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244 rows where experiment.library_selection = "cDNA", technology = "unknown" and tissue_curation = "Kidney"

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devstage_curation_coarse 5

devstage_curation 5

experiment.platform 4

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Kidney · 244 ✖

technology 1

  • unknown · 244 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • cDNA · 244 ✖
Link 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>2</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>85</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP000447 Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing ENA FIRST PUBLIC:2011 06 14|ENA LAST UPDATE:2018 11 16 5625_3.srf srf 3610226240.0 22563914.0 E MTAB 460 part2:5625 3.srf 0:76 1:8 2:76 A:924866194;C:782403420;G:781277214;T:934812782;N:6355318 76 8 76   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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP000447 Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing ENA FIRST PUBLIC:2011 02 03|ENA LAST UPDATE:2018 11 16 3212_8.srf srf 1030624600.0 6780425.0 E MTAB 460:3212 8.srf 0:76 1:76 A:349845451;C:160945226;G:157028856;T:352888853;N:9916214 76 76     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP000447 Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing ENA FIRST PUBLIC:2011 02 03|ENA LAST UPDATE:2018 11 16 4191_6.srf srf 3888911336.0 25584943.0 E MTAB 460:4191 6.srf 0:76 1:76 A:1359993097;C:582070992;G:582686161;T:1356976166;N:7184920 76 76     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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
32611 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 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 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 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 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 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 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 tr…   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 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 tr…   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 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 tr…   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 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 tr…   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 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 tr…   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 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 tr…   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 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 tr…   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 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 tr…   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 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 tr…   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 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 tr…   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 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 tr…   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 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 tr…   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 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 tr…   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 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 tr…   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 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 tr…   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 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 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 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 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 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 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
34535 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP044781     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 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 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 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 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 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 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 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 &amp; Stem Cell Therapy Program Centenary Institute 2 0.97153 0.98059 0.09216 0.09282 0.72679 0.7234 0.46875 0.47002 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Australia 2017-04-19 Adult Adult Kidney Renal System
41873 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 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 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 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 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 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
47595 47595 SRR6661145 SRX3638241 SRS2904492 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidWTPHZ 3 GSM2975189   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type KidWTPHZ 3 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type GSM2975189 GSM2975189: KidWTPHZ 3; Danio rerio; RNA Seq GSM2975189   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975189 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidWTPHZ_3.fastq.gz fastq 858099990.0 16825490.0 GSM2975189 r1 0:51 A:231903062;C:197865548;G:200825484;T:227491985;N:13911 51       231903062 197865548 200825484 227491985 13911 SRX3638241 SRS2904492 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.9605   0.10316   0.70721   0.51089   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47596 47596 SRR6661144 SRX3638240 SRS2904491 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidWTPHZ 2 GSM2975188   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type KidWTPHZ 2 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type GSM2975188 GSM2975188: KidWTPHZ 2; Danio rerio; RNA Seq GSM2975188   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975188 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidWTPHZ_2.fastq.gz fastq 799571013.0 15677863.0 GSM2975188 r1 0:51 A:217401512;C:183178629;G:185275617;T:213702318;N:12937 51       217401512 183178629 185275617 213702318 12937 SRX3638240 SRS2904491 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.96209   0.10882   0.70861   0.5149   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47597 47597 SRR6661143 SRX3638239 SRS2904490 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidWTPHZ 1 GSM2975187   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type KidWTPHZ 1 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type GSM2975187 GSM2975187: KidWTPHZ 1; Danio rerio; RNA Seq GSM2975187   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975187 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidWTPHZ_1.fastq.gz fastq 816038505.0 16000755.0 GSM2975187 r1 0:51 A:218420574;C:190260181;G:192288409;T:215056318;N:13023 51       218420574 190260181 192288409 215056318 13023 SRX3638239 SRS2904490 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.96264   0.09527   0.70834   0.51477   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47598 47598 SRR6661142 SRX3638238 SRS2904489 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidWT 3 GSM2975186   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type KidWT 3 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type GSM2975186 GSM2975186: KidWT 3; Danio rerio; RNA Seq GSM2975186   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975186 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidWT_3.fastq.gz fastq 852094026.0 16707726.0 GSM2975186 r1 0:51 A:234167802;C:192807979;G:194651214;T:230453461;N:13570 51       234167802 192807979 194651214 230453461 13570 SRX3638238 SRS2904489 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.95788   0.12336   0.70258   0.48964   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47599 47599 SRR6661141 SRX3638237 SRS2904488 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidWT 2 GSM2975185   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type KidWT 2 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type GSM2975185 GSM2975185: KidWT 2; Danio rerio; RNA Seq GSM2975185   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975185 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidWT_2.fastq.gz fastq 969772038.0 19015138.0 GSM2975185 r1 0:51 A:265582126;C:219526888;G:222468938;T:262178447;N:15639 51       265582126 219526888 222468938 262178447 15639 SRX3638237 SRS2904488 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.95803   0.12522   0.69794   0.50805   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47600 47600 SRR6661140 SRX3638236 SRS2904487 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidWT 1 GSM2975184   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type KidWT 1 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Wild type GSM2975184 GSM2975184: KidWT 1; Danio rerio; RNA Seq GSM2975184   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975184 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidWT_1.fastq.gz fastq 815590011.0 15991961.0 GSM2975184 r1 0:51 A:224190865;C:184406547;G:186159880;T:220819162;N:13557 51       224190865 184406547 186159880 220819162 13557 SRX3638236 SRS2904487 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.95883   0.13181   0.7023   0.49523   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47601 47601 SRR6661139 SRX3638235 SRS2904486 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidDKOPHZ 3 GSM2975183   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO KidDKOPHZ 3 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO GSM2975183 GSM2975183: KidDKOPHZ 3; Danio rerio; RNA Seq GSM2975183   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975183 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidDKOPHZ_3.fastq.gz fastq 789588885.0 15482135.0 GSM2975183 r1 0:51 A:215354577;C:180286176;G:181162894;T:212772248;N:12990 51       215354577 180286176 181162894 212772248 12990 SRX3638235 SRS2904486 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.92385   0.10405   0.70471   0.50985   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47602 47602 SRR6661138 SRX3638234 SRS2904485 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidDKOPHZ 2 GSM2975182   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO KidDKOPHZ 2 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO GSM2975182 GSM2975182: KidDKOPHZ 2; Danio rerio; RNA Seq GSM2975182   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975182 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidDKOPHZ_2.fastq.gz fastq 866844552.0 16996952.0 GSM2975182 r1 0:51 A:235445628;C:198901971;G:200334068;T:232148841;N:14044 51       235445628 198901971 200334068 232148841 14044 SRX3638234 SRS2904485 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.92657   0.10886   0.71112   0.52093   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47603 47603 SRR6661137 SRX3638233 SRS2904484 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidDKOPHZ 1 GSM2975181   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO KidDKOPHZ 1 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO GSM2975181 GSM2975181: KidDKOPHZ 1; Danio rerio; RNA Seq GSM2975181   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975181 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidDKOPHZ_1.fastq.gz fastq 795526560.0 15598560.0 GSM2975181 r1 0:51 A:216666052;C:181785239;G:183159054;T:213903089;N:13126 51       216666052 181785239 183159054 213903089 13126 SRX3638233 SRS2904484 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.92522   0.10277   0.7121   0.51721   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47604 47604 SRR6661136 SRX3638232 SRS2904483 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidDKO 3 GSM2975180   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO KidDKO 3 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO GSM2975180 GSM2975180: KidDKO 3; Danio rerio; RNA Seq GSM2975180   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975180 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidDKO_3.fastq.gz fastq 699170577.0 13709227.0 GSM2975180 r1 0:51 A:191094810;C:157413925;G:158857752;T:191792628;N:11462 51       191094810 157413925 158857752 191792628 11462 SRX3638232 SRS2904483 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.9183   0.12207   0.7083   0.52994   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47605 47605 SRR6661135 SRX3638231 SRS2904482 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidDKO 2 GSM2975179   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO KidDKO 2 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO GSM2975179 GSM2975179: KidDKO 2; Danio rerio; RNA Seq GSM2975179   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975179 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidDKO_2.fastq.gz fastq 720757194.0 14132494.0 GSM2975179 r1 0:51 A:198433339;C:163064446;G:163967236;T:195280391;N:11782 51       198433339 163064446 163967236 195280391 11782 SRX3638231 SRS2904482 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.92921   0.11261   0.7063   0.52644   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
47606 47606 SRR6661134 SRX3638230 SRS2904481 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   KidDKO 1 GSM2975178   source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO KidDKO 1 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO GSM2975178 GSM2975178: KidDKO 1; Danio rerio; RNA Seq GSM2975178   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975178 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     KidDKO_1.fastq.gz fastq 835548606.0 16383306.0 GSM2975178 r1 0:51 A:227900020;C:191118125;G:192603640;T:223913065;N:13756 51       227900020 191118125 192603640 223913065 13756 SRX3638230 SRS2904481 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.93166   0.10926   0.7063   0.50705   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Kidney Renal System
48074 48074 SRR7008287 SRX3940775 SRS3171576 SRP140471 PRJNA450343 A Zebrafish Acromegaly Model Elevates DNA Damage and Impairs DNA Repair Pathways GSE113169 Transcriptome Analysis Acromegaly is a pathological condition due to excess growth hormone GH secretion. Acromegaly patients exhibit a deterioration of health and many associated complications such as cardiovascular issues arthritis kidney diseases muscular weakness and colon cancer. Since these complications are generalized throughout the body we investigated the effect of GH excess on cellular integrity. Here we established stable acromegaly model zebrafish lines that overexpress tilapia GH and the red fluorescence protein RFP reporter gene for tracking GH gene expression throughout generations and performed RNA Seq data analysis from different organs. Intriguingly heatmap and Expression2Kinases X2K analysis revealed the enrichment of DNA damage markers in various organs. Moreover H2A.X immunostaining analysis in acromegaly zebrafish larvae and the adult acromegaly model brain and muscle showed a robust increase in the number of DNA damaged cells. Using Gene Set Enrichment Analysis GSEA we found that the acromegaly zebrafish model had impaired DNA repair pathways in the liver such as double strand break DSB homologous recombination repair HRR non homologous end joining NHEJ nucleotide excision repair NER and translesion synthesis TLS. Interestingly the impairment of DNA repair was even more prominent in acromegaly model than in aged zebrafish three years old. Thus our study demonstrates that affection of cellular integrity is characteristic of acromegaly Overall design: Total mRNA obtained from 1 years old acromegaly zebrafish model muscle brain kidney liver and 3 dpf larvae compared to wild type WT zebrafish were generated by deep sequencing using Illumina.   pubmed:30336646;pubmed:32517323;pubmed:33849304   Kidney WT rep2 GSM3098423   source name:Kidney|genotype:wild type|tissue:Kidney|age:1 year old Kidney WT rep2 Illumina Casava1.7 software used for basecalling. HISAT2 software was used according to the instructions from the program designers to map the raw reads of acromegaly and WT samples to zebrafish genome reference GRCz10 retrieved from Ensembl database together with the annotation file. The Cufflinks pipeline was used to assign reads to known transcripts and test for differential expression between acromegaly model and the WT samples. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads FPKM. Genome build: GRCz10 Supplementary files format and content: One tab delimited text file containing all FPKM values for all Samples. Kidney   tissues were removed and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.   genotype:wild type|tissue:Kidney|age:1 year old GSM3098423 GSM3098423: Kidney WT rep2; Danio rerio; RNA Seq GSM3098423   1 tissues were removed and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide. GEO Accession:GSM3098423 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP140471     WT_K6_Kidney_21_1.fq.gz WT_K6_Kidney_21_2.fq.gz fastq fastq 452219400.0 2261097.0 GSM3098423 r1 0:100 1:100 A:119997841;C:105588197;G:105552577;T:121010097;N:70688 100 100     119997841 105588197 105552577 121010097 70688 SRX3940775 SRS3171576 SRA690975 GEO Aquatic Molecular Biology and Biotechnology, Aquatic Bioscience, The University of Tokyo 2 0.93414 0.93513 0.07437 0.07244 0.71622 0.71593 0.5221 0.52872 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-04-16 Adult Adult Kidney Renal System
48075 48075 SRR7008286 SRX3940774 SRS3171575 SRP140471 PRJNA450343 A Zebrafish Acromegaly Model Elevates DNA Damage and Impairs DNA Repair Pathways GSE113169 Transcriptome Analysis Acromegaly is a pathological condition due to excess growth hormone GH secretion. Acromegaly patients exhibit a deterioration of health and many associated complications such as cardiovascular issues arthritis kidney diseases muscular weakness and colon cancer. Since these complications are generalized throughout the body we investigated the effect of GH excess on cellular integrity. Here we established stable acromegaly model zebrafish lines that overexpress tilapia GH and the red fluorescence protein RFP reporter gene for tracking GH gene expression throughout generations and performed RNA Seq data analysis from different organs. Intriguingly heatmap and Expression2Kinases X2K analysis revealed the enrichment of DNA damage markers in various organs. Moreover H2A.X immunostaining analysis in acromegaly zebrafish larvae and the adult acromegaly model brain and muscle showed a robust increase in the number of DNA damaged cells. Using Gene Set Enrichment Analysis GSEA we found that the acromegaly zebrafish model had impaired DNA repair pathways in the liver such as double strand break DSB homologous recombination repair HRR non homologous end joining NHEJ nucleotide excision repair NER and translesion synthesis TLS. Interestingly the impairment of DNA repair was even more prominent in acromegaly model than in aged zebrafish three years old. Thus our study demonstrates that affection of cellular integrity is characteristic of acromegaly Overall design: Total mRNA obtained from 1 years old acromegaly zebrafish model muscle brain kidney liver and 3 dpf larvae compared to wild type WT zebrafish were generated by deep sequencing using Illumina.   pubmed:30336646;pubmed:32517323;pubmed:33849304   Kidney WT rep1 GSM3098422   source name:Kidney|genotype:wild type|tissue:Kidney|age:1 year old Kidney WT rep1 Illumina Casava1.7 software used for basecalling. HISAT2 software was used according to the instructions from the program designers to map the raw reads of acromegaly and WT samples to zebrafish genome reference GRCz10 retrieved from Ensembl database together with the annotation file. The Cufflinks pipeline was used to assign reads to known transcripts and test for differential expression between acromegaly model and the WT samples. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads FPKM. Genome build: GRCz10 Supplementary files format and content: One tab delimited text file containing all FPKM values for all Samples. Kidney   tissues were removed and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.   genotype:wild type|tissue:Kidney|age:1 year old GSM3098422 GSM3098422: Kidney WT rep1; Danio rerio; RNA Seq GSM3098422   1 tissues were removed and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide. GEO Accession:GSM3098422 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP140471     WT_K4_Kidney_20_1.fq.gz WT_K4_Kidney_20_2.fq.gz fastq fastq 468105400.0 2340527.0 GSM3098422 r1 0:100 1:100 A:125918771;C:107695952;G:107289472;T:127127892;N:73313 100 100     125918771 107695952 107289472 127127892 73313 SRX3940774 SRS3171575 SRA690975 GEO Aquatic Molecular Biology and Biotechnology, Aquatic Bioscience, The University of Tokyo 2 0.93618 0.93627 0.08989 0.08801 0.73026 0.72971 0.54855 0.55327 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-04-16 Adult Adult Kidney Renal System
48076 48076 SRR7008285 SRX3940773 SRS3171574 SRP140471 PRJNA450343 A Zebrafish Acromegaly Model Elevates DNA Damage and Impairs DNA Repair Pathways GSE113169 Transcriptome Analysis Acromegaly is a pathological condition due to excess growth hormone GH secretion. Acromegaly patients exhibit a deterioration of health and many associated complications such as cardiovascular issues arthritis kidney diseases muscular weakness and colon cancer. Since these complications are generalized throughout the body we investigated the effect of GH excess on cellular integrity. Here we established stable acromegaly model zebrafish lines that overexpress tilapia GH and the red fluorescence protein RFP reporter gene for tracking GH gene expression throughout generations and performed RNA Seq data analysis from different organs. Intriguingly heatmap and Expression2Kinases X2K analysis revealed the enrichment of DNA damage markers in various organs. Moreover H2A.X immunostaining analysis in acromegaly zebrafish larvae and the adult acromegaly model brain and muscle showed a robust increase in the number of DNA damaged cells. Using Gene Set Enrichment Analysis GSEA we found that the acromegaly zebrafish model had impaired DNA repair pathways in the liver such as double strand break DSB homologous recombination repair HRR non homologous end joining NHEJ nucleotide excision repair NER and translesion synthesis TLS. Interestingly the impairment of DNA repair was even more prominent in acromegaly model than in aged zebrafish three years old. Thus our study demonstrates that affection of cellular integrity is characteristic of acromegaly Overall design: Total mRNA obtained from 1 years old acromegaly zebrafish model muscle brain kidney liver and 3 dpf larvae compared to wild type WT zebrafish were generated by deep sequencing using Illumina.   pubmed:30336646;pubmed:32517323;pubmed:33849304   Kidney ACRO rep3 GSM3098421   source name:Kidney|genotype:Acromegaly zebrafish model|tissue:Kidney|age:1 year old Kidney ACRO rep3 Illumina Casava1.7 software used for basecalling. HISAT2 software was used according to the instructions from the program designers to map the raw reads of acromegaly and WT samples to zebrafish genome reference GRCz10 retrieved from Ensembl database together with the annotation file. The Cufflinks pipeline was used to assign reads to known transcripts and test for differential expression between acromegaly model and the WT samples. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads FPKM. Genome build: GRCz10 Supplementary files format and content: One tab delimited text file containing all FPKM values for all Samples. Kidney   tissues were removed and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.   genotype:Acromegaly zebrafish model|tissue:Kidney|age:1 year old GSM3098421 GSM3098421: Kidney ACRO rep3; Danio rerio; RNA Seq GSM3098421   1 tissues were removed and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide. GEO Accession:GSM3098421 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP140471     GH_K3_Kidney_19_1.fq.gz GH_K3_Kidney_19_2.fq.gz fastq fastq 516366800.0 2581834.0 GSM3098421 r1 0:100 1:100 A:139000034;C:118629581;G:117673967;T:140984276;N:78942 100 100     139000034 118629581 117673967 140984276 78942 SRX3940773 SRS3171574 SRA690975 GEO Aquatic Molecular Biology and Biotechnology, Aquatic Bioscience, The University of Tokyo 2 0.93368 0.93424 0.08046 0.07881 0.73032 0.73125 0.52305 0.51853 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-04-16 Adult Adult Kidney Renal System
48077 48077 SRR7008284 SRX3940772 SRS3171573 SRP140471 PRJNA450343 A Zebrafish Acromegaly Model Elevates DNA Damage and Impairs DNA Repair Pathways GSE113169 Transcriptome Analysis Acromegaly is a pathological condition due to excess growth hormone GH secretion. Acromegaly patients exhibit a deterioration of health and many associated complications such as cardiovascular issues arthritis kidney diseases muscular weakness and colon cancer. Since these complications are generalized throughout the body we investigated the effect of GH excess on cellular integrity. Here we established stable acromegaly model zebrafish lines that overexpress tilapia GH and the red fluorescence protein RFP reporter gene for tracking GH gene expression throughout generations and performed RNA Seq data analysis from different organs. Intriguingly heatmap and Expression2Kinases X2K analysis revealed the enrichment of DNA damage markers in various organs. Moreover H2A.X immunostaining analysis in acromegaly zebrafish larvae and the adult acromegaly model brain and muscle showed a robust increase in the number of DNA damaged cells. Using Gene Set Enrichment Analysis GSEA we found that the acromegaly zebrafish model had impaired DNA repair pathways in the liver such as double strand break DSB homologous recombination repair HRR non homologous end joining NHEJ nucleotide excision repair NER and translesion synthesis TLS. Interestingly the impairment of DNA repair was even more prominent in acromegaly model than in aged zebrafish three years old. Thus our study demonstrates that affection of cellular integrity is characteristic of acromegaly Overall design: Total mRNA obtained from 1 years old acromegaly zebrafish model muscle brain kidney liver and 3 dpf larvae compared to wild type WT zebrafish were generated by deep sequencing using Illumina.   pubmed:30336646;pubmed:32517323;pubmed:33849304   Kidney ACRO rep2 GSM3098420   source name:Kidney|genotype:Acromegaly zebrafish model|tissue:Kidney|age:1 year old Kidney ACRO rep2 Illumina Casava1.7 software used for basecalling. HISAT2 software was used according to the instructions from the program designers to map the raw reads of acromegaly and WT samples to zebrafish genome reference GRCz10 retrieved from Ensembl database together with the annotation file. The Cufflinks pipeline was used to assign reads to known transcripts and test for differential expression between acromegaly model and the WT samples. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads FPKM. Genome build: GRCz10 Supplementary files format and content: One tab delimited text file containing all FPKM values for all Samples. Kidney   tissues were removed and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.   genotype:Acromegaly zebrafish model|tissue:Kidney|age:1 year old GSM3098420 GSM3098420: Kidney ACRO rep2; Danio rerio; RNA Seq GSM3098420   1 tissues were removed and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide. GEO Accession:GSM3098420 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP140471     GH_K2_Kidney_18_1.fq.gz GH_K2_Kidney_18_2.fq.gz fastq fastq 554022000.0 2770110.0 GSM3098420 r1 0:100 1:100 A:145695233;C:130810207;G:130333919;T:147099701;N:82940 100 100     145695233 130810207 130333919 147099701 82940 SRX3940772 SRS3171573 SRA690975 GEO Aquatic Molecular Biology and Biotechnology, Aquatic Bioscience, The University of Tokyo 2 0.94063 0.94251 0.08052 0.07972 0.72316 0.72372 0.51706 0.53029 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-04-16 Adult Adult Kidney Renal System
48078 48078 SRR7008283 SRX3940771 SRS3171572 SRP140471 PRJNA450343 A Zebrafish Acromegaly Model Elevates DNA Damage and Impairs DNA Repair Pathways GSE113169 Transcriptome Analysis Acromegaly is a pathological condition due to excess growth hormone GH secretion. Acromegaly patients exhibit a deterioration of health and many associated complications such as cardiovascular issues arthritis kidney diseases muscular weakness and colon cancer. Since these complications are generalized throughout the body we investigated the effect of GH excess on cellular integrity. Here we established stable acromegaly model zebrafish lines that overexpress tilapia GH and the red fluorescence protein RFP reporter gene for tracking GH gene expression throughout generations and performed RNA Seq data analysis from different organs. Intriguingly heatmap and Expression2Kinases X2K analysis revealed the enrichment of DNA damage markers in various organs. Moreover H2A.X immunostaining analysis in acromegaly zebrafish larvae and the adult acromegaly model brain and muscle showed a robust increase in the number of DNA damaged cells. Using Gene Set Enrichment Analysis GSEA we found that the acromegaly zebrafish model had impaired DNA repair pathways in the liver such as double strand break DSB homologous recombination repair HRR non homologous end joining NHEJ nucleotide excision repair NER and translesion synthesis TLS. Interestingly the impairment of DNA repair was even more prominent in acromegaly model than in aged zebrafish three years old. Thus our study demonstrates that affection of cellular integrity is characteristic of acromegaly Overall design: Total mRNA obtained from 1 years old acromegaly zebrafish model muscle brain kidney liver and 3 dpf larvae compared to wild type WT zebrafish were generated by deep sequencing using Illumina.   pubmed:30336646;pubmed:32517323;pubmed:33849304   Kidney ACRO rep1 GSM3098419   source name:Kidney|genotype:Acromegaly zebrafish model|tissue:Kidney|age:1 year old Kidney ACRO rep1 Illumina Casava1.7 software used for basecalling. HISAT2 software was used according to the instructions from the program designers to map the raw reads of acromegaly and WT samples to zebrafish genome reference GRCz10 retrieved from Ensembl database together with the annotation file. The Cufflinks pipeline was used to assign reads to known transcripts and test for differential expression between acromegaly model and the WT samples. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads FPKM. Genome build: GRCz10 Supplementary files format and content: One tab delimited text file containing all FPKM values for all Samples. Kidney   tissues were removed and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide.   genotype:Acromegaly zebrafish model|tissue:Kidney|age:1 year old GSM3098419 GSM3098419: Kidney ACRO rep1; Danio rerio; RNA Seq GSM3098419   1 tissues were removed and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep KitCat# RS 122 2101 was used with 1 ug of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina TruSeq Stranded mRNA Sample Preparation guide. GEO Accession:GSM3098419 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP140471     GH_K1_Kidney_17_1.fq.gz GH_K1_Kidney_17_2.fq.gz fastq fastq 421518000.0 2107590.0 GSM3098419 r1 0:100 1:100 A:108267615;C:102016623;G:102089011;T:109080343;N:64408 100 100     108267615 102016623 102089011 109080343 64408 SRX3940771 SRS3171572 SRA690975 GEO Aquatic Molecular Biology and Biotechnology, Aquatic Bioscience, The University of Tokyo 2 0.93823 0.94043 0.08003 0.07811 0.72508 0.72502 0.49632 0.50453 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-04-16 Adult Adult Kidney Renal System
49079 49079 SRR7659034 SRX4520651 SRS3639026 SRP156734 PRJNA485080 Characterization of the immune response to Mycobacterium marinum infection in zebrafish GSE118288 Transcriptome Analysis Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. As expected based on the literature our results showed the induction of genes coding proteins associated to immune signaling cell migration and acute phase response indicating that the immune response to M. marinum infection in zebrafish is similar than the response to tuberculosis causing Mycobacterium tuberculosis in humans. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 8 samples were analyzed four biological replicates in each group.   pubmed:31626817   ABc 4: WT control rep4 GSM3324252   source name:zebrafish kidney|genotype:wild type AB|agent:n1 control|tissue:zebrafish kidney ABc 4: WT control rep4 Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts  Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 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 Gencode id. The remaining columns indicate the read counts such that each column represents a sample. zebrafish kidney 5 mpf to 6 mpf zebrafish were infected with 5 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. Control samples were collected from unchallenged wild type AB fish of the smame litter which was used for infections. Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. The zebrafish were maintained according to the standard protocols. genotype:wild type AB|agent:n1 control|tissue:zebrafish kidney GSM3324252 GSM3324252: ABc 4: WT control rep4; Danio rerio; RNA Seq GSM3324252   1 Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. GEO Accession:GSM3324252 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP156734     ABc_4_1.fq.gz ABc_4_2.fq.gz fastq fastq 8338149600.0 27793832.0 GSM3324252 r1 0:150 1:150 A:2217593021;C:1962526726;G:1956500797;T:2200674254;N:854802 150 150     2217593021 1962526726 1956500797 2200674254 854802 SRX4520651 SRS3639026 SRA755536 GEO University of Tampere 2 0.92493 0.91975 0.05312 0.0528 0.69603 0.70005 0.52953 0.5259 150 150 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   Finland 2018-08-08 Multi-stage Multi-stage Kidney Renal System
49080 49080 SRR7659033 SRX4520650 SRS3639025 SRP156734 PRJNA485080 Characterization of the immune response to Mycobacterium marinum infection in zebrafish GSE118288 Transcriptome Analysis Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. As expected based on the literature our results showed the induction of genes coding proteins associated to immune signaling cell migration and acute phase response indicating that the immune response to M. marinum infection in zebrafish is similar than the response to tuberculosis causing Mycobacterium tuberculosis in humans. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 8 samples were analyzed four biological replicates in each group.   pubmed:31626817   ABc 3: WT control rep3 GSM3324251   source name:zebrafish kidney|genotype:wild type AB|agent:n1 control|tissue:zebrafish kidney ABc 3: WT control rep3 Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts  Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 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 Gencode id. The remaining columns indicate the read counts such that each column represents a sample. zebrafish kidney 5 mpf to 6 mpf zebrafish were infected with 5 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. Control samples were collected from unchallenged wild type AB fish of the smame litter which was used for infections. Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. The zebrafish were maintained according to the standard protocols. genotype:wild type AB|agent:n1 control|tissue:zebrafish kidney GSM3324251 GSM3324251: ABc 3: WT control rep3; Danio rerio; RNA Seq GSM3324251   1 Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. GEO Accession:GSM3324251 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP156734     ABc_3_1.fq.gz ABc_3_2.fq.gz fastq fastq 7748608500.0 25828695.0 GSM3324251 r1 0:150 1:150 A:2069797407;C:1816718033;G:1809358876;T:2051944143;N:790041 150 150     2069797407 1816718033 1809358876 2051944143 790041 SRX4520650 SRS3639025 SRA755536 GEO University of Tampere 2 0.91798 0.90987 0.04896 0.04859 0.74166 0.74418 0.53544 0.54232 150 150 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   Finland 2018-08-08 Multi-stage Multi-stage Kidney Renal System
49081 49081 SRR7659032 SRX4520649 SRS3639024 SRP156734 PRJNA485080 Characterization of the immune response to Mycobacterium marinum infection in zebrafish GSE118288 Transcriptome Analysis Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. As expected based on the literature our results showed the induction of genes coding proteins associated to immune signaling cell migration and acute phase response indicating that the immune response to M. marinum infection in zebrafish is similar than the response to tuberculosis causing Mycobacterium tuberculosis in humans. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 8 samples were analyzed four biological replicates in each group.   pubmed:31626817   ABc 2: WT control rep2 GSM3324250   source name:zebrafish kidney|genotype:wild type AB|agent:n1 control|tissue:zebrafish kidney ABc 2: WT control rep2 Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts  Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 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 Gencode id. The remaining columns indicate the read counts such that each column represents a sample. zebrafish kidney 5 mpf to 6 mpf zebrafish were infected with 5 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. Control samples were collected from unchallenged wild type AB fish of the smame litter which was used for infections. Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. The zebrafish were maintained according to the standard protocols. genotype:wild type AB|agent:n1 control|tissue:zebrafish kidney GSM3324250 GSM3324250: ABc 2: WT control rep2; Danio rerio; RNA Seq GSM3324250   1 Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. GEO Accession:GSM3324250 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP156734     ABc_2_1.fq.gz ABc_2_2.fq.gz fastq fastq 8114032500.0 27046775.0 GSM3324250 r1 0:150 1:150 A:2194610150;C:1876718372;G:1867025193;T:2174858493;N:820292 150 150     2194610150 1876718372 1867025193 2174858493 820292 SRX4520649 SRS3639024 SRA755536 GEO University of Tampere 2 0.91423 0.90996 0.06031 0.05939 0.73095 0.7345 0.53902 0.53559 150 150 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   Finland 2018-08-08 Multi-stage Multi-stage Kidney Renal System
49082 49082 SRR7659031 SRX4520648 SRS3639023 SRP156734 PRJNA485080 Characterization of the immune response to Mycobacterium marinum infection in zebrafish GSE118288 Transcriptome Analysis Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. As expected based on the literature our results showed the induction of genes coding proteins associated to immune signaling cell migration and acute phase response indicating that the immune response to M. marinum infection in zebrafish is similar than the response to tuberculosis causing Mycobacterium tuberculosis in humans. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 8 samples were analyzed four biological replicates in each group.   pubmed:31626817   ABc 1: WT control rep1 GSM3324249   source name:zebrafish kidney|genotype:wild type AB|agent:n1 control|tissue:zebrafish kidney ABc 1: WT control rep1 Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts  Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 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 Gencode id. The remaining columns indicate the read counts such that each column represents a sample. zebrafish kidney 5 mpf to 6 mpf zebrafish were infected with 5 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. Control samples were collected from unchallenged wild type AB fish of the smame litter which was used for infections. Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. The zebrafish were maintained according to the standard protocols. genotype:wild type AB|agent:n1 control|tissue:zebrafish kidney GSM3324249 GSM3324249: ABc 1: WT control rep1; Danio rerio; RNA Seq GSM3324249   1 Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. GEO Accession:GSM3324249 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP156734     ABc_1_2.fq.gz ABc_1_1.fq.gz fastq fastq 7048214700.0 23494049.0 GSM3324249 r1 0:150 1:150 A:1872405650;C:1662441748;G:1654726958;T:1857920176;N:720168 150 150     1872405650 1662441748 1654726958 1857920176 720168 SRX4520648 SRS3639023 SRA755536 GEO University of Tampere 2 0.90831 0.89864 0.04895 0.04839 0.7419 0.74501 0.54589 0.55048 150 150 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   Finland 2018-08-08 Multi-stage Multi-stage Kidney Renal System
49083 49083 SRR7659030 SRX4520647 SRS3639020 SRP156734 PRJNA485080 Characterization of the immune response to Mycobacterium marinum infection in zebrafish GSE118288 Transcriptome Analysis Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. As expected based on the literature our results showed the induction of genes coding proteins associated to immune signaling cell migration and acute phase response indicating that the immune response to M. marinum infection in zebrafish is similar than the response to tuberculosis causing Mycobacterium tuberculosis in humans. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 8 samples were analyzed four biological replicates in each group.   pubmed:31626817   AB 4: WT inf rep4 GSM3324248   source name:zebrafish kidney|genotype:wild type AB|agent:Mycobacterium marinum|tissue:zebrafish kidney AB 4: WT inf rep4 Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts  Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 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 Gencode id. The remaining columns indicate the read counts such that each column represents a sample. zebrafish kidney 5 mpf to 6 mpf zebrafish were infected with 5 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. Control samples were collected from unchallenged wild type AB fish of the smame litter which was used for infections. Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. The zebrafish were maintained according to the standard protocols. genotype:wild type AB|agent:Mycobacterium marinum|tissue:zebrafish kidney GSM3324248 GSM3324248: AB 4: WT inf rep4; Danio rerio; RNA Seq GSM3324248   1 Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. GEO Accession:GSM3324248 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP156734     AB_4_1.fq.gz AB_4_2.fq.gz fastq fastq 7339619100.0 24465397.0 GSM3324248 r1 0:150 1:150 A:1956014376;C:1724124671;G:1723654528;T:1935080058;N:745467 150 150     1956014376 1724124671 1723654528 1935080058 745467 SRX4520647 SRS3639020 SRA755536 GEO University of Tampere 2 0.91872 0.90787 0.04809 0.04729 0.74241 0.74698 0.5326 0.53365 150 150 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   Finland 2018-08-08 Multi-stage Multi-stage Kidney Renal System
49084 49084 SRR7659029 SRX4520646 SRS3639022 SRP156734 PRJNA485080 Characterization of the immune response to Mycobacterium marinum infection in zebrafish GSE118288 Transcriptome Analysis Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. As expected based on the literature our results showed the induction of genes coding proteins associated to immune signaling cell migration and acute phase response indicating that the immune response to M. marinum infection in zebrafish is similar than the response to tuberculosis causing Mycobacterium tuberculosis in humans. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 8 samples were analyzed four biological replicates in each group.   pubmed:31626817   AB 3: WT inf rep3 GSM3324247   source name:zebrafish kidney|genotype:wild type AB|agent:Mycobacterium marinum|tissue:zebrafish kidney AB 3: WT inf rep3 Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts  Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 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 Gencode id. The remaining columns indicate the read counts such that each column represents a sample. zebrafish kidney 5 mpf to 6 mpf zebrafish were infected with 5 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. Control samples were collected from unchallenged wild type AB fish of the smame litter which was used for infections. Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. The zebrafish were maintained according to the standard protocols. genotype:wild type AB|agent:Mycobacterium marinum|tissue:zebrafish kidney GSM3324247 GSM3324247: AB 3: WT inf rep3; Danio rerio; RNA Seq GSM3324247   1 Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. GEO Accession:GSM3324247 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP156734     AB_3_1.fq.gz AB_3_2.fq.gz fastq fastq 7424949300.0 24749831.0 GSM3324247 r1 0:150 1:150 A:1964882946;C:1754326057;G:1752010860;T:1952971662;N:757775 150 150     1964882946 1754326057 1752010860 1952971662 757775 SRX4520646 SRS3639022 SRA755536 GEO University of Tampere 2 0.9196 0.91227 0.04829 0.04781 0.72232 0.72594 0.52261 0.51343 150 150 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   Finland 2018-08-08 Multi-stage Multi-stage Kidney Renal System
49085 49085 SRR7659028 SRX4520645 SRS3639021 SRP156734 PRJNA485080 Characterization of the immune response to Mycobacterium marinum infection in zebrafish GSE118288 Transcriptome Analysis Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. As expected based on the literature our results showed the induction of genes coding proteins associated to immune signaling cell migration and acute phase response indicating that the immune response to M. marinum infection in zebrafish is similar than the response to tuberculosis causing Mycobacterium tuberculosis in humans. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 8 samples were analyzed four biological replicates in each group.   pubmed:31626817   AB 2: WT inf rep2 GSM3324246   source name:zebrafish kidney|genotype:wild type AB|agent:Mycobacterium marinum|tissue:zebrafish kidney AB 2: WT inf rep2 Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts  Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 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 Gencode id. The remaining columns indicate the read counts such that each column represents a sample. zebrafish kidney 5 mpf to 6 mpf zebrafish were infected with 5 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. Control samples were collected from unchallenged wild type AB fish of the smame litter which was used for infections. Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. The zebrafish were maintained according to the standard protocols. genotype:wild type AB|agent:Mycobacterium marinum|tissue:zebrafish kidney GSM3324246 GSM3324246: AB 2: WT inf rep2; Danio rerio; RNA Seq GSM3324246   1 Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. GEO Accession:GSM3324246 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP156734     AB_2_2.fq.gz AB_2_1.fq.gz fastq fastq 7060829400.0 23536098.0 GSM3324246 r1 0:150 1:150 A:1875609739;C:1663056551;G:1660410877;T:1861028532;N:723701 150 150     1875609739 1663056551 1660410877 1861028532 723701 SRX4520645 SRS3639021 SRA755536 GEO University of Tampere 2 0.92483 0.9177 0.04614 0.04584 0.73012 0.73389 0.52324 0.52808 150 150 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   Finland 2018-08-08 Multi-stage Multi-stage Kidney Renal System
49086 49086 SRR7659027 SRX4520644 SRS3639019 SRP156734 PRJNA485080 Characterization of the immune response to Mycobacterium marinum infection in zebrafish GSE118288 Transcriptome Analysis Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. As expected based on the literature our results showed the induction of genes coding proteins associated to immune signaling cell migration and acute phase response indicating that the immune response to M. marinum infection in zebrafish is similar than the response to tuberculosis causing Mycobacterium tuberculosis in humans. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 8 samples were analyzed four biological replicates in each group.   pubmed:31626817   AB 1: WT inf rep1 GSM3324245   source name:zebrafish kidney|genotype:wild type AB|agent:Mycobacterium marinum|tissue:zebrafish kidney AB 1: WT inf rep1 Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts  Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 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 Gencode id. The remaining columns indicate the read counts such that each column represents a sample. zebrafish kidney 5 mpf to 6 mpf zebrafish were infected with 5 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. Control samples were collected from unchallenged wild type AB fish of the smame litter which was used for infections. Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. The zebrafish were maintained according to the standard protocols. genotype:wild type AB|agent:Mycobacterium marinum|tissue:zebrafish kidney GSM3324245 GSM3324245: AB 1: WT inf rep1; Danio rerio; RNA Seq GSM3324245   1 Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. GEO Accession:GSM3324245 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP156734     AB_1_1.fq.gz AB_1_2.fq.gz fastq fastq 7909740000.0 26365800.0 GSM3324245 r1 0:150 1:150 A:2093646099;C:1870851418;G:1866389764;T:2078055144;N:797575 150 150     2093646099 1870851418 1866389764 2078055144 797575 SRX4520644 SRS3639019 SRA755536 GEO University of Tampere 2 0.92137 0.90717 0.04875 0.04769 0.73783 0.74219 0.53376 0.5364 150 150 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   Finland 2018-08-08 Multi-stage Multi-stage Kidney Renal System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;