{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"cDNA\", experiment.library_strategy = \"RNA-Seq\" and tissue_curation = \"Kidney\"", "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"], [25326, "SRR25868015", "SRX21589423", "SRS18766996", "SRP457977", "PRJNA1011833", "Single cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity", "GSE242133", "Transcriptome Analysis", "The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides  the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However  knowledge about the properties of kidney hematopoietic cells  and the functionality of kidney in fish immune systems remain to be elucidated. To this end  our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell HSPC and immune cell types from zebrafish kidney via single cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity  and displayed differential responses to viral infection  indicating their diverse functional roles in antiviral immunity. Remarkably  HSPCs were found to have extensive reactivities to viral infection  and the trained immunity can be effectively induced in certain HSPCs. In addition  the antigen stimulated adaptive immunity can be fully generated in kidney  suggesting kidney acting as a secondary lymphoid organ. These results indicated that fish kidney is a dual functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune system  and highlighted the multifaced biology of kidney in ancient vertebrates. Overall design: Kidney leukocyte PBS administered control  SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:38497789", null, "vaccinated+SVCV  scRNAseq Kidney leukocyte", "GSM7749529", null, "source name:Kidney|cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:vaccinated+SVCV|geo loc name:missing|collection date:missing", "vaccinated+SVCV  scRNAseq Kidney leukocyte", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files", "Kidney", null, "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 \u03bcg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:vaccinated+SVCV", "GSM7749529", "GSM7749529: vaccinated+SVCV  scRNAseq Kidney leukocyte; Danio rerio; RNA Seq", "GSM7749529 r1", "GSM7749529", "1", "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 \u03bcg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP457977", null, null, "vaccinated+SVCV_S1_L001_R1_001.fastq.gz vaccinated+SVCV_S1_L001_R2_001.fastq.gz", "fastq fastq", 48964415682.0, 411465678.0, "GSM7749529 r1", "0:28 1:91", "A:13575624351;C:10984755198;G:11582424564;T:12820058148;N:1553421", 28, 91, null, null, 13575624351, 10984755198, 11582424564, 12820058148, 1553421, "SRX21589423", "SRS18766996", "SRA1703997", "College of Life Sciences, Zhejiang University", "College of Life Sciences, Zhejiang University", 2, 0.00754, 0.93029, 0.00274, 0.13414, 0.99168, 0.81527, 0.35, 0.50044, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-09-01", "Juvenile", "Juvenile", "Kidney", "Renal System"], [25327, "SRR25868016", "SRX21589422", "SRS18766995", "SRP457977", "PRJNA1011833", "Single cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity", "GSE242133", "Transcriptome Analysis", "The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides  the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However  knowledge about the properties of kidney hematopoietic cells  and the functionality of kidney in fish immune systems remain to be elucidated. To this end  our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell HSPC and immune cell types from zebrafish kidney via single cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity  and displayed differential responses to viral infection  indicating their diverse functional roles in antiviral immunity. Remarkably  HSPCs were found to have extensive reactivities to viral infection  and the trained immunity can be effectively induced in certain HSPCs. In addition  the antigen stimulated adaptive immunity can be fully generated in kidney  suggesting kidney acting as a secondary lymphoid organ. These results indicated that fish kidney is a dual functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune system  and highlighted the multifaced biology of kidney in ancient vertebrates. Overall design: Kidney leukocyte PBS administered control  SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:38497789", null, "SVCV  scRNAseq Kidney leukocyte", "GSM7749528", null, "source name:Kidney|cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:SVCV|geo loc name:missing|collection date:missing", "SVCV  scRNAseq Kidney leukocyte", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files", "Kidney", null, "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 \u03bcg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:SVCV", "GSM7749528", "GSM7749528: SVCV  scRNAseq Kidney leukocyte; Danio rerio; RNA Seq", "GSM7749528 r1", "GSM7749528", "1", "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 \u03bcg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP457977", null, null, "SVCV_S1_L001_R2_001.fastq.gz SVCV_S1_L001_R1_001.fastq.gz", "fastq fastq", 48037908933.0, 403679907.0, "GSM7749528 r1", "0:28 1:91", "A:13476452185;C:10712519121;G:11200837365;T:12646404590;N:1695672", 28, 91, null, null, 13476452185, 10712519121, 11200837365, 12646404590, 1695672, "SRX21589422", "SRS18766995", "SRA1703997", "College of Life Sciences, Zhejiang University", "College of Life Sciences, Zhejiang University", 2, 0.00795, 0.92383, 0.00261, 0.14, 0.98948, 0.7806, 0.36862, 0.54549, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-09-01", "Juvenile", "Juvenile", "Kidney", "Renal System"], [25328, "SRR25868017", "SRX21589421", "SRS18766994", "SRP457977", "PRJNA1011833", "Single cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity", "GSE242133", "Transcriptome Analysis", "The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides  the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However  knowledge about the properties of kidney hematopoietic cells  and the functionality of kidney in fish immune systems remain to be elucidated. To this end  our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell HSPC and immune cell types from zebrafish kidney via single cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity  and displayed differential responses to viral infection  indicating their diverse functional roles in antiviral immunity. Remarkably  HSPCs were found to have extensive reactivities to viral infection  and the trained immunity can be effectively induced in certain HSPCs. In addition  the antigen stimulated adaptive immunity can be fully generated in kidney  suggesting kidney acting as a secondary lymphoid organ. These results indicated that fish kidney is a dual functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune system  and highlighted the multifaced biology of kidney in ancient vertebrates. Overall design: Kidney leukocyte PBS administered control  SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.", null, "pubmed:38497789", null, "PBS  scRNAseq Kidney leukocyte", "GSM7749527", null, "source name:Kidney|cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:PBS|geo loc name:missing|collection date:missing", "PBS  scRNAseq Kidney leukocyte", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files", "Kidney", null, "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 \u03bcg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter\u2019s instructions single cell 3\u2019 v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:PBS", "GSM7749527", "GSM7749527: PBS  scRNAseq Kidney leukocyte; Danio rerio; RNA Seq", "GSM7749527 r1", "GSM7749527", "1", "Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly  zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 \u03bcm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 \u03bcg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP457977", null, null, "PBS_S1_L001_R1_001.fastq.gz PBS_S1_L001_R2_001.fastq.gz", "fastq fastq", 49559940115.0, 416470085.0, "GSM7749527 r1", "0:28 1:91", "A:13856071803;C:11114011608;G:11616674427;T:12971434952;N:1747325", 28, 91, null, null, 13856071803, 11114011608, 11616674427, 12971434952, 1747325, "SRX21589421", "SRS18766994", "SRA1703997", "College of Life Sciences, Zhejiang University", "College of Life Sciences, Zhejiang University", 2, 0.00648, 0.92681, 0.00213, 0.1376, 0.99056, 0.79866, 0.40117, 0.5487, 28, 91, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-09-01", "Juvenile", "Juvenile", "Kidney", "Renal System"], [28589, "SRR26491369", "SRX22195232", "SRS19251247", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "KM eos", "GSM7854254", null, "source name:eosinophils|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing", "KM eos", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "eosinophils", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP", "GSM7854254", "GSM7854254: KM eos; Danio rerio; RNA Seq", "GSM7854254 r1", "GSM7854254", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, "loader:fastq load.py", "LGF-2-LGF-2-1_L1_1.fq.gz LGF-2-LGF-2-1_L1_2.fq.gz", "fastq fastq", 25680257100.0, 85600857.0, "GSM7854254 r1", "0:150 1:150", "A:8025239149;C:3737115767;G:4237725481;T:9679701617;N:475086", 150, 150, null, null, 8025239149, 3737115767, 4237725481, 9679701617, 475086, "SRX22195232", "SRS19251247", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.21477, 0.87303, 0.06136, 0.18991, 0.99084, 0.83187, 0.58742, 0.60309, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28590, "SRR26491370", "SRX22195232", "SRS19251247", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "KM eos", "GSM7854254", null, "source name:eosinophils|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing", "KM eos", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "eosinophils", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP", "GSM7854254", "GSM7854254: KM eos; Danio rerio; RNA Seq", "GSM7854254 r1", "GSM7854254", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, "loader:fastq load.py", "LGF-2-LGF-2-2_L1_1.fq.gz LGF-2-LGF-2-2_L1_2.fq.gz", "fastq fastq", 30035236200.0, 100117454.0, "GSM7854254 r2", "0:150 1:150", "A:9382913917;C:4364910890;G:4955266285;T:11331735278;N:409830", 150, 150, null, null, 9382913917, 4364910890, 4955266285, 11331735278, 409830, "SRX22195232", "SRS19251247", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.20279, 0.87187, 0.05971, 0.19015, 0.99068, 0.83108, 0.6129, 0.60029, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28591, "SRR26491371", "SRX22195232", "SRS19251247", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "KM eos", "GSM7854254", null, "source name:eosinophils|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing", "KM eos", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "eosinophils", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP", "GSM7854254", "GSM7854254: KM eos; Danio rerio; RNA Seq", "GSM7854254 r1", "GSM7854254", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, "loader:fastq load.py", "LGF-2-LGF-2-3_L1_1.fq.gz LGF-2-LGF-2-3_L1_2.fq.gz", "fastq fastq", 29383046400.0, 97943488.0, "GSM7854254 r3", "0:150 1:150", "A:9183968085;C:4275116661;G:4844377300;T:11079048598;N:535756", 150, 150, null, null, 9183968085, 4275116661, 4844377300, 11079048598, 535756, "SRX22195232", "SRS19251247", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.19524, 0.87384, 0.06096, 0.19095, 0.99188, 0.83293, 0.58701, 0.58361, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28592, "SRR26491372", "SRX22195232", "SRS19251247", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "KM eos", "GSM7854254", null, "source name:eosinophils|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing", "KM eos", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "eosinophils", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP", "GSM7854254", "GSM7854254: KM eos; Danio rerio; RNA Seq", "GSM7854254 r1", "GSM7854254", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, "loader:fastq load.py", "LGF-2-LGF-2-4_L1_1.fq.gz LGF-2-LGF-2-4_L1_2.fq.gz", "fastq fastq", 33167265900.0, 110557553.0, "GSM7854254 r4", "0:150 1:150", "A:10380451186;C:4827987987;G:5467300098;T:12490912690;N:613939", 150, 150, null, null, 10380451186, 4827987987, 5467300098, 12490912690, 613939, "SRX22195232", "SRS19251247", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.21222, 0.87102, 0.06704, 0.18877, 0.99052, 0.83343, 0.56053, 0.58249, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28593, "SRR26491373", "SRX22195231", "SRS19251246", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebpb mut KM 3", "GSM7854253", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing", "cebpb mut KM 3", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1", "GSM7854253", "GSM7854253: cebpb mut KM 3; Danio rerio; RNA Seq", "GSM7854253 r1", "GSM7854253", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, "loader:fastq load.py", "b3_S0_L003_R2_001.fastq.gz b3_S0_L003_R1_001.fastq.gz", "fastq fastq", 112688609700.0, 375628699.0, "GSM7854253 r1", "0:150 1:150", "A:38960384866;C:23864873253;G:24209853889;T:25652339570;N:1158122", 150, 150, null, null, 38960384866, 23864873253, 24209853889, 25652339570, 1158122, "SRX22195231", "SRS19251246", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.89036, 0.0, 0.11804, 1.0, 0.86318, null, 0.69315, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28594, "SRR26491374", "SRX22195230", "SRS19251245", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebpb mut KM 2", "GSM7854252", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing", "cebpb mut KM 2", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1", "GSM7854252", "GSM7854252: cebpb mut KM 2; Danio rerio; RNA Seq", "GSM7854252 r1", "GSM7854252", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, "loader:fastq load.py", "b2_S0_L003_R1_001.fastq.gz b2_S0_L003_R2_001.fastq.gz", "fastq fastq", 115982411700.0, 386608039.0, "GSM7854252 r1", "0:150 1:150", "A:39966143944;C:23813985234;G:22925287805;T:29275806145;N:1188572", 150, 150, null, null, 39966143944, 23813985234, 22925287805, 29275806145, 1188572, "SRX22195230", "SRS19251245", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.86607, 0.0, 0.12954, 1.0, 0.83132, null, 0.631, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28595, "SRR26491375", "SRX22195229", "SRS19251244", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebpb mut KM 1", "GSM7854251", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing", "cebpb mut KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1", "GSM7854251", "GSM7854251: cebpb mut KM 1; Danio rerio; RNA Seq", "GSM7854251 r1", "GSM7854251", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "KMB-KMB-1_FKDL210332848-1a-AK4437_1.fq.gz KMB-KMB-1_FKDL210332848-1a-AK4437_2.fq.gz", "fastq fastq", 17042007300.0, 56806691.0, "GSM7854251 r1", "0:150 1:150", "A:5668533017;C:3385304499;G:3366957982;T:4620992880;N:218922", 150, 150, null, null, 5668533017, 3385304499, 3366957982, 4620992880, 218922, "SRX22195229", "SRS19251244", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.03184, 0.89149, 0.00867, 0.11757, 0.99758, 0.82077, 0.751, 0.57147, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28596, "SRR26491376", "SRX22195229", "SRS19251244", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebpb mut KM 1", "GSM7854251", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing", "cebpb mut KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1", "GSM7854251", "GSM7854251: cebpb mut KM 1; Danio rerio; RNA Seq", "GSM7854251 r1", "GSM7854251", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "KMB-KMB-2_FKDL210332848-1a-AK4438_1.fq.gz KMB-KMB-2_FKDL210332848-1a-AK4438_2.fq.gz", "fastq fastq", 16343762400.0, 54479208.0, "GSM7854251 r2", "0:150 1:150", "A:5450512159;C:3242501005;G:3220219102;T:4430319009;N:211125", 150, 150, null, null, 5450512159, 3242501005, 3220219102, 4430319009, 211125, "SRX22195229", "SRS19251244", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.02568, 0.8936, 0.00694, 0.11929, 0.99776, 0.82235, 0.66666, 0.57382, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28597, "SRR26491377", "SRX22195229", "SRS19251244", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebpb mut KM 1", "GSM7854251", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing", "cebpb mut KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1", "GSM7854251", "GSM7854251: cebpb mut KM 1; Danio rerio; RNA Seq", "GSM7854251 r1", "GSM7854251", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "KMB-KMB-3_FKDL210332848-1a-AK4439_1.fq.gz KMB-KMB-3_FKDL210332848-1a-AK4439_2.fq.gz", "fastq fastq", 10959163500.0, 36530545.0, "GSM7854251 r3", "0:150 1:150", "A:3642539220;C:2179136896;G:2168295053;T:2969053386;N:138945", 150, 150, null, null, 3642539220, 2179136896, 2168295053, 2969053386, 138945, "SRX22195229", "SRS19251244", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.03232, 0.89137, 0.00922, 0.12039, 0.9974, 0.82171, 0.58775, 0.57177, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28598, "SRR26491378", "SRX22195229", "SRS19251244", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebpb mut KM 1", "GSM7854251", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing", "cebpb mut KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1", "GSM7854251", "GSM7854251: cebpb mut KM 1; Danio rerio; RNA Seq", "GSM7854251 r1", "GSM7854251", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "KMB-KMB-4_FKDL210332848-1a-AK4440_1.fq.gz KMB-KMB-4_FKDL210332848-1a-AK4440_2.fq.gz", "fastq fastq", 18130067100.0, 60433557.0, "GSM7854251 r4", "0:150 1:150", "A:6030347851;C:3607618024;G:3589047945;T:4902820241;N:233039", 150, 150, null, null, 6030347851, 3607618024, 3589047945, 4902820241, 233039, "SRX22195229", "SRS19251244", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.02563, 0.89333, 0.00745, 0.11784, 0.99805, 0.82156, 0.71568, 0.56377, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28599, "SRR26491379", "SRX22195228", "SRS19251243", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebp1 mut KM 3", "GSM7854250", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing", "cebp1 mut KM 3", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1", "GSM7854250", "GSM7854250: cebp1 mut KM 3; Danio rerio; RNA Seq", "GSM7854250 r1", "GSM7854250", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, "loader:fastq load.py", "e3_S0_L003_R1_001.fastq.gz e3_S0_L003_R2_001.fastq.gz", "fastq fastq", 106692684600.0, 355642282.0, "GSM7854250 r1", "0:150 1:150", "A:43760768907;C:19045349028;G:18701042387;T:25183159362;N:2364916", 150, 150, null, null, 43760768907, 19045349028, 18701042387, 25183159362, 2364916, "SRX22195228", "SRS19251243", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.90163, 0.0, 0.08054, 1.0, 0.7908, null, 0.55652, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28600, "SRR26491380", "SRX22195227", "SRS19251242", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebp1 mut KM 2", "GSM7854249", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing", "cebp1 mut KM 2", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1", "GSM7854249", "GSM7854249: cebp1 mut KM 2; Danio rerio; RNA Seq", "GSM7854249 r1", "GSM7854249", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, "loader:fastq load.py", "e2_S0_L003_R2_001.fastq.gz e2_S0_L003_R1_001.fastq.gz", "fastq fastq", 126515726100.0, 421719087.0, "GSM7854249 r1", "0:150 1:150", "A:44391473513;C:24602183317;G:23721160983;T:33799587611;N:1320676", 150, 150, null, null, 44391473513, 24602183317, 23721160983, 33799587611, 1320676, "SRX22195227", "SRS19251242", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.90423, 0.0, 0.07758, 1.0, 0.81509, null, 0.5598, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28601, "SRR26491381", "SRX22195226", "SRS19251241", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebp1 mut KM 1", "GSM7854248", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing", "cebp1 mut KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1", "GSM7854248", "GSM7854248: cebp1 mut KM 1; Danio rerio; RNA Seq", "GSM7854248 r1", "GSM7854248", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "KM1-KM1-1_FKDL210332847-1a-AK4772_2.fq.gz KM1-KM1-1_FKDL210332847-1a-AK4772_1.fq.gz", "fastq fastq", 18653393400.0, 62177978.0, "GSM7854248 r1", "0:150 1:150", "A:6381285195;C:3802506730;G:3637919666;T:4831413881;N:267928", 150, 150, null, null, 6381285195, 3802506730, 3637919666, 4831413881, 267928, "SRX22195226", "SRS19251241", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.86906, 0.0, 0.0958, 1.0, 0.84423, null, 0.5956, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28602, "SRR26491382", "SRX22195226", "SRS19251241", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebp1 mut KM 1", "GSM7854248", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing", "cebp1 mut KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1", "GSM7854248", "GSM7854248: cebp1 mut KM 1; Danio rerio; RNA Seq", "GSM7854248 r1", "GSM7854248", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "KM1-KM1-2_FKDL210332847-1a-AK4773_1.fq.gz KM1-KM1-2_FKDL210332847-1a-AK4773_2.fq.gz", "fastq fastq", 18326971500.0, 61089905.0, "GSM7854248 r2", "0:150 1:150", "A:6267364051;C:3758542961;G:3587627310;T:4713172477;N:264701", 150, 150, null, null, 6267364051, 3758542961, 3587627310, 4713172477, 264701, "SRX22195226", "SRS19251241", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.86638, 0.0, 0.09499, 1.0, 0.84526, null, 0.60651, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28603, "SRR26491383", "SRX22195226", "SRS19251241", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebp1 mut KM 1", "GSM7854248", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing", "cebp1 mut KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1", "GSM7854248", "GSM7854248: cebp1 mut KM 1; Danio rerio; RNA Seq", "GSM7854248 r1", "GSM7854248", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "KM1-KM1-3_FKDL210332847-1a-AK4774_1.fq.gz KM1-KM1-3_FKDL210332847-1a-AK4774_2.fq.gz", "fastq fastq", 11808660600.0, 39362202.0, "GSM7854248 r3", "0:150 1:150", "A:4038900150;C:2417395586;G:2308989220;T:3043205908;N:169736", 150, 150, null, null, 4038900150, 2417395586, 2308989220, 3043205908, 169736, "SRX22195226", "SRS19251241", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.86661, 0.0, 0.09574, 1.0, 0.84542, null, 0.57797, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28604, "SRR26491384", "SRX22195226", "SRS19251241", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebp1 mut KM 1", "GSM7854248", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing", "cebp1 mut KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1", "GSM7854248", "GSM7854248: cebp1 mut KM 1; Danio rerio; RNA Seq", "GSM7854248 r1", "GSM7854248", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "KM1-KM1-4_FKDL210332847-1a-AK4775_1.fq.gz KM1-KM1-4_FKDL210332847-1a-AK4775_2.fq.gz", "fastq fastq", 13766583900.0, 45888613.0, "GSM7854248 r4", "0:150 1:150", "A:4706562659;C:2817183636;G:2693650162;T:3548993544;N:193899", 150, 150, null, null, 4706562659, 2817183636, 2693650162, 3548993544, 193899, "SRX22195226", "SRS19251241", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.86464, 0.0, 0.09455, 1.0, 0.84453, null, 0.59712, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28605, "SRR26491385", "SRX22195225", "SRS19251240", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "WT KM 3", "GSM7854247", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing", "WT KM 3", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1", "GSM7854247", "GSM7854247: WT KM 3; Danio rerio; RNA Seq", "GSM7854247 r1", "GSM7854247", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, "loader:fastq load.py", "w3_S0_L003_R1_001.fastq.gz w3_S0_L003_R2_001.fastq.gz", "fastq fastq", 142550442300.0, 475168141.0, "GSM7854247 r1", "0:150 1:150", "A:56961713939;C:27160797921;G:25876430130;T:32548386896;N:3113414", 150, 150, null, null, 56961713939, 27160797921, 25876430130, 32548386896, 3113414, "SRX22195225", "SRS19251240", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.84672, 0.0, 0.09057, 1.0, 0.84893, null, 0.64916, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28606, "SRR26491386", "SRX22195224", "SRS19251239", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "WT KM 2", "GSM7854246", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing", "WT KM 2", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1", "GSM7854246", "GSM7854246: WT KM 2; Danio rerio; RNA Seq", "GSM7854246 r1", "GSM7854246", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, "loader:fastq load.py", "w2_S0_L003_R2_001.fastq.gz w2_S0_L003_R1_001.fastq.gz", "fastq fastq", 110520161400.0, 368400538.0, "GSM7854246 r1", "0:150 1:150", "A:44333853620;C:20994101993;G:19951597607;T:25238178463;N:2429717", 150, 150, null, null, 44333853620, 20994101993, 19951597607, 25238178463, 2429717, "SRX22195224", "SRS19251239", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.84344, 0.0, 0.0961, 1.0, 0.83485, null, 0.63275, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28607, "SRR26491387", "SRX22195223", "SRS19251238", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "WT KM 1", "GSM7854245", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing", "WT KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1", "GSM7854245", "GSM7854245: WT KM 1; Danio rerio; RNA Seq", "GSM7854245 r1", "GSM7854245", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "WKM-WKM-1_BKDL190841222-1a-AK650_1.fq.gz WKM-WKM-1_BKDL190841222-1a-AK650_2.fq.gz", "fastq fastq", 20481536700.0, 68271789.0, "GSM7854245 r1", "0:150 1:150", "A:4681473958;C:3918612929;G:6623380714;T:5257792172;N:276927", 150, 150, null, null, 4681473958, 3918612929, 6623380714, 5257792172, 276927, "SRX22195223", "SRS19251238", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.91381, 0.0, 0.08281, 1.0, 0.82386, null, 0.55976, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28608, "SRR26491388", "SRX22195223", "SRS19251238", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "WT KM 1", "GSM7854245", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing", "WT KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1", "GSM7854245", "GSM7854245: WT KM 1; Danio rerio; RNA Seq", "GSM7854245 r1", "GSM7854245", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "WKM-WKM-2_BKDL190841222-1a-AK651_2.fq.gz WKM-WKM-2_BKDL190841222-1a-AK651_1.fq.gz", "fastq fastq", 24824596500.0, 82748655.0, "GSM7854245 r2", "0:150 1:150", "A:5675288010;C:4753602834;G:8033499593;T:6361861422;N:344641", 150, 150, null, null, 5675288010, 4753602834, 8033499593, 6361861422, 344641, "SRX22195223", "SRS19251238", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.9121, 0.0, 0.08282, 1.0, 0.82613, null, 0.56378, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28609, "SRR26491389", "SRX22195223", "SRS19251238", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "WT KM 1", "GSM7854245", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing", "WT KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1", "GSM7854245", "GSM7854245: WT KM 1; Danio rerio; RNA Seq", "GSM7854245 r1", "GSM7854245", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "WKM-WKM-3_BKDL190841222-1a-AK652_1.fq.gz WKM-WKM-3_BKDL190841222-1a-AK652_2.fq.gz", "fastq fastq", 20574633600.0, 68582112.0, "GSM7854245 r3", "0:150 1:150", "A:4698580031;C:3942306152;G:6657096764;T:5276366726;N:283927", 150, 150, null, null, 4698580031, 3942306152, 6657096764, 5276366726, 283927, "SRX22195223", "SRS19251238", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.9136, 0.0, 0.08366, 1.0, 0.82373, null, 0.55683, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "Adult", "Adult", "Kidney", "Renal System"], [28610, "SRR26491390", "SRX22195223", "SRS19251238", "SRP468071", "PRJNA1031138", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq]", "GSE246039", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model  we have identified an eosinophil lineage specific marker  eslec. Using this marker we have established a Tgeslec:eGFP reporter line  which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells  tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis  in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary  this study characterized eosinophil development in multiple dimensions including spatial temporal patterns  expression profiles  and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT  cebp1 /   and cebpb /  KM cells were integrated and analyzed together.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "WT KM 1", "GSM7854245", null, "source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing", "WT KM 1", "Post basecalling  the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package \"Seurat\". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the \"IntegrateData\" function of Seurat. Further analyses was performed based on the instructions of \"Seurat\" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell  cell and gene metadata for integrated KM cells and KM eosinophils  and the relevant Seurat objects rds files.", "renal cells", null, "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer\u2019s instructions 10x Genomics  USA.", null, "strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1", "GSM7854245", "GSM7854245: WT KM 1; Danio rerio; RNA Seq", "GSM7854245 r1", "GSM7854245", "1", "For scRNA Seq analysis of eosinophils from kidney  eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes  kidneys were collected from WT  cebp1 /   and cebpb /  individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation  the library construction was performed strictly based on the manufacturer's instructions 10x Genomics  USA.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468071", null, null, "WKM-WKM-4_BKDL190841222-1a-AK653_2.fq.gz WKM-WKM-4_BKDL190841222-1a-AK653_1.fq.gz", "fastq fastq", 25381641600.0, 84605472.0, "GSM7854245 r4", "0:150 1:150", "A:5785664179;C:4874470993;G:8220023956;T:6501127037;N:355435", 150, 150, null, null, 5785664179, 4874470993, 8220023956, 6501127037, 355435, "SRX22195223", "SRS19251238", "SRA1739642", "South China University of Technology", "South China University of Technology", 2, 0.0, 0.91371, 0.0, 0.08381, 1.0, 0.8244, null, 0.57179, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-10-23", "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"], [33649, "SRR30353607", "SRX25811748", "SRS22442019", "SRP528282", "PRJNA1151637", "Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [scRNA seq]", "GSE275537", "Transcriptome Analysis", "Single cell transcriptome analyses of whole kidney marrow cells isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: Single Cell RNA sequencing on whole kidney marrow cells isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171  which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. Single cell RNA sequencing was carried out in duplicates and each replicate consisted of cells dissociated from a pool of 2 4 adult whole kidney marrow.", null, "pubmed:39548947", null, "Rad21het rep2", "GSM8479120", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:rad21+/ |geo loc name:missing|collection date:missing", "Rad21het rep2", "Fastq files were aligned to the Danio Rerio GRCz11 genome NCBI:GCA 000002035.4 using CellRanger version 6.0.1 with chemistry mode: SC3Pv3. Gene annotation came from Ensembl version 98. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: Tab seperated barcodes  features and matrix files", "Whole kidney marrow", null, "Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 \u00b5m filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3\u2032 GEM library and Gel bead Kit v3.1 10x Genomics.", null, "tissue:Whole kidney marrow|genotype:rad21+/ ", "GSM8479120", "GSM8479120: Rad21het rep2; Danio rerio; RNA Seq", "GSM8479120 r1", "GSM8479120", "1", "Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 \u00b5m filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3\u2032 GEM library and Gel bead Kit v3.1 10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP528282", null, null, "Rad21het_rep2_S1_L001_R2_001.fastq.gz Rad21het_rep2_S1_L001_R1_001.fastq.gz", "fastq fastq", 25307099168.0, 218164648.0, "GSM8479120 r1", "0:27 1:89", "A:6829044594;C:5976366733;G:6024781695;T:6476303884;N:602262", 27, 89, null, null, 6829044594, 5976366733, 6024781695, 6476303884, 602262, "SRX25811748", "SRS22442019", "SRA1954153", "Horsfield, Pathology, University of Otago", "Horsfield, Pathology, University of Otago", 2, 0.00381, 0.89166, 0.00123, 0.07968, 0.99279, 0.82956, 0.36032, 0.51023, 27, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "New Zealand", "2024-08-23", "Adult", "Adult", "Kidney", "Renal System"], [33650, "SRR30353608", "SRX25811747", "SRS22442018", "SRP528282", "PRJNA1151637", "Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [scRNA seq]", "GSE275537", "Transcriptome Analysis", "Single cell transcriptome analyses of whole kidney marrow cells isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: Single Cell RNA sequencing on whole kidney marrow cells isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171  which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. Single cell RNA sequencing was carried out in duplicates and each replicate consisted of cells dissociated from a pool of 2 4 adult whole kidney marrow.", null, "pubmed:39548947", null, "Rad21het rep1", "GSM8479119", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:rad21+/ |geo loc name:missing|collection date:missing", "Rad21het rep1", "Fastq files were aligned to the Danio Rerio GRCz11 genome NCBI:GCA 000002035.4 using CellRanger version 6.0.1 with chemistry mode: SC3Pv3. Gene annotation came from Ensembl version 98. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: Tab seperated barcodes  features and matrix files", "Whole kidney marrow", null, "Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 \u00b5m filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3\u2032 GEM library and Gel bead Kit v3.1 10x Genomics.", null, "tissue:Whole kidney marrow|genotype:rad21+/ ", "GSM8479119", "GSM8479119: Rad21het rep1; Danio rerio; RNA Seq", "GSM8479119 r1", "GSM8479119", "1", "Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 \u00b5m filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3\u2032 GEM library and Gel bead Kit v3.1 10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP528282", null, null, "Rad21het_rep1_S1_L001_R2_001.fastq.gz Rad21het_rep1_S1_L001_R1_001.fastq.gz", "fastq fastq", 22413519188.0, 193219993.0, "GSM8479119 r1", "0:27 1:89", "A:6260052051;C:5058503439;G:5315821015;T:5778634222;N:508461", 27, 89, null, null, 6260052051, 5058503439, 5315821015, 5778634222, 508461, "SRX25811747", "SRS22442018", "SRA1954153", "Horsfield, Pathology, University of Otago", "Horsfield, Pathology, University of Otago", 2, 0.00394, 0.90508, 0.00119, 0.09071, 0.99162, 0.82942, 0.3619, 0.54526, 27, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "New Zealand", "2024-08-23", "Adult", "Adult", "Kidney", "Renal System"], [33651, "SRR30353609", "SRX25811746", "SRS22442017", "SRP528282", "PRJNA1151637", "Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [scRNA seq]", "GSE275537", "Transcriptome Analysis", "Single cell transcriptome analyses of whole kidney marrow cells isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: Single Cell RNA sequencing on whole kidney marrow cells isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171  which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. Single cell RNA sequencing was carried out in duplicates and each replicate consisted of cells dissociated from a pool of 2 4 adult whole kidney marrow.", null, "pubmed:39548947", null, "WT rep2", "GSM8479118", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:wild type|geo loc name:missing|collection date:missing", "WT rep2", "Fastq files were aligned to the Danio Rerio GRCz11 genome NCBI:GCA 000002035.4 using CellRanger version 6.0.1 with chemistry mode: SC3Pv3. Gene annotation came from Ensembl version 98. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: Tab seperated barcodes  features and matrix files", "Whole kidney marrow", null, "Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 \u00b5m filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3\u2032 GEM library and Gel bead Kit v3.1 10x Genomics.", null, "tissue:Whole kidney marrow|genotype:wild type", "GSM8479118", "GSM8479118: WT rep2; Danio rerio; RNA Seq", "GSM8479118 r1", "GSM8479118", "1", "Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 \u00b5m filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3\u2032 GEM library and Gel bead Kit v3.1 10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP528282", null, null, "WT_rep2_S1_L001_R1_001.fastq.gz WT_rep2_S1_L001_R2_001.fastq.gz", "fastq fastq", 23457592964.0, 202220629.0, "GSM8479118 r1", "0:27 1:89", "A:6426793246;C:5417323760;G:5551103780;T:6061805923;N:566255", 27, 89, null, null, 6426793246, 5417323760, 5551103780, 6061805923, 566255, "SRX25811746", "SRS22442017", "SRA1954153", "Horsfield, Pathology, University of Otago", "Horsfield, Pathology, University of Otago", 2, 0.00406, 0.91487, 0.00142, 0.09007, 0.99283, 0.82641, 0.37549, 0.51858, 27, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "New Zealand", "2024-08-23", "Adult", "Adult", "Kidney", "Renal System"], [33652, "SRR30353610", "SRX25811745", "SRS22442016", "SRP528282", "PRJNA1151637", "Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [scRNA seq]", "GSE275537", "Transcriptome Analysis", "Single cell transcriptome analyses of whole kidney marrow cells isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: Single Cell RNA sequencing on whole kidney marrow cells isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171  which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. Single cell RNA sequencing was carried out in duplicates and each replicate consisted of cells dissociated from a pool of 2 4 adult whole kidney marrow.", null, "pubmed:39548947", null, "WT rep1", "GSM8479117", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:wild type|geo loc name:missing|collection date:missing", "WT rep1", "Fastq files were aligned to the Danio Rerio GRCz11 genome NCBI:GCA 000002035.4 using CellRanger version 6.0.1 with chemistry mode: SC3Pv3. Gene annotation came from Ensembl version 98. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: Tab seperated barcodes  features and matrix files", "Whole kidney marrow", null, "Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 \u00b5m filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3\u2032 GEM library and Gel bead Kit v3.1 10x Genomics.", null, "tissue:Whole kidney marrow|genotype:wild type", "GSM8479117", "GSM8479117: WT rep1; Danio rerio; RNA Seq", "GSM8479117 r1", "GSM8479117", "1", "Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 \u00b5m filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3\u2032 GEM library and Gel bead Kit v3.1 10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP528282", null, null, "WT_rep1_S1_L001_R2_001.fastq.gz WT_rep1_S1_L001_R1_001.fastq.gz", "fastq fastq", 26909031908.0, 231974413.0, "GSM8479117 r1", "0:27 1:89", "A:7272478752;C:6312728360;G:6433038501;T:6890198195;N:588100", 27, 89, null, null, 7272478752, 6312728360, 6433038501, 6890198195, 588100, "SRX25811745", "SRS22442016", "SRA1954153", "Horsfield, Pathology, University of Otago", "Horsfield, Pathology, University of Otago", 2, 0.00366, 0.93902, 0.00134, 0.0858, 0.99318, 0.82769, 0.35, 0.51885, 27, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "New Zealand", "2024-08-23", "Adult", "Adult", "Kidney", "Renal System"], [33653, "SRR30355362", "SRX25813460", "SRS22443728", "SRP528295", "PRJNA1151638", "Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA seq]", "GSE275536", "Transcriptome Analysis", "Bulk RNA sequencing analyses of whole kidney marrow tissue isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: RNA sequencing was carried out on whole kidney marrow tissue isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171  which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. RNA sequencing was carried out in triplicates and each replicate consisted of whole kidney marrow pooled from three adult zebrafish.", null, "pubmed:39548947", null, "Rad21het rep3", "GSM8479116", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:rad21+/ |geo loc name:missing|collection date:missing", "Rad21het rep3", "Sequencing reads were QC using FastQC. Sequencing adapter and low quality Q<20 were removed using fastq mcf. Cleaned reads were aligned using HISAT2 version 2.0.4. Read count were retrieved using FeatureCount summarising data at gene id level. Transcript per milion were generated using featureCount read count using R. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: tab delimited text file  contains the transcript parts million countsTPM for each sample", "Whole kidney marrow", null, "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "tissue:Whole kidney marrow|genotype:rad21+/ ", "GSM8479116", "GSM8479116: Rad21het rep3; Danio rerio; RNA Seq", "GSM8479116 r1", "GSM8479116", "1", "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP528295", null, null, "Rad21het_rep3_L001_R1_001.fastq.gz Rad21het_rep3_L001_R2_001.fastq.gz", "fastq fastq", 11739699756.0, 38873178.0, "GSM8479116 r1", "0:151 1:151", "A:3023039412;C:2849320583;G:2949255547;T:2917120212;N:964002", 151, 151, null, null, 3023039412, 2849320583, 2949255547, 2917120212, 964002, "SRX25813460", "SRS22443728", "SRA1954177", "Horsfield, Pathology, University of Otago", "Horsfield, Pathology, University of Otago", 2, 0.91949, 0.91921, 0.02856, 0.02841, 0.72287, 0.72969, 0.50988, 0.50739, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "New Zealand", "2024-08-23", "Adult", "Adult", "Kidney", "Renal System"], [33654, "SRR30355363", "SRX25813459", "SRS22443727", "SRP528295", "PRJNA1151638", "Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA seq]", "GSE275536", "Transcriptome Analysis", "Bulk RNA sequencing analyses of whole kidney marrow tissue isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: RNA sequencing was carried out on whole kidney marrow tissue isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171  which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. RNA sequencing was carried out in triplicates and each replicate consisted of whole kidney marrow pooled from three adult zebrafish.", null, "pubmed:39548947", null, "Rad21het rep2", "GSM8479115", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:rad21+/ |geo loc name:missing|collection date:missing", "Rad21het rep2", "Sequencing reads were QC using FastQC. Sequencing adapter and low quality Q<20 were removed using fastq mcf. Cleaned reads were aligned using HISAT2 version 2.0.4. Read count were retrieved using FeatureCount summarising data at gene id level. Transcript per milion were generated using featureCount read count using R. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: tab delimited text file  contains the transcript parts million countsTPM for each sample", "Whole kidney marrow", null, "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "tissue:Whole kidney marrow|genotype:rad21+/ ", "GSM8479115", "GSM8479115: Rad21het rep2; Danio rerio; RNA Seq", "GSM8479115 r1", "GSM8479115", "1", "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP528295", null, null, "Rad21het_rep2_L001_R1_001.fastq.gz Rad21het_rep2_L001_R2_001.fastq.gz", "fastq fastq", 15263700610.0, 50542055.0, "GSM8479115 r1", "0:151 1:151", "A:3934169632;C:3701506984;G:3857649812;T:3769115522;N:1258660", 151, 151, null, null, 3934169632, 3701506984, 3857649812, 3769115522, 1258660, "SRX25813459", "SRS22443727", "SRA1954177", "Horsfield, Pathology, University of Otago", "Horsfield, Pathology, University of Otago", 2, 0.9227, 0.92195, 0.02689, 0.02669, 0.72547, 0.73196, 0.47904, 0.48582, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "New Zealand", "2024-08-23", "Adult", "Adult", "Kidney", "Renal System"], [33655, "SRR30355364", "SRX25813458", "SRS22443726", "SRP528295", "PRJNA1151638", "Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA seq]", "GSE275536", "Transcriptome Analysis", "Bulk RNA sequencing analyses of whole kidney marrow tissue isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: RNA sequencing was carried out on whole kidney marrow tissue isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171  which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. RNA sequencing was carried out in triplicates and each replicate consisted of whole kidney marrow pooled from three adult zebrafish.", null, "pubmed:39548947", null, "Rad21het rep1", "GSM8479114", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:rad21+/ |geo loc name:missing|collection date:missing", "Rad21het rep1", "Sequencing reads were QC using FastQC. Sequencing adapter and low quality Q<20 were removed using fastq mcf. Cleaned reads were aligned using HISAT2 version 2.0.4. Read count were retrieved using FeatureCount summarising data at gene id level. Transcript per milion were generated using featureCount read count using R. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: tab delimited text file  contains the transcript parts million countsTPM for each sample", "Whole kidney marrow", null, "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "tissue:Whole kidney marrow|genotype:rad21+/ ", "GSM8479114", "GSM8479114: Rad21het rep1; Danio rerio; RNA Seq", "GSM8479114 r1", "GSM8479114", "1", "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP528295", null, null, "Rad21het_rep1_L001_R1_001.fastq.gz Rad21het_rep1_L001_R2_001.fastq.gz", "fastq fastq", 12383733782.0, 41005741.0, "GSM8479114 r1", "0:151 1:151", "A:3185412651;C:3011130011;G:3135728222;T:3050446997;N:1015901", 151, 151, null, null, 3185412651, 3011130011, 3135728222, 3050446997, 1015901, "SRX25813458", "SRS22443726", "SRA1954177", "Horsfield, Pathology, University of Otago", "Horsfield, Pathology, University of Otago", 2, 0.9242, 0.92383, 0.0273, 0.02728, 0.72151, 0.72683, 0.47619, 0.48803, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "New Zealand", "2024-08-23", "Adult", "Adult", "Kidney", "Renal System"], [33656, "SRR30355365", "SRX25813457", "SRS22443744", "SRP528295", "PRJNA1151638", "Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA seq]", "GSE275536", "Transcriptome Analysis", "Bulk RNA sequencing analyses of whole kidney marrow tissue isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: RNA sequencing was carried out on whole kidney marrow tissue isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171  which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. RNA sequencing was carried out in triplicates and each replicate consisted of whole kidney marrow pooled from three adult zebrafish.", null, "pubmed:39548947", null, "WT rep3", "GSM8479113", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:wild type|geo loc name:missing|collection date:missing", "WT rep3", "Sequencing reads were QC using FastQC. Sequencing adapter and low quality Q<20 were removed using fastq mcf. Cleaned reads were aligned using HISAT2 version 2.0.4. Read count were retrieved using FeatureCount summarising data at gene id level. Transcript per milion were generated using featureCount read count using R. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: tab delimited text file  contains the transcript parts million countsTPM for each sample", "Whole kidney marrow", null, "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "tissue:Whole kidney marrow|genotype:wild type", "GSM8479113", "GSM8479113: WT rep3; Danio rerio; RNA Seq", "GSM8479113 r1", "GSM8479113", "1", "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP528295", null, null, "WT_rep3_L001_R1_001.fastq.gz WT_rep3_L001_R2_001.fastq.gz", "fastq fastq", 13242216498.0, 43848399.0, "GSM8479113 r1", "0:151 1:151", "A:3400902046;C:3224156106;G:3363313174;T:3252754642;N:1090530", 151, 151, null, null, 3400902046, 3224156106, 3363313174, 3252754642, 1090530, "SRX25813457", "SRS22443744", "SRA1954177", "Horsfield, Pathology, University of Otago", "Horsfield, Pathology, University of Otago", 2, 0.91607, 0.91443, 0.02817, 0.02789, 0.705, 0.7107, 0.51363, 0.49767, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "New Zealand", "2024-08-23", "Adult", "Adult", "Kidney", "Renal System"], [33657, "SRR30355366", "SRX25813456", "SRS22443725", "SRP528295", "PRJNA1151638", "Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA seq]", "GSE275536", "Transcriptome Analysis", "Bulk RNA sequencing analyses of whole kidney marrow tissue isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: RNA sequencing was carried out on whole kidney marrow tissue isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171  which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. RNA sequencing was carried out in triplicates and each replicate consisted of whole kidney marrow pooled from three adult zebrafish.", null, "pubmed:39548947", null, "WT rep2", "GSM8479112", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:wild type|geo loc name:missing|collection date:missing", "WT rep2", "Sequencing reads were QC using FastQC. Sequencing adapter and low quality Q<20 were removed using fastq mcf. Cleaned reads were aligned using HISAT2 version 2.0.4. Read count were retrieved using FeatureCount summarising data at gene id level. Transcript per milion were generated using featureCount read count using R. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: tab delimited text file  contains the transcript parts million countsTPM for each sample", "Whole kidney marrow", null, "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "tissue:Whole kidney marrow|genotype:wild type", "GSM8479112", "GSM8479112: WT rep2; Danio rerio; RNA Seq", "GSM8479112 r1", "GSM8479112", "1", "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP528295", null, null, "WT_rep2_L001_R1_001.fastq.gz WT_rep2_L001_R2_001.fastq.gz", "fastq fastq", 10248296614.0, 33934757.0, "GSM8479112 r1", "0:151 1:151", "A:2636593190;C:2486812997;G:2585808493;T:2538244274;N:837660", 151, 151, null, null, 2636593190, 2486812997, 2585808493, 2538244274, 837660, "SRX25813456", "SRS22443725", "SRA1954177", "Horsfield, Pathology, University of Otago", "Horsfield, Pathology, University of Otago", 2, 0.91112, 0.91075, 0.02202, 0.02161, 0.70942, 0.71719, 0.47568, 0.49773, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "New Zealand", "2024-08-23", "Adult", "Adult", "Kidney", "Renal System"], [33658, "SRR30355367", "SRX25813455", "SRS22443724", "SRP528295", "PRJNA1151638", "Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA seq]", "GSE275536", "Transcriptome Analysis", "Bulk RNA sequencing analyses of whole kidney marrow tissue isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: RNA sequencing was carried out on whole kidney marrow tissue isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171  which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. RNA sequencing was carried out in triplicates and each replicate consisted of whole kidney marrow pooled from three adult zebrafish.", null, "pubmed:39548947", null, "WT rep1", "GSM8479111", null, "source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:wild type|geo loc name:missing|collection date:missing", "WT rep1", "Sequencing reads were QC using FastQC. Sequencing adapter and low quality Q<20 were removed using fastq mcf. Cleaned reads were aligned using HISAT2 version 2.0.4. Read count were retrieved using FeatureCount summarising data at gene id level. Transcript per milion were generated using featureCount read count using R. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: tab delimited text file  contains the transcript parts million countsTPM for each sample", "Whole kidney marrow", null, "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "tissue:Whole kidney marrow|genotype:wild type", "GSM8479111", "GSM8479111: WT rep1; Danio rerio; RNA Seq", "GSM8479111 r1", "GSM8479111", "1", "Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq\u00ae RNA Sample Preparation v2", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP528295", null, null, "WT_rep1_L001_R1_001.fastq.gz WT_rep1_L001_R2_001.fastq.gz", "fastq fastq", 11368938584.0, 37645492.0, "GSM8479111 r1", "0:151 1:151", "A:2896983545;C:2796736516;G:2916252779;T:2758034822;N:930922", 151, 151, null, null, 2896983545, 2796736516, 2916252779, 2758034822, 930922, "SRX25813455", "SRS22443724", "SRA1954177", "Horsfield, Pathology, University of Otago", "Horsfield, Pathology, University of Otago", 2, 0.91882, 0.91785, 0.02974, 0.02968, 0.72105, 0.72693, 0.50274, 0.49954, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "New Zealand", "2024-08-23", "Adult", "Adult", "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"]], "truncated": false, "filtered_table_rows_count": 885, "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_selection\" = :p0 and \"experiment.library_strategy\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "cDNA", "p1": "RNA-Seq", "p2": "Kidney"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 885, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&tissue_curation=Kidney", "selected": true}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 837, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&experiment.library_source=TRANSCRIPTOMIC", "selected": false}, {"value": "TRANSCRIPTOMIC SINGLE CELL", "label": "TRANSCRIPTOMIC SINGLE CELL", "count": 48, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney", "results": [{"value": "cDNA", "label": "cDNA", "count": 885, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_strategy=RNA-Seq&tissue_curation=Kidney", "selected": true}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 786, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&experiment.library_layout=PAIRED", "selected": false}, {"value": "SINGLE", "label": "SINGLE", "count": 99, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&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_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 858, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&experiment.platform=ILLUMINA", "selected": false}, {"value": "BGISEQ", "label": "BGISEQ", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&experiment.platform=BGISEQ", "selected": false}, {"value": "DNBSEQ", "label": "DNBSEQ", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&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_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&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_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney", "results": [{"value": "Adult", "label": "Adult", "count": 546, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&devstage_curation_coarse=Adult", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 145, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&devstage_curation_coarse=Undetermined", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 119, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&devstage_curation_coarse=Multi-stage", "selected": false}, {"value": "Larval", "label": "Larval", "count": 64, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&devstage_curation_coarse=Larval", "selected": false}, {"value": "Juvenile", "label": "Juvenile", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&devstage_curation_coarse=Juvenile", "selected": false}, {"value": "Embryo", "label": "Embryo", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&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_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney", "results": [{"value": "Undetermined", "label": "Undetermined", "count": 489, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&devstage_curation=Undetermined", "selected": false}, {"value": "Adult", "label": "Adult", "count": 263, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&devstage_curation=Adult", "selected": false}, {"value": "Larval", "label": "Larval", "count": 64, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&devstage_curation=Larval", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 58, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&devstage_curation=Multi-stage", "selected": false}, {"value": "Juvenile", "label": "Juvenile", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&devstage_curation=Juvenile", "selected": false}, {"value": "Pharyngula", "label": "Pharyngula", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&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_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney", "results": [{"value": "Renal System", "label": "Renal System", "count": 885, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&tissue_curation_coarse=Renal+System", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney", "results": [{"value": "Kidney", "label": "Kidney", "count": 885, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney", "results": [{"value": "smartseq", "label": "smartseq", "count": 261, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&technology=smartseq", "selected": false}, {"value": "unknown", "label": "unknown", "count": 244, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&technology=unknown", "selected": false}, {"value": "celseq", "label": "celseq", "count": 132, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&technology=celseq", "selected": false}, {"value": "10x", "label": "10x", "count": 89, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&technology=10x", "selected": false}, {"value": "bulk", "label": "bulk", "count": 66, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&technology=bulk", "selected": false}, {"value": "scartrace", "label": "scartrace", "count": 48, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&technology=scartrace", "selected": false}, {"value": "indrops", "label": "indrops", "count": 19, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&technology=indrops", "selected": false}, {"value": "quartzseq", "label": "quartzseq", "count": 15, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&technology=quartzseq", "selected": false}, {"value": "generic-scrnaseq-only", "label": "generic-scrnaseq-only", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&technology=generic-scrnaseq-only", "selected": false}, {"value": "microwellseq", "label": "microwellseq", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&technology=microwellseq", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": "38268", "next_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.library_strategy=RNA-Seq&tissue_curation=Kidney&_next=38268", "private": false, "allow_execute_sql": true, "query_ms": 173.82810400158633}