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
8067,ERR035547,ERX013537,ERS017858,ERP000447,PRJEB2368,Sanger zebrafish sequencing,E-MTAB-460,Other,,,,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,,,,,,,,,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,1600Application ReadForward11Technical ReadReverse772Application ReadReverse85,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,,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,,United Kingdom,2011-02-03,Adult,Adult,Kidney,Renal System
8072,ERR023146,ERX009446,ERS017858,ERP000447,PRJEB2368,Sanger zebrafish sequencing,E-MTAB-460,Other,,,,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,,,,,,,,,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,1520Application ReadForward11Application ReadReverse77,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,,,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,,United Kingdom,2011-02-03,Adult,Adult,Kidney,Renal System
8075,ERR023149,ERX009443,ERS017858,ERP000447,PRJEB2368,Sanger zebrafish sequencing,E-MTAB-460,Other,,,,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,,,,,,,,,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,1520Application ReadForward11Application ReadReverse77,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,,,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,,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,,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,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 10 08 2022 10:54:39:372 85553,MF4,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,,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,,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,,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,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 10 08 2022 10:54:39:372 85551,MF3,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,,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,,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,,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,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 10 08 2022 10:54:39:372 85549,MF2,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,,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,,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,,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,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 10 08 2022 10:54:39:372 85547,MF1,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,,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,,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,,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,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 10 08 2022 10:54:39:371 85545,MM4,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,,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,,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,,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,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 10 08 2022 10:54:39:371 85543,MM3,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,,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,,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,,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,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 10 08 2022 10:54:39:371 85541,MM2,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,,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,,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,,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,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 10 08 2022 10:54:39:371 85539,MM1,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,,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,,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,,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,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 10 08 2022 10:54:39:370 85537,WF4,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,,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,,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,,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,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 10 08 2022 10:54:39:370 85535,WF3,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,,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,,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,,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,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 10 08 2022 10:54:39:370 85533,WF2,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,,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,,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,,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,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 10 08 2022 10:54:39:370 85531,WF1,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,,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,,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,,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,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 10 08 2022 10:54:39:369 85529,WM4,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,,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,,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,,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,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 10 08 2022 10:54:39:369 85527,WM3,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,,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,,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,,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,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 10 08 2022 10:54:39:369 85525,WM2,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,,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,,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,,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,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 10 08 2022 10:54:39:368 85523,WM1,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,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,,,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,,Unknown,2022-09-15,Undetermined,Undetermined,Kidney,Renal System
32162,SRR29095835,SRX24619914,SRS21357066,SRP508906,PRJNA1113956,A zebrafish model of diabetic nephropathy,PRJNA1113956,Other,We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.,,,,6 month zebrafish kidney 1,DN zebrafish,,strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal,,,,,,,,,6 month zebrafish with proteinuria kidney 4,OF 4,OF 4,6 month zebrafish with proteinuria kidney 4,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP508906,,,OF_4_1.fq OF_4_2.fq,fastq fastq,4377669000.0,14592230.0,OF 4 1.fq,0:150 1:150,A:1194166573;C:999239529;G:1001594280;T:1182651631;N:16987,150,150,,,1194166573,999239529,1001594280,1182651631,16987,SRX24619914,SRS21357066,SRA1872692,Mie Univeristy|School of Medicine,Mie Univeristy,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Japan,2024-05-21,Adult,Adult,Kidney,Renal System
32163,SRR29095836,SRX24619913,SRS21357066,SRP508906,PRJNA1113956,A zebrafish model of diabetic nephropathy,PRJNA1113956,Other,We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.,,,,6 month zebrafish kidney 1,DN zebrafish,,strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal,,,,,,,,,6 month zebrafish with proteinuria kidney 3,OF 3,OF 3,6 month zebrafish with proteinuria kidney 3,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP508906,,,OF_3_1.fq OF_3_2.fq,fastq fastq,4798165200.0,15993884.0,OF 3 1.fq,0:150 1:150,A:1290466714;C:1114007506;G:1115137813;T:1278535708;N:17459,150,150,,,1290466714,1114007506,1115137813,1278535708,17459,SRX24619913,SRS21357066,SRA1872692,Mie Univeristy|School of Medicine,Mie Univeristy,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Japan,2024-05-21,Adult,Adult,Kidney,Renal System
32164,SRR29095837,SRX24619912,SRS21357066,SRP508906,PRJNA1113956,A zebrafish model of diabetic nephropathy,PRJNA1113956,Other,We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.,,,,6 month zebrafish kidney 1,DN zebrafish,,strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal,,,,,,,,,6 month zebrafish with proteinuria kidney 2,OF 2,OF 2,6 month zebrafish with proteinuria kidney 2,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP508906,,,OF_2_1.fq OF_2_2.fq,fastq fastq,5661202800.0,18870676.0,OF 2 1.fq,0:150 1:150,A:1549085619;C:1287400217;G:1288853902;T:1535841249;N:21813,150,150,,,1549085619,1287400217,1288853902,1535841249,21813,SRX24619912,SRS21357066,SRA1872692,Mie Univeristy|School of Medicine,Mie Univeristy,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Japan,2024-05-21,Adult,Adult,Kidney,Renal System
32165,SRR29095838,SRX24619911,SRS21357066,SRP508906,PRJNA1113956,A zebrafish model of diabetic nephropathy,PRJNA1113956,Other,We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.,,,,6 month zebrafish kidney 1,DN zebrafish,,strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal,,,,,,,,,6 month zebrafish with proteinuria kidney 1,OF 1,OF 1,6 month zebrafish with proteinuria kidney 1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP508906,,,OF_1_1.fq OF_1_2.fq,fastq fastq,5957895600.0,19859652.0,OF 1 1.fq,0:150 1:150,A:1627320757;C:1359602784;G:1360982917;T:1609967331;N:21811,150,150,,,1627320757,1359602784,1360982917,1609967331,21811,SRX24619911,SRS21357066,SRA1872692,Mie Univeristy|School of Medicine,Mie Univeristy,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Japan,2024-05-21,Adult,Adult,Kidney,Renal System
32166,SRR29095839,SRX24619910,SRS21357066,SRP508906,PRJNA1113956,A zebrafish model of diabetic nephropathy,PRJNA1113956,Other,We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.,,,,6 month zebrafish kidney 1,DN zebrafish,,strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal,,,,,,,,,6 month zebrafish kidney 4,NF 6,NF 6,6 month zebrafish kidney 4,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP508906,,,NF_6_1.fq NF_6_2.fq,fastq fastq,5469504900.0,18231683.0,NF 6 1.fq,0:150 1:150,A:1480833386;C:1260945093;G:1261275041;T:1466430429;N:20951,150,150,,,1480833386,1260945093,1261275041,1466430429,20951,SRX24619910,SRS21357066,SRA1872692,Mie Univeristy|School of Medicine,Mie Univeristy,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Japan,2024-05-21,Adult,Adult,Kidney,Renal System
32167,SRR29095840,SRX24619909,SRS21357066,SRP508906,PRJNA1113956,A zebrafish model of diabetic nephropathy,PRJNA1113956,Other,We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.,,,,6 month zebrafish kidney 1,DN zebrafish,,strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal,,,,,,,,,6 month zebrafish kidney 3,NF 5,NF 5,6 month zebrafish kidney 3,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP508906,,,NF_5_1.fq NF_5_2.fq,fastq fastq,6386781900.0,21289273.0,NF 5 1.fq,0:150 1:150,A:1743273279;C:1458330156;G:1460747658;T:1724406616;N:24191,150,150,,,1743273279,1458330156,1460747658,1724406616,24191,SRX24619909,SRS21357066,SRA1872692,Mie Univeristy|School of Medicine,Mie Univeristy,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Japan,2024-05-21,Adult,Adult,Kidney,Renal System
32168,SRR29095841,SRX24619908,SRS21357066,SRP508906,PRJNA1113956,A zebrafish model of diabetic nephropathy,PRJNA1113956,Other,We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.,,,,6 month zebrafish kidney 1,DN zebrafish,,strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal,,,,,,,,,6 month zebrafish kidney 2,NF 2,NF 2,6 month zebrafish kidney 2,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP508906,,,NF_2_1.fq NF_2_2.fq,fastq fastq,5747851800.0,19159506.0,NF 2 1.fq,0:150 1:150,A:1564796254;C:1316015979;G:1317516650;T:1549501774;N:21143,150,150,,,1564796254,1316015979,1317516650,1549501774,21143,SRX24619908,SRS21357066,SRA1872692,Mie Univeristy|School of Medicine,Mie Univeristy,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Japan,2024-05-21,Adult,Adult,Kidney,Renal System
32169,SRR29095842,SRX24619907,SRS21357066,SRP508906,PRJNA1113956,A zebrafish model of diabetic nephropathy,PRJNA1113956,Other,We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.,,,,6 month zebrafish kidney 1,DN zebrafish,,strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal,,,,,,,,,6 month zebrafish kidney 1,NF 1,NF 1,6 month zebrafish kidney 1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP508906,,,NF_1_1.fq NF_1_2.fq,fastq fastq,5369089800.0,17896966.0,NF 1 1.fq,0:150 1:150,A:1413369042;C:1273865602;G:1277141372;T:1404694133;N:19651,150,150,,,1413369042,1273865602,1277141372,1404694133,19651,SRX24619907,SRS21357066,SRA1872692,Mie Univeristy|School of Medicine,Mie Univeristy,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Japan,2024-05-21,Adult,Adult,Kidney,Renal System
32611,SRR29356860,SRX24871764,SRS21581236,SRP513122,PRJNA1122499,An mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy,GSE269547,Transcriptome Analysis,Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune protective mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from zebrafish immunized with the mRNA vaccine and the LPP control. For mRNA vaccination mRNA candidate vaccines were injected with 1µg 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.,,pubmed:39759874,,kidneys LPP immunized sample3,GSM8321946,,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 mpf 15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 μL for intramuscular i.m immunization. 1μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP513122,,,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,,,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,,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 1µg 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.,,pubmed:39759874,,kidneys LPP immunized sample2,GSM8321945,,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 mpf 15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 μL for intramuscular i.m immunization. 1μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP513122,,,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,,,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,,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 1µg 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.,,pubmed:39759874,,kidneys LPP immunized sample1,GSM8321944,,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 mpf 15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 μL for intramuscular i.m immunization. 1μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP513122,,,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,,,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,,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 1µg 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.,,pubmed:39759874,,kidneys L3T immunized sample3,GSM8321943,,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 mpf 15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 μL for intramuscular i.m immunization. 1μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP513122,,,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,,,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,,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 1µg 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.,,pubmed:39759874,,kidneys L3T immunized sample2,GSM8321942,,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 mpf 15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 μL for intramuscular i.m immunization. 1μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP513122,,,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,,,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,,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 1µg 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.,,pubmed:39759874,,kidneys L3T immunized sample1,GSM8321941,,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 mpf 15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 μL for intramuscular i.m immunization. 1μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP513122,,,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,,,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,,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 0.5µg 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.,,pubmed:39759874,,M.m infection sample3,GSM8334559,,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 mpf 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 0.5μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514436,,,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,,,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,,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 0.5µg 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.,,pubmed:39759874,,M.m infection sample2,GSM8334558,,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 mpf 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 0.5μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514436,,,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,,,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,,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 0.5µg 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.,,pubmed:39759874,,M.m infection sample1,GSM8334557,,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 mpf 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 0.5μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514436,,,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,,,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,,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 0.5µg 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.,,pubmed:39759874,,Blank sample3,GSM8334556,,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 mpf 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 0.5μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514436,,,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,,,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,,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 0.5µg 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.,,pubmed:39759874,,Blank sample2,GSM8334555,,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 mpf 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 0.5μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514436,,,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,,,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,,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 0.5µg 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.,,pubmed:39759874,,Blank sample1,GSM8334554,,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 mpf 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 0.5μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514436,,,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,,,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,,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 0.5µg 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.,,pubmed:39759874,,PBS treated sample3,GSM8334553,,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 mpf 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 0.5μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514436,,,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,,,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,,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 0.5µg 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.,,pubmed:39759874,,PBS treated sample2,GSM8334552,,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 mpf 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 0.5μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514436,,,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,,,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,,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 0.5µg 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.,,pubmed:39759874,,PBS treated sample1,GSM8334551,,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 mpf 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 0.5μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514436,,,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,,,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,,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 0.5µg 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.,,pubmed:39759874,,LPP treated sample3,GSM8334550,,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 mpf 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 0.5μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514436,,,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,,,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,,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 0.5µg 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.,,pubmed:39759874,,LPP treated sample2,GSM8334549,,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 mpf 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 0.5μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514436,,,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,,,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,,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 0.5µg 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.,,pubmed:39759874,,LPP treated sample1,GSM8334548,,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 mpf 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 0.5μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514436,,,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,,,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,,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 0.5µg 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.,,pubmed:39759874,,L3T treated sample3,GSM8334547,,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 mpf 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 0.5μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514436,,,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,,,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,,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 0.5µg 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.,,pubmed:39759874,,L3T treated sample2,GSM8334546,,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 mpf 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 0.5μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514436,,,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,,,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,,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 0.5µg 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.,,pubmed:39759874,,L3T treated sample1,GSM8334545,,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 mpf 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 0.5μg 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’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.,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 ∼28°C pH ∼7.4 and conductivity ∼1500μS.,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514436,,,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,,,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,,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.,,pubmed:39916610,,kidney derived neutrophils homozygous Mm infected rep3,GSM8335407,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514613,,,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,,,1920522839,1515700169,1537191557,1927497878,97057,SRX24965357,SRS21668889,SRA1902200,University of Tampere,University of Tampere,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,pubmed:39916610,,kidney derived neutrophils homozygous Mm infected rep2,GSM8335406,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514613,,,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,,,1901340557,1516911325,1537883236,1921186807,91675,SRX24965356,SRS21668888,SRA1902200,University of Tampere,University of Tampere,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,pubmed:39916610,,kidney derived neutrophils homozygous Mm infected rep1,GSM8335405,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514613,,,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,,,1923648919,1520702661,1540739284,1936060582,91254,SRX24965355,SRS21668887,SRA1902200,University of Tampere,University of Tampere,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,pubmed:39916610,,kidney derived neutrophils wt Mm infected rep3,GSM8335404,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514613,,,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,,,1866248606,1494647864,1513464764,1881229301,92365,SRX24965354,SRS21668886,SRA1902200,University of Tampere,University of Tampere,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,pubmed:39916610,,kidney derived neutrophils wt Mm infected rep2,GSM8335403,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514613,,,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,,,1897407228,1488944523,1508394915,1907051254,88280,SRX24965353,SRS21668885,SRA1902200,University of Tampere,University of Tampere,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,pubmed:39916610,,kidney derived neutrophils wt Mm infected rep1,GSM8335402,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP514613,,,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,,,1863279045,1498858984,1519081612,1879233731,91028,SRX24965352,SRS21668884,SRA1902200,University of Tampere,University of Tampere,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2024-06-18,Larval,Larval,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.,,pubmed:39548947,,Rad21het rep3,GSM8479116,,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,,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® RNA Sample Preparation v2,,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® RNA Sample Preparation v2,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Five,,SRP528295,,,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,,,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,,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.,,pubmed:39548947,,Rad21het rep2,GSM8479115,,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,,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® RNA Sample Preparation v2,,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® RNA Sample Preparation v2,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Five,,SRP528295,,,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,,,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,,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.,,pubmed:39548947,,Rad21het rep1,GSM8479114,,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,,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® RNA Sample Preparation v2,,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® RNA Sample Preparation v2,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Five,,SRP528295,,,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,,,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,,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.,,pubmed:39548947,,WT rep3,GSM8479113,,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,,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® RNA Sample Preparation v2,,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® RNA Sample Preparation v2,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Five,,SRP528295,,,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,,,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,,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.,,pubmed:39548947,,WT rep2,GSM8479112,,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,,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® RNA Sample Preparation v2,,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® RNA Sample Preparation v2,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Five,,SRP528295,,,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,,,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,,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.,,pubmed:39548947,,WT rep1,GSM8479111,,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,,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® RNA Sample Preparation v2,,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® RNA Sample Preparation v2,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Five,,SRP528295,,,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,,,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,,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.,,pubmed:39916610,,kidney derived neutrophils homozygous Mm infected rep6,GSM8748663,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP558767,,,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,,,1920598119,1565819640,1566891465,1896911503,231473,SRX27413530,SRS23843189,SRA2056436,University of Tampere,University of Tampere,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,pubmed:39916610,,kidney derived neutrophils homozygous Mm infected rep5,GSM8748662,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP558767,,,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,,,1831236930,1510631608,1510442962,1810728281,668219,SRX27413529,SRS23843188,SRA2056436,University of Tampere,University of Tampere,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,pubmed:39916610,,kidney derived neutrophils homozygous Mm infected rep4,GSM8748661,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP558767,,,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,,,1736278764,1437925823,1439447440,1714587759,627114,SRX27413528,SRS23843187,SRA2056436,University of Tampere,University of Tampere,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,pubmed:39916610,,kidney derived neutrophils homozygous Mm infected rep3,GSM8748660,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP558767,,,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,,,1647964217,1357673528,1357262640,1631490903,217712,SRX27413527,SRS23843186,SRA2056436,University of Tampere,University of Tampere,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,pubmed:39916610,,kidney derived neutrophils homozygous Mm infected rep2,GSM8748659,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP558767,,,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,,,1650140619,1346802182,1348552488,1627259927,680084,SRX27413526,SRS23843185,SRA2056436,University of Tampere,University of Tampere,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,pubmed:39916610,,kidney derived neutrophils homozygous Mm infected rep1,GSM8748658,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP558767,,,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,,,1798422932,1471942244,1470322290,1774672386,642548,SRX27413525,SRS23843184,SRA2056436,University of Tampere,University of Tampere,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,pubmed:39916610,,kidney derived neutrophils wt Mm infected rep6,GSM8748657,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP558767,,,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,,,1785469029,1447831778,1441059581,1765446885,218027,SRX27413524,SRS23843183,SRA2056436,University of Tampere,University of Tampere,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,pubmed:39916610,,kidney derived neutrophils wt Mm infected rep5,GSM8748656,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP558767,,,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,,,1786241571,1451411588,1447987838,1764221339,654864,SRX27413523,SRS23843182,SRA2056436,University of Tampere,University of Tampere,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,pubmed:39916610,,kidney derived neutrophils wt Mm infected rep4,GSM8748655,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP558767,,,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,,,1748779929,1415200694,1412343882,1729784544,662851,SRX27413522,SRS23843181,SRA2056436,University of Tampere,University of Tampere,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,pubmed:39916610,,kidney derived neutrophils wt Mm infected rep3,GSM8748654,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP558767,,,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,,,1907309824,1546968275,1546306637,1879237297,234567,SRX27413521,SRS23843180,SRA2056436,University of Tampere,University of Tampere,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,pubmed:39916610,,kidney derived neutrophils wt Mm infected rep2,GSM8748653,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP558767,,,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,,,1768453408,1440642021,1438187733,1744118899,380239,SRX27413520,SRS23843179,SRA2056436,University of Tampere,University of Tampere,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,pubmed:39916610,,kidney derived neutrophils wt Mm infected rep1,GSM8748652,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP558767,,,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,,,1824710129,1507871608,1512676495,1791435639,675329,SRX27413519,SRS23843178,SRA2056436,University of Tampere,University of Tampere,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,,,Iso Seq RNA from Danio rerio,C2 F2 F K,,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,,,,,,,,,Iso Seq RNA from kidney,C2 F2 F K,C2 F2 F K,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,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,,,,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,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,,,Iso Seq RNA from Danio rerio,C2 F2 M K22,,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,,,,,,,,,Iso Seq RNA from kidney,C2 F2 M K22,C2 F2 M K22,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,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,,,,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,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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.,,,,Iso Seq RNA from Danio rerio,C2 F2 M K21,,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,,,,,,,,,Iso Seq RNA from kidney,C2 F2 M K21,C2 F2 M K21,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,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,,,,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,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,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,,strain:AB|age:5 month|biomaterial provider:INRA|sex:male and female|tissue:Kidney|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Kidney,F Dr 7,F Dr 7,Total RNA was qualified using an Agilent BioAnalyzer and 1 µg 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,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,SRP044781,,,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,,,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,,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°C to mild 18°C and severe 10°C 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 ‘negative regulation of endopeptidase activity’ 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,,pubmed:26227973,,kidney10,GSM1523044,,source name:kidney|tissue:kidney|temperature:10°C|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,,tissue:kidney|temperature:10°C|strain:Tubingen|age:6 mpf,GSM1523044,GSM1523044: kidney10; Danio rerio; RNA Seq,GSM1523044,,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,,SRP048807,,,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,,,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,,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°C to mild 18°C and severe 10°C 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 ‘negative regulation of endopeptidase activity’ 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,,pubmed:26227973,,kidney18,GSM1523043,,source name:kidney|tissue:kidney|temperature:18°C|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,,tissue:kidney|temperature:18°C|strain:Tubingen|age:6 mpf,GSM1523043,GSM1523043: kidney18; Danio rerio; RNA Seq,GSM1523043,,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,,SRP048807,,,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,,,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,,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°C to mild 18°C and severe 10°C 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 ‘negative regulation of endopeptidase activity’ 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,,pubmed:26227973,,kidney28,GSM1523042,,source name:kidney|tissue:kidney|temperature:28°C|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,,tissue:kidney|temperature:28°C|strain:Tubingen|age:6 mpf,GSM1523042,GSM1523042: kidney28; Danio rerio; RNA Seq,GSM1523042,,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,,SRP048807,,,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,,,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,,China,2014-10-09,Adult,Adult,Kidney,Renal System
38296,SRR1647681,SRX756916,SRS742120,SRP049663,PRJNA266803,Spring Varaemia of Carp Virus SVCV infection of adult zebrafish,GSE63133,Transcriptome Analysis,During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.,,pubmed:25535281,,24K,GSM1541905,,source name:head kidney|tissue:head kidney|disease state:24h post SVCV infection,24K,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,head kidney,,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:head kidney|disease state:24h post SVCV infection,GSM1541905,GSM1541905: 24K; Danio rerio; RNA Seq,GSM1541905,,1,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1541905,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP049663,,,24K_GTGAAA_L003_R1.fastq,fastq,1020487560.0,20009560.0,GSM1541905 r1,0:51,A:266117014;C:246797067;G:240014464;T:267491299;N:67716,51,,,,266117014,246797067,240014464,267491299,67716,SRX756916,SRS742120,SRA200717,GEO,"Institute of Hydrobiology, Chinese Academy of Sciences",1,0.92411,,0.07686,,0.68647,,0.4627,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2014-11-10,Undetermined,Adult,Kidney,Renal System
38297,SRR1647680,SRX756915,SRS742117,SRP049663,PRJNA266803,Spring Varaemia of Carp Virus SVCV infection of adult zebrafish,GSE63133,Transcriptome Analysis,During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.,,pubmed:25535281,,6K,GSM1541904,,source name:head kidney|tissue:head kidney|disease state:6h post SVCV infection,6K,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,head kidney,,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:head kidney|disease state:6h post SVCV infection,GSM1541904,GSM1541904: 6K; Danio rerio; RNA Seq,GSM1541904,,1,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1541904,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP049663,,,6K_GTCCGC_L003_R1.fastq,fastq,929436036.0,18224236.0,GSM1541904 r1,0:51,A:242005719;C:225485975;G:219890494;T:241993975;N:59873,51,,,,242005719,225485975,219890494,241993975,59873,SRX756915,SRS742117,SRA200717,GEO,"Institute of Hydrobiology, Chinese Academy of Sciences",1,0.92547,,0.09105,,0.69264,,0.49166,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2014-11-10,Undetermined,Adult,Kidney,Renal System
38298,SRR1647679,SRX756914,SRS742116,SRP049663,PRJNA266803,Spring Varaemia of Carp Virus SVCV infection of adult zebrafish,GSE63133,Transcriptome Analysis,During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.,,pubmed:25535281,,0K,GSM1541903,,source name:head kidney|tissue:head kidney|disease state:un infected,0K,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,head kidney,,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:head kidney|disease state:un infected,GSM1541903,GSM1541903: 0K; Danio rerio; RNA Seq,GSM1541903,,1,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1541903,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP049663,,,0K_CCGTCC_L003_R1.fastq,fastq,1077979095.0,21136845.0,GSM1541903 r1,0:51,A:280277150;C:261348733;G:255721013;T:280562071;N:70128,51,,,,280277150,261348733,255721013,280562071,70128,SRX756914,SRS742116,SRA200717,GEO,"Institute of Hydrobiology, Chinese Academy of Sciences",1,0.92545,,0.08181,,0.68373,,0.49408,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2014-11-10,Undetermined,Adult,Kidney,Renal System
41473,SRR5457065,SRX2745133,SRS1761840,SRP092128,PRJNA350712,Phylogenetic analysis of intron retention in vertebrates,PRJNA350712,Other,Our study is detailing new evidence for transcriptomic complexity realized by a mechanism of orchestrated intron retention.,,,,zebrafish granulocytes,dre granulocytes,,strain: |age:3 month 6 month|sex:male|tissue:kidney marrow|biomaterial provider:Graham Lieschke|cell type:granulocyte|health state:healthy|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish granulocytes,dre gran TruSeq RNA paired Ill HiSeq2000,dre gran TruSeq RNA paired Ill HiSeq2000,RNA seq libraries were prepared from >1 g of total RNA using TruSeq RNA sample prep kit Illumina according to the manufacturersÍ instructions,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP092128,,,Zebrafish-1_ZF1_1.fastq.gz Zebrafish-1_ZF1_2.fastq.gz Zebrafish-1_ZF3_1.fastq.gz Zebrafish-1_ZF3_2.fastq.gz,fastq fastq fastq fastq,27103033264.0,134173432.0,Zebrafish 1 ZF3 2.fastq.gz,0:101 1:101,A:7205178092;C:6377884075;G:6326441274;T:7192445241;N:1084582,101,101,,,7205178092,6377884075,6326441274,7192445241,1084582,SRX2745133,SRS1761840,SRA555068,Centenary Institute|Gene & Stem Cell Therapy Program,Centenary Institute,2,0.97153,0.98059,0.09216,0.09282,0.72679,0.7234,0.46875,0.47002,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Australia,2017-04-19,Adult,Adult,Kidney,Renal System
41873,SRR5320505,SRX2619910,SRS2029873,SRP101556,PRJNA378487,Transcriptional profiling of the zebrafish proximal tubule,GSE95808,Transcriptome Analysis,The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney the pronephros represents a simplified form of the mammalian organ yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here we establish a high resolution expression profile of isolated GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue,,pubmed:31188030,,Morpholino 7,GSM2526320,,tissue:larval kidney|line:tgPT::EGFP|genotype/variation:Hnf1b depleted,Morpholino 7,Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts.,larval kidney,,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,,line:tgPT::EGFP|genotype/variation:Hnf1b depleted,GSM2526320,GSM2526320: Morpholino 7; Danio rerio; RNA Seq,GSM2526320,,1,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,GEO Accession:GSM2526320,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP101556,,,C6H9AANXX-1531-06-1-1_CTTGTAAT_L001_R1_001.fastq.gz C6H9AANXX-1531-06-1-1_CTTGTAAT_L001_R2_001.fastq.gz,fastq fastq,8670821250.0,34683285.0,GSM2526320 r1,0:125 1:125,A:2285357364;C:2049868144;G:2107192972;T:2225558024;N:2844746,125,125,,,2285357364,2049868144,2107192972,2225558024,2844746,SRX2619910,SRS2029873,SRA543390,GEO,"Molecular Medicine and Pathology, University of Auckland",2,0.96682,0.96763,0.08369,0.08426,0.69296,0.69493,0.47739,0.47931,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-03-08,Multi-stage,Multi-stage,Kidney,Renal System
41874,SRR5320504,SRX2619909,SRS2029872,SRP101556,PRJNA378487,Transcriptional profiling of the zebrafish proximal tubule,GSE95808,Transcriptome Analysis,The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney the pronephros represents a simplified form of the mammalian organ yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here we establish a high resolution expression profile of isolated GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue,,pubmed:31188030,,Morpholino 5,GSM2526319,,tissue:larval kidney|line:tgPT::EGFP|genotype/variation:Hnf1b depleted,Morpholino 5,Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts.,larval kidney,,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,,line:tgPT::EGFP|genotype/variation:Hnf1b depleted,GSM2526319,GSM2526319: Morpholino 5; Danio rerio; RNA Seq,GSM2526319,,1,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,GEO Accession:GSM2526319,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP101556,,,C6H9AANXX-1531-05-1-1_CAGATCAT_L001_R1_001.fastq.gz C6H9AANXX-1531-05-1-1_CAGATCAT_L001_R2_001.fastq.gz,fastq fastq,9864273500.0,39457094.0,GSM2526319 r1,0:125 1:125,A:2628741477;C:2304848464;G:2364915536;T:2562525014;N:3243009,125,125,,,2628741477,2304848464,2364915536,2562525014,3243009,SRX2619909,SRS2029872,SRA543390,GEO,"Molecular Medicine and Pathology, University of Auckland",2,0.96115,0.96161,0.10876,0.10854,0.67495,0.67616,0.45304,0.45767,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-03-08,Multi-stage,Multi-stage,Kidney,Renal System
41875,SRR5320503,SRX2619908,SRS2029871,SRP101556,PRJNA378487,Transcriptional profiling of the zebrafish proximal tubule,GSE95808,Transcriptome Analysis,The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney the pronephros represents a simplified form of the mammalian organ yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here we establish a high resolution expression profile of isolated GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue,,pubmed:31188030,,Morpholino 4,GSM2526318,,tissue:larval kidney|line:tgPT::EGFP|genotype/variation:Hnf1b depleted,Morpholino 4,Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts.,larval kidney,,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,,line:tgPT::EGFP|genotype/variation:Hnf1b depleted,GSM2526318,GSM2526318: Morpholino 4; Danio rerio; RNA Seq,GSM2526318,,1,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,GEO Accession:GSM2526318,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP101556,,,C6H9AANXX-1531-04-1-1_GCCAATAT_L001_R1_001.fastq.gz C6H9AANXX-1531-04-1-1_GCCAATAT_L001_R2_001.fastq.gz,fastq fastq,8503939500.0,34015758.0,GSM2526318 r1,0:125 1:125,A:2251120561;C:2002327793;G:2052310864;T:2195401798;N:2778484,125,125,,,2251120561,2002327793,2052310864,2195401798,2778484,SRX2619908,SRS2029871,SRA543390,GEO,"Molecular Medicine and Pathology, University of Auckland",2,0.96344,0.96379,0.09973,0.09974,0.68043,0.68264,0.46613,0.46851,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-03-08,Multi-stage,Multi-stage,Kidney,Renal System
41876,SRR5320502,SRX2619907,SRS2029870,SRP101556,PRJNA378487,Transcriptional profiling of the zebrafish proximal tubule,GSE95808,Transcriptome Analysis,The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney the pronephros represents a simplified form of the mammalian organ yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here we establish a high resolution expression profile of isolated GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue,,pubmed:31188030,,Control 3,GSM2526317,,tissue:larval kidney|line:tgPT::EGFP|genotype/variation:wild type,Control 3,Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts.,larval kidney,,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,,line:tgPT::EGFP|genotype/variation:wild type,GSM2526317,GSM2526317: Control 3; Danio rerio; RNA Seq,GSM2526317,,1,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,GEO Accession:GSM2526317,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP101556,,,C6H9AANXX-1531-03-1-1_ACAGTGAT_L001_R1_001.fastq.gz C6H9AANXX-1531-03-1-1_ACAGTGAT_L001_R2_001.fastq.gz,fastq fastq,9619758500.0,38479034.0,GSM2526317 r1,0:125 1:125,A:2561625595;C:2249183851;G:2312313710;T:2493482524;N:3152820,125,125,,,2561625595,2249183851,2312313710,2493482524,3152820,SRX2619907,SRS2029870,SRA543390,GEO,"Molecular Medicine and Pathology, University of Auckland",2,0.96067,0.96218,0.10832,0.10898,0.66675,0.66866,0.47609,0.47441,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-03-08,Multi-stage,Multi-stage,Kidney,Renal System
41877,SRR5320501,SRX2619906,SRS2029869,SRP101556,PRJNA378487,Transcriptional profiling of the zebrafish proximal tubule,GSE95808,Transcriptome Analysis,The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney the pronephros represents a simplified form of the mammalian organ yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here we establish a high resolution expression profile of isolated GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue,,pubmed:31188030,,Control 2,GSM2526316,,tissue:larval kidney|line:tgPT::EGFP|genotype/variation:wild type,Control 2,Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts.,larval kidney,,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,,line:tgPT::EGFP|genotype/variation:wild type,GSM2526316,GSM2526316: Control 2; Danio rerio; RNA Seq,GSM2526316,,1,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,GEO Accession:GSM2526316,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP101556,,,C6H9AANXX-1531-02-1-1_TGACCAAT_L001_R1_001.fastq.gz C6H9AANXX-1531-02-1-1_TGACCAAT_L001_R2_001.fastq.gz,fastq fastq,8939151000.0,35756604.0,GSM2526316 r1,0:125 1:125,A:2379909844;C:2090182914;G:2143061952;T:2323063658;N:2932632,125,125,,,2379909844,2090182914,2143061952,2323063658,2932632,SRX2619906,SRS2029869,SRA543390,GEO,"Molecular Medicine and Pathology, University of Auckland",2,0.96176,0.96203,0.10658,0.10717,0.67087,0.67194,0.45961,0.46137,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-03-08,Multi-stage,Multi-stage,Kidney,Renal System
41878,SRR5320500,SRX2619905,SRS2029868,SRP101556,PRJNA378487,Transcriptional profiling of the zebrafish proximal tubule,GSE95808,Transcriptome Analysis,The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney the pronephros represents a simplified form of the mammalian organ yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here we establish a high resolution expression profile of isolated GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue,,pubmed:31188030,,Control 1,GSM2526315,,tissue:larval kidney|line:tgPT::EGFP|genotype/variation:wild type,Control 1,Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts.,larval kidney,,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,,line:tgPT::EGFP|genotype/variation:wild type,GSM2526315,GSM2526315: Control 1; Danio rerio; RNA Seq,GSM2526315,,1,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,GEO Accession:GSM2526315,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP101556,,,C6H9AANXX-1531-01-1-1_CGATGTAT_L001_R1_001.fastq.gz C6H9AANXX-1531-01-1-1_CGATGTAT_L001_R2_001.fastq.gz,fastq fastq,9579790250.0,38319161.0,GSM2526315 r1,0:125 1:125,A:2520690618;C:2269535412;G:2326632146;T:2459796830;N:3135244,125,125,,,2520690618,2269535412,2326632146,2459796830,3135244,SRX2619905,SRS2029868,SRA543390,GEO,"Molecular Medicine and Pathology, University of Auckland",2,0.96456,0.96615,0.08928,0.09003,0.68373,0.6856,0.46544,0.46416,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-03-08,Multi-stage,Multi-stage,Kidney,Renal System
41902,SRR5337748,SRX2635098,SRS2043910,SRP101756,PRJNA378882,Transcriptome of the distal late segment of the zebrafish mesonephros,GSE96519,Transcriptome Analysis,We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.,,pubmed:28656378,,YS6,GSM2534771,,tissue:Mes1phros DL|transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult,YS6,none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts,Mesonephros DL,,DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.,,transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult,GSM2534771,GSM2534771: YS6; Danio rerio; RNA Seq,GSM2534771,,1,DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.,GEO Accession:GSM2534771,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP101756,,,20150717.A-YS6_R1.fastq.gz,fastq,5434051896.0,43127396.0,GSM2534771 r1,0:126,A:1185876928;C:1354521221;G:1643633065;T:1249907593;N:113089,126,,,,1185876928,1354521221,1643633065,1249907593,113089,SRX2635098,SRS2043910,SRA544882,GEO,"Drummond, Nephrology, Massachusetts General Hospital",1,0.97351,,0.17501,,0.85303,,0.75625,,126,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2017-03-12,Adult,Adult,Kidney,Renal System
41903,SRR5337747,SRX2635097,SRS2043909,SRP101756,PRJNA378882,Transcriptome of the distal late segment of the zebrafish mesonephros,GSE96519,Transcriptome Analysis,We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.,,pubmed:28656378,,YS5,GSM2534770,,tissue:DL segments|transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult,YS5,none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts,DL segments,,DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.,,transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult,GSM2534770,GSM2534770: YS5; Danio rerio; RNA Seq,GSM2534770,,1,DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.,GEO Accession:GSM2534770,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP101756,,,20150717.A-YS5_R1.fastq(1).gz,fastq,2297696058.0,18235683.0,GSM2534770 r1,0:126,A:648837532;C:505738661;G:568578688;T:574489076;N:52101,126,,,,648837532,505738661,568578688,574489076,52101,SRX2635097,SRS2043909,SRA544882,GEO,"Drummond, Nephrology, Massachusetts General Hospital",1,0.94402,,0.1927,,0.77585,,0.67728,,126,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2017-03-12,Adult,Adult,Kidney,Renal System
41904,SRR5337746,SRX2635096,SRS2043908,SRP101756,PRJNA378882,Transcriptome of the distal late segment of the zebrafish mesonephros,GSE96519,Transcriptome Analysis,We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.,,pubmed:28656378,,YS4,GSM2534769,,tissue:Mes1phros DL|transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult,YS4,none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts,Mesonephros DL,,DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.,,transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult,GSM2534769,GSM2534769: YS4; Danio rerio; RNA Seq,GSM2534769,,1,DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.,GEO Accession:GSM2534769,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP101756,,,20150717.A-YS4_R1.fastq.gz,fastq,4570634754.0,36274879.0,GSM2534769 r1,0:126,A:1179398927;C:1024363944;G:1239125274;T:1127644877;N:101732,126,,,,1179398927,1024363944,1239125274,1127644877,101732,SRX2635096,SRS2043908,SRA544882,GEO,"Drummond, Nephrology, Massachusetts General Hospital",1,0.93083,,0.27465,,0.78102,,0.70638,,126,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2017-03-12,Adult,Adult,Kidney,Renal System
41905,SRR5337745,SRX2635095,SRS2043907,SRP101756,PRJNA378882,Transcriptome of the distal late segment of the zebrafish mesonephros,GSE96519,Transcriptome Analysis,We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.,,pubmed:28656378,,YS3,GSM2534768,,tissue:DL segments|transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult,YS3,none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts,DL segments,,DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.,,transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult,GSM2534768,GSM2534768: YS3; Danio rerio; RNA Seq,GSM2534768,,1,DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.,GEO Accession:GSM2534768,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP101756,,,20150717.A-YS3_R1.fastq.gz,fastq,5648398686.0,44828561.0,GSM2534768 r1,0:126,A:1607436982;C:1222995706;G:1369036558;T:1448805498;N:123942,126,,,,1607436982,1222995706,1369036558,1448805498,123942,SRX2635095,SRS2043907,SRA544882,GEO,"Drummond, Nephrology, Massachusetts General Hospital",1,0.93399,,0.20266,,0.78076,,0.73978,,126,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2017-03-12,Adult,Adult,Kidney,Renal System
41906,SRR5337744,SRX2635094,SRS2043906,SRP101756,PRJNA378882,Transcriptome of the distal late segment of the zebrafish mesonephros,GSE96519,Transcriptome Analysis,We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.,,pubmed:28656378,,YS2,GSM2534767,,tissue:Mes1phros DL|transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult,YS2,none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts,Mesonephros DL,,DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.,,transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult,GSM2534767,GSM2534767: YS2; Danio rerio; RNA Seq,GSM2534767,,1,DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.,GEO Accession:GSM2534767,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP101756,,,20150717.A-YS2_R1.fastq.gz,fastq,4680679374.0,37148249.0,GSM2534767 r1,0:126,A:1320151433;C:986429614;G:1112497899;T:1261495719;N:104709,126,,,,1320151433,986429614,1112497899,1261495719,104709,SRX2635094,SRS2043906,SRA544882,GEO,"Drummond, Nephrology, Massachusetts General Hospital",1,0.91952,,0.24724,,0.73884,,0.63985,,126,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2017-03-12,Adult,Adult,Kidney,Renal System
41907,SRR5337743,SRX2635093,SRS2043905,SRP101756,PRJNA378882,Transcriptome of the distal late segment of the zebrafish mesonephros,GSE96519,Transcriptome Analysis,We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.,,pubmed:28656378,,YS1,GSM2534766,,tissue:DL segments|transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult,YS1,none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts,DL segments,,DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.,,transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult,GSM2534766,GSM2534766: YS1; Danio rerio; RNA Seq,GSM2534766,,1,DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.,GEO Accession:GSM2534766,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP101756,,,20150717.A-YS1_R1.fastq.gz,fastq,7000703892.0,55561142.0,GSM2534766 r1,0:126,A:1521231890;C:1760818628;G:2148863730;T:1569634203;N:155441,126,,,,1521231890,1760818628,2148863730,1569634203,155441,SRX2635093,SRS2043905,SRA544882,GEO,"Drummond, Nephrology, Massachusetts General Hospital",1,0.96016,,0.1982,,0.86261,,0.75572,,126,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2017-03-12,Adult,Adult,Kidney,Renal System
42599,SRR5810682,SRX2989237,SRS2341160,SRP111339,PRJNA393429,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops],GSE100910,Transcriptome Analysis,Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.,parent bioproject:PRJNA393415,pubmed:28878000,,inDrop sequencing of multiple samples 2,GSM2696104,,source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes,inDrop sequencing of multiple samples 2,"Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file ""inDrop GEO supplementary.xlsx "" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.",Whole kidney marrow,,RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.,,indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes,GSM2696104,GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq,GSM2696104,,1,RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.,GEO Accession:GSM2696104,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP111339,,,inDrop_v3_run2_R1.fastq.gz,fastq,23315853588.0,382227108.0,GSM2696104 r1,0:61 1:0,A:6573828142;C:5137891481;G:5021324431;T:6582457296;N:352238,61,0,,,6573828142,5137891481,5021324431,6582457296,352238,SRX2989237,SRS2341160,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.83828,,0.08537,,0.83552,,0.56658,,61,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42600,SRR5810683,SRX2989237,SRS2341160,SRP111339,PRJNA393429,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops],GSE100910,Transcriptome Analysis,Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.,parent bioproject:PRJNA393415,pubmed:28878000,,inDrop sequencing of multiple samples 2,GSM2696104,,source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes,inDrop sequencing of multiple samples 2,"Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file ""inDrop GEO supplementary.xlsx "" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.",Whole kidney marrow,,RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.,,indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes,GSM2696104,GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq,GSM2696104,,1,RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.,GEO Accession:GSM2696104,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP111339,,,inDrop_v3_run2_R2.fastq.gz,fastq,3057816864.0,382227108.0,GSM2696104 r2,0:0 1:8,A:743619897;C:720488231;G:1031094190;T:562297818;N:316728,0,8,,,743619897,720488231,1031094190,562297818,316728,SRX2989237,SRS2341160,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42601,SRR5810684,SRX2989237,SRS2341160,SRP111339,PRJNA393429,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops],GSE100910,Transcriptome Analysis,Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.,parent bioproject:PRJNA393415,pubmed:28878000,,inDrop sequencing of multiple samples 2,GSM2696104,,source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes,inDrop sequencing of multiple samples 2,"Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file ""inDrop GEO supplementary.xlsx "" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.",Whole kidney marrow,,RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.,,indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes,GSM2696104,GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq,GSM2696104,,1,RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.,GEO Accession:GSM2696104,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP111339,,,inDrop_v3_run2_R3.fastq.gz,fastq,3057816864.0,382227108.0,GSM2696104 r3,0:8,A:913664473;C:577895371;G:646194239;T:918893384;N:1169397,8,,,,913664473,577895371,646194239,918893384,1169397,SRX2989237,SRS2341160,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42602,SRR5810685,SRX2989237,SRS2341160,SRP111339,PRJNA393429,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops],GSE100910,Transcriptome Analysis,Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.,parent bioproject:PRJNA393415,pubmed:28878000,,inDrop sequencing of multiple samples 2,GSM2696104,,source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes,inDrop sequencing of multiple samples 2,"Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file ""inDrop GEO supplementary.xlsx "" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.",Whole kidney marrow,,RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.,,indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes,GSM2696104,GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq,GSM2696104,,1,RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.,GEO Accession:GSM2696104,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP111339,,,inDrop_v3_run2_R4.fastq.gz,fastq,5351179512.0,382227108.0,GSM2696104 r4,0:14,A:1351470715;C:1294400719;G:1379073889;T:1322397488;N:3836701,14,,,,1351470715,1294400719,1379073889,1322397488,3836701,SRX2989237,SRS2341160,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.0,,0.0,,1.0,,,,14,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System
42603,SRR5810678,SRX2989236,SRS2341159,SRP111339,PRJNA393429,Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops],GSE100910,Transcriptome Analysis,Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals n=2 068 cells and prkdcD3612fs il2rgaY91fs double compound mutant fish N=2 animals n=2 276 cells. Lastly we identified seven structural and functional cell lineages of kidney identities in the whole kidney marrow n=1 699 kidney cells.,parent bioproject:PRJNA393415,pubmed:28878000,,inDrop sequencing of multiple samples 1,GSM2696103,,source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes,inDrop sequencing of multiple samples 1,"Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file ""inDrop GEO supplementary.xlsx "" available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts.",Whole kidney marrow,,RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.,,indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes,GSM2696103,GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq,GSM2696103,,1,RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.,GEO Accession:GSM2696103,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP111339,,,inDrop_v3_run1_R1.fastq.gz,fastq,26868371039.0,440465099.0,GSM2696103 r1,0:61 1:0,A:7598044404;C:5948542485;G:5746339343;T:7575168754;N:276053,61,0,,,7598044404,5948542485,5746339343,7575168754,276053,SRX2989236,SRS2341159,SRA584587,GEO,"Pathology, Massachusetts General Hospital",1,0.83437,,0.08222,,0.82658,,0.54569,,61,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,indrops,,United States,2017-07-07,Undetermined,Adult,Kidney,Renal System