coarse=Undetermined", "selected": false}, {"value": "Embryo", "label": "Embryo", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&devstage_curation_coarse=Embryo", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System", "results": [{"value": "Adult", "label": "Adult", "count": 234, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&devstage_curation=Adult", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 69, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&devstage_curation=Undetermined", "selected": false}, {"value": "Larval", "label": "Larval", "count": 49, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&devstage_curation=Larval", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 48, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&devstage_curation=Multi-stage", "selected": false}, {"value": "Pharyngula", "label": "Pharyngula", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&devstage_curation=Pharyngula", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System", "results": [{"value": "Renal System", "label": "Renal System", "count": 402, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown", "selected": true}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System", "results": [{"value": "Kidney", "label": "Kidney", "count": 402, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&tissue_curation=Kidney", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System", "results": [{"value": "unknown", "label": "unknown", "count": 402, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&tissue_curation_coarse=Renal+System", "selected": true}], "truncated": false}}, "suggested_facets": [], "next": "48078", "next_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=unknown&tissue_curation_coarse=Renal+System&_next=48078", "private": false, "allow_execute_sql": true, "query_ms": 164.9544940009946}