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
32611,SRR29356860,SRX24871764,SRS21581236,SRP513122,PRJNA1122499,An mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy,GSE269547,Transcriptome Analysis,Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune protective mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from zebrafish immunized with the mRNA vaccine and the LPP control.  For mRNA vaccination  mRNA candidate vaccines were injected with 1µg LPP mRNA in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL  negative control zebrafish were immunized with LPP GFP mRNA  immunized twice with two week intervals week 0 and 2.post 12 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group.,,pubmed:39759874,,kidneys  LPP immunized sample3,GSM8321946,,source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Vector control immunized group|treatment:2 dose of LPP GFP mRNA immunized|geo loc name:missing|collection date:missing,kidneys  LPP immunized sample3,The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes FPKM counts for each Sample,kidneys,For determination of the host immune response induced by mRNA vaccine immunization  adult zebrafish AB strain  3 to 4 mpf  15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 μL for intramuscular i.m immunization. 1μg L3T mRNA vaccine or LPP GFP mRNA were injected in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL. post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction.,post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions.,The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C  pH ∼7.4  and conductivity ∼1500μS.,tissue:kidneys|cell type:whole cell immune cell|group:Vector control immunized group|treatment:2 dose of LPP GFP mRNA immunized,GSM8321946,GSM8321946: kidneys  LPP immunized sample3; Danio rerio; RNA Seq,GSM8321946 r1,GSM8321946,1,post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP513122,,,LPP3.R1.fq.gz LPP3.R2.fq.gz,fastq fastq,6930388402.0,24028386.0,GSM8321946 r1,0:144.22 1:144.21,A:1741896633;C:1718081658;G:1728245814;T:1742156412;N:7885,144,144,,,1741896633,1718081658,1728245814,1742156412,7885,SRX24871764,SRS21581236,SRA1896369,"Zhang Lab, Department of Microbiology, Fudan University","Zhang Lab, Department of Microbiology, Fudan University",2,0.95561,0.95769,0.04873,0.04831,0.70556,0.705,0.50774,0.50807,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-06-11,Multi-stage,Multi-stage,Kidney,Renal System
32612,SRR29356861,SRX24871763,SRS21581235,SRP513122,PRJNA1122499,An mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy,GSE269547,Transcriptome Analysis,Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune protective mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from zebrafish immunized with the mRNA vaccine and the LPP control.  For mRNA vaccination  mRNA candidate vaccines were injected with 1µg LPP mRNA in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL  negative control zebrafish were immunized with LPP GFP mRNA  immunized twice with two week intervals week 0 and 2.post 12 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group.,,pubmed:39759874,,kidneys  LPP immunized sample2,GSM8321945,,source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Vector control immunized group|treatment:2 dose of LPP GFP mRNA immunized|geo loc name:missing|collection date:missing,kidneys  LPP immunized sample2,The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes FPKM counts for each Sample,kidneys,For determination of the host immune response induced by mRNA vaccine immunization  adult zebrafish AB strain  3 to 4 mpf  15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 μL for intramuscular i.m immunization. 1μg L3T mRNA vaccine or LPP GFP mRNA were injected in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL. post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction.,post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions.,The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C  pH ∼7.4  and conductivity ∼1500μS.,tissue:kidneys|cell type:whole cell immune cell|group:Vector control immunized group|treatment:2 dose of LPP GFP mRNA immunized,GSM8321945,GSM8321945: kidneys  LPP immunized sample2; Danio rerio; RNA Seq,GSM8321945 r1,GSM8321945,1,post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP513122,,,LPP2.R1.fq.gz LPP2.R2.fq.gz,fastq fastq,6970934950.0,24067775.0,GSM8321945 r1,0:144.82 1:144.82,A:1750927361;C:1729272618;G:1740379247;T:1750348140;N:7584,144,144,,,1750927361,1729272618,1740379247,1750348140,7584,SRX24871763,SRS21581235,SRA1896369,"Zhang Lab, Department of Microbiology, Fudan University","Zhang Lab, Department of Microbiology, Fudan University",2,0.95562,0.95799,0.04685,0.04619,0.7067,0.7051,0.50198,0.49861,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-06-11,Multi-stage,Multi-stage,Kidney,Renal System
32613,SRR29356862,SRX24871762,SRS21581234,SRP513122,PRJNA1122499,An mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy,GSE269547,Transcriptome Analysis,Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune protective mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from zebrafish immunized with the mRNA vaccine and the LPP control.  For mRNA vaccination  mRNA candidate vaccines were injected with 1µg LPP mRNA in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL  negative control zebrafish were immunized with LPP GFP mRNA  immunized twice with two week intervals week 0 and 2.post 12 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group.,,pubmed:39759874,,kidneys  LPP immunized sample1,GSM8321944,,source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Vector control immunized group|treatment:2 dose of LPP GFP mRNA immunized|geo loc name:missing|collection date:missing,kidneys  LPP immunized sample1,The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes FPKM counts for each Sample,kidneys,For determination of the host immune response induced by mRNA vaccine immunization  adult zebrafish AB strain  3 to 4 mpf  15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 μL for intramuscular i.m immunization. 1μg L3T mRNA vaccine or LPP GFP mRNA were injected in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL. post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction.,post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions.,The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C  pH ∼7.4  and conductivity ∼1500μS.,tissue:kidneys|cell type:whole cell immune cell|group:Vector control immunized group|treatment:2 dose of LPP GFP mRNA immunized,GSM8321944,GSM8321944: kidneys  LPP immunized sample1; Danio rerio; RNA Seq,GSM8321944 r1,GSM8321944,1,post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP513122,,,LPP1.R1.fq.gz LPP1.R2.fq.gz,fastq fastq,6946964789.0,24016865.0,GSM8321944 r1,0:144.63 1:144.62,A:1753009524;C:1714194993;G:1724914785;T:1754837582;N:7905,144,144,,,1753009524,1714194993,1724914785,1754837582,7905,SRX24871762,SRS21581234,SRA1896369,"Zhang Lab, Department of Microbiology, Fudan University","Zhang Lab, Department of Microbiology, Fudan University",2,0.94958,0.95243,0.05857,0.05785,0.70181,0.70074,0.5058,0.50491,150,145,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-06-11,Multi-stage,Multi-stage,Kidney,Renal System
32614,SRR29356863,SRX24871761,SRS21581233,SRP513122,PRJNA1122499,An mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy,GSE269547,Transcriptome Analysis,Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune protective mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from zebrafish immunized with the mRNA vaccine and the LPP control.  For mRNA vaccination  mRNA candidate vaccines were injected with 1µg LPP mRNA in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL  negative control zebrafish were immunized with LPP GFP mRNA  immunized twice with two week intervals week 0 and 2.post 12 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group.,,pubmed:39759874,,kidneys  L3T immunized sample3,GSM8321943,,source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:L3T immunized group|treatment:2 dose of L3T mRNA immunized|geo loc name:missing|collection date:missing,kidneys  L3T immunized sample3,The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes FPKM counts for each Sample,kidneys,For determination of the host immune response induced by mRNA vaccine immunization  adult zebrafish AB strain  3 to 4 mpf  15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 μL for intramuscular i.m immunization. 1μg L3T mRNA vaccine or LPP GFP mRNA were injected in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL. post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction.,post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions.,The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C  pH ∼7.4  and conductivity ∼1500μS.,tissue:kidneys|cell type:whole cell immune cell|group:L3T immunized group|treatment:2 dose of L3T mRNA immunized,GSM8321943,GSM8321943: kidneys  L3T immunized sample3; Danio rerio; RNA Seq,GSM8321943 r1,GSM8321943,1,post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP513122,,,L3T3.R1.fq.gz L3T3.R2.fq.gz,fastq fastq,7056672882.0,24530821.0,GSM8321943 r1,0:143.84 1:143.83,A:1768243408;C:1755016636;G:1763993995;T:1769411088;N:7755,143,143,,,1768243408,1755016636,1763993995,1769411088,7755,SRX24871761,SRS21581233,SRA1896369,"Zhang Lab, Department of Microbiology, Fudan University","Zhang Lab, Department of Microbiology, Fudan University",2,0.95045,0.95387,0.04717,0.04638,0.712,0.71125,0.52106,0.51883,106,106,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-06-11,Multi-stage,Multi-stage,Kidney,Renal System
32615,SRR29356864,SRX24871760,SRS21581232,SRP513122,PRJNA1122499,An mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy,GSE269547,Transcriptome Analysis,Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune protective mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from zebrafish immunized with the mRNA vaccine and the LPP control.  For mRNA vaccination  mRNA candidate vaccines were injected with 1µg LPP mRNA in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL  negative control zebrafish were immunized with LPP GFP mRNA  immunized twice with two week intervals week 0 and 2.post 12 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group.,,pubmed:39759874,,kidneys  L3T immunized sample2,GSM8321942,,source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:L3T immunized group|treatment:2 dose of L3T mRNA immunized|geo loc name:missing|collection date:missing,kidneys  L3T immunized sample2,The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes FPKM counts for each Sample,kidneys,For determination of the host immune response induced by mRNA vaccine immunization  adult zebrafish AB strain  3 to 4 mpf  15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 μL for intramuscular i.m immunization. 1μg L3T mRNA vaccine or LPP GFP mRNA were injected in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL. post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction.,post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions.,The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C  pH ∼7.4  and conductivity ∼1500μS.,tissue:kidneys|cell type:whole cell immune cell|group:L3T immunized group|treatment:2 dose of L3T mRNA immunized,GSM8321942,GSM8321942: kidneys  L3T immunized sample2; Danio rerio; RNA Seq,GSM8321942 r1,GSM8321942,1,post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP513122,,,L3T2.R1.fq.gz L3T2.R2.fq.gz,fastq fastq,7021833716.0,24281953.0,GSM8321942 r1,0:144.59 1:144.59,A:1777129692;C:1728181109;G:1738562098;T:1777953935;N:6882,144,144,,,1777129692,1728181109,1738562098,1777953935,6882,SRX24871760,SRS21581232,SRA1896369,"Zhang Lab, Department of Microbiology, Fudan University","Zhang Lab, Department of Microbiology, Fudan University",2,0.9484,0.9523,0.0532,0.05294,0.7052,0.70362,0.51282,0.50716,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-06-11,Multi-stage,Multi-stage,Kidney,Renal System
32616,SRR29356865,SRX24871759,SRS21581231,SRP513122,PRJNA1122499,An mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy,GSE269547,Transcriptome Analysis,Effective vaccines are urgently needed for the control of tuberculosis TB. Here  we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB.  Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge  and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity  but not the canonical DNA damage responses that promote cell death  demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably  the mRNA vaccine induced autophagy in granulomas  coinciding with bacterial killing and cell survival.  Collectively  these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity  conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune protective mechanisms mediated by the L3T vaccine  we performed RNA seq analysis of kidneys isolated from zebrafish immunized with the mRNA vaccine and the LPP control.  For mRNA vaccination  mRNA candidate vaccines were injected with 1µg LPP mRNA in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL  negative control zebrafish were immunized with LPP GFP mRNA  immunized twice with two week intervals week 0 and 2.post 12 days of  the final immunization  kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group.,,pubmed:39759874,,kidneys  L3T immunized sample1,GSM8321941,,source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:L3T immunized group|treatment:2 dose of L3T mRNA immunized|geo loc name:missing|collection date:missing,kidneys  L3T immunized sample1,The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.  The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes FPKM counts for each Sample,kidneys,For determination of the host immune response induced by mRNA vaccine immunization  adult zebrafish AB strain  3 to 4 mpf  15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 μL for intramuscular i.m immunization. 1μg L3T mRNA vaccine or LPP GFP mRNA were injected in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments  Sarasota  FL. post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction.,post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions.,The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co.  Ltd. Qingdao  China  and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C  pH ∼7.4  and conductivity ∼1500μS.,tissue:kidneys|cell type:whole cell immune cell|group:L3T immunized group|treatment:2 dose of L3T mRNA immunized,GSM8321941,GSM8321941: kidneys  L3T immunized sample1; Danio rerio; RNA Seq,GSM8321941 r1,GSM8321941,1,post 12 days of the secondary immunization  kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen  CA  USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific  USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies  Santa Clara  CA  USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP513122,,,L3T1.R1.fq.gz L3T1.R2.fq.gz,fastq fastq,6941829152.0,24117590.0,GSM8321941 r1,0:143.92 1:143.91,A:1756734172;C:1708781793;G:1718505186;T:1757800293;N:7708,143,143,,,1756734172,1708781793,1718505186,1757800293,7708,SRX24871759,SRS21581231,SRA1896369,"Zhang Lab, Department of Microbiology, Fudan University","Zhang Lab, Department of Microbiology, Fudan University",2,0.95019,0.95324,0.05797,0.05755,0.70013,0.69934,0.5137,0.5148,147,147,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-06-11,Multi-stage,Multi-stage,Kidney,Renal System
41873,SRR5320505,SRX2619910,SRS2029873,SRP101556,PRJNA378487,Transcriptional profiling of the zebrafish proximal tubule,GSE95808,Transcriptome Analysis,The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney  the pronephros  represents a simplified form of the mammalian organ  yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here  we establish a high resolution expression profile of isolated  GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation  proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue,,pubmed:31188030,,Morpholino 7,GSM2526320,,tissue:larval kidney|line:tgPT::EGFP|genotype/variation:Hnf1b depleted,Morpholino 7,Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts.,larval kidney,,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,,line:tgPT::EGFP|genotype/variation:Hnf1b depleted,GSM2526320,GSM2526320: Morpholino 7; Danio rerio; RNA Seq,GSM2526320,,1,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,GEO Accession:GSM2526320,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP101556,,,C6H9AANXX-1531-06-1-1_CTTGTAAT_L001_R1_001.fastq.gz C6H9AANXX-1531-06-1-1_CTTGTAAT_L001_R2_001.fastq.gz,fastq fastq,8670821250.0,34683285.0,GSM2526320 r1,0:125 1:125,A:2285357364;C:2049868144;G:2107192972;T:2225558024;N:2844746,125,125,,,2285357364,2049868144,2107192972,2225558024,2844746,SRX2619910,SRS2029873,SRA543390,GEO,"Molecular Medicine and Pathology, University of Auckland",2,0.96682,0.96763,0.08369,0.08426,0.69296,0.69493,0.47739,0.47931,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-03-08,Multi-stage,Multi-stage,Kidney,Renal System
41874,SRR5320504,SRX2619909,SRS2029872,SRP101556,PRJNA378487,Transcriptional profiling of the zebrafish proximal tubule,GSE95808,Transcriptome Analysis,The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney  the pronephros  represents a simplified form of the mammalian organ  yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here  we establish a high resolution expression profile of isolated  GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation  proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue,,pubmed:31188030,,Morpholino 5,GSM2526319,,tissue:larval kidney|line:tgPT::EGFP|genotype/variation:Hnf1b depleted,Morpholino 5,Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts.,larval kidney,,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,,line:tgPT::EGFP|genotype/variation:Hnf1b depleted,GSM2526319,GSM2526319: Morpholino 5; Danio rerio; RNA Seq,GSM2526319,,1,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,GEO Accession:GSM2526319,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP101556,,,C6H9AANXX-1531-05-1-1_CAGATCAT_L001_R1_001.fastq.gz C6H9AANXX-1531-05-1-1_CAGATCAT_L001_R2_001.fastq.gz,fastq fastq,9864273500.0,39457094.0,GSM2526319 r1,0:125 1:125,A:2628741477;C:2304848464;G:2364915536;T:2562525014;N:3243009,125,125,,,2628741477,2304848464,2364915536,2562525014,3243009,SRX2619909,SRS2029872,SRA543390,GEO,"Molecular Medicine and Pathology, University of Auckland",2,0.96115,0.96161,0.10876,0.10854,0.67495,0.67616,0.45304,0.45767,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-03-08,Multi-stage,Multi-stage,Kidney,Renal System
41875,SRR5320503,SRX2619908,SRS2029871,SRP101556,PRJNA378487,Transcriptional profiling of the zebrafish proximal tubule,GSE95808,Transcriptome Analysis,The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney  the pronephros  represents a simplified form of the mammalian organ  yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here  we establish a high resolution expression profile of isolated  GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation  proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue,,pubmed:31188030,,Morpholino 4,GSM2526318,,tissue:larval kidney|line:tgPT::EGFP|genotype/variation:Hnf1b depleted,Morpholino 4,Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts.,larval kidney,,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,,line:tgPT::EGFP|genotype/variation:Hnf1b depleted,GSM2526318,GSM2526318: Morpholino 4; Danio rerio; RNA Seq,GSM2526318,,1,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,GEO Accession:GSM2526318,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP101556,,,C6H9AANXX-1531-04-1-1_GCCAATAT_L001_R1_001.fastq.gz C6H9AANXX-1531-04-1-1_GCCAATAT_L001_R2_001.fastq.gz,fastq fastq,8503939500.0,34015758.0,GSM2526318 r1,0:125 1:125,A:2251120561;C:2002327793;G:2052310864;T:2195401798;N:2778484,125,125,,,2251120561,2002327793,2052310864,2195401798,2778484,SRX2619908,SRS2029871,SRA543390,GEO,"Molecular Medicine and Pathology, University of Auckland",2,0.96344,0.96379,0.09973,0.09974,0.68043,0.68264,0.46613,0.46851,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-03-08,Multi-stage,Multi-stage,Kidney,Renal System
41876,SRR5320502,SRX2619907,SRS2029870,SRP101556,PRJNA378487,Transcriptional profiling of the zebrafish proximal tubule,GSE95808,Transcriptome Analysis,The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney  the pronephros  represents a simplified form of the mammalian organ  yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here  we establish a high resolution expression profile of isolated  GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation  proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue,,pubmed:31188030,,Control 3,GSM2526317,,tissue:larval kidney|line:tgPT::EGFP|genotype/variation:wild type,Control 3,Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts.,larval kidney,,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,,line:tgPT::EGFP|genotype/variation:wild type,GSM2526317,GSM2526317: Control 3; Danio rerio; RNA Seq,GSM2526317,,1,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,GEO Accession:GSM2526317,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP101556,,,C6H9AANXX-1531-03-1-1_ACAGTGAT_L001_R1_001.fastq.gz C6H9AANXX-1531-03-1-1_ACAGTGAT_L001_R2_001.fastq.gz,fastq fastq,9619758500.0,38479034.0,GSM2526317 r1,0:125 1:125,A:2561625595;C:2249183851;G:2312313710;T:2493482524;N:3152820,125,125,,,2561625595,2249183851,2312313710,2493482524,3152820,SRX2619907,SRS2029870,SRA543390,GEO,"Molecular Medicine and Pathology, University of Auckland",2,0.96067,0.96218,0.10832,0.10898,0.66675,0.66866,0.47609,0.47441,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-03-08,Multi-stage,Multi-stage,Kidney,Renal System
41877,SRR5320501,SRX2619906,SRS2029869,SRP101556,PRJNA378487,Transcriptional profiling of the zebrafish proximal tubule,GSE95808,Transcriptome Analysis,The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney  the pronephros  represents a simplified form of the mammalian organ  yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here  we establish a high resolution expression profile of isolated  GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation  proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue,,pubmed:31188030,,Control 2,GSM2526316,,tissue:larval kidney|line:tgPT::EGFP|genotype/variation:wild type,Control 2,Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts.,larval kidney,,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,,line:tgPT::EGFP|genotype/variation:wild type,GSM2526316,GSM2526316: Control 2; Danio rerio; RNA Seq,GSM2526316,,1,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,GEO Accession:GSM2526316,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP101556,,,C6H9AANXX-1531-02-1-1_TGACCAAT_L001_R1_001.fastq.gz C6H9AANXX-1531-02-1-1_TGACCAAT_L001_R2_001.fastq.gz,fastq fastq,8939151000.0,35756604.0,GSM2526316 r1,0:125 1:125,A:2379909844;C:2090182914;G:2143061952;T:2323063658;N:2932632,125,125,,,2379909844,2090182914,2143061952,2323063658,2932632,SRX2619906,SRS2029869,SRA543390,GEO,"Molecular Medicine and Pathology, University of Auckland",2,0.96176,0.96203,0.10658,0.10717,0.67087,0.67194,0.45961,0.46137,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-03-08,Multi-stage,Multi-stage,Kidney,Renal System
41878,SRR5320500,SRX2619905,SRS2029868,SRP101556,PRJNA378487,Transcriptional profiling of the zebrafish proximal tubule,GSE95808,Transcriptome Analysis,The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney  the pronephros  represents a simplified form of the mammalian organ  yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here  we establish a high resolution expression profile of isolated  GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation  proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue,,pubmed:31188030,,Control 1,GSM2526315,,tissue:larval kidney|line:tgPT::EGFP|genotype/variation:wild type,Control 1,Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts.,larval kidney,,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,,line:tgPT::EGFP|genotype/variation:wild type,GSM2526315,GSM2526315: Control 1; Danio rerio; RNA Seq,GSM2526315,,1,Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes  the E3 embryo medium removed  replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette  the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage  the larvae are disintegrated into chunks of tissue with intact  bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel  and instantly frozen to  80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols,GEO Accession:GSM2526315,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP101556,,,C6H9AANXX-1531-01-1-1_CGATGTAT_L001_R1_001.fastq.gz C6H9AANXX-1531-01-1-1_CGATGTAT_L001_R2_001.fastq.gz,fastq fastq,9579790250.0,38319161.0,GSM2526315 r1,0:125 1:125,A:2520690618;C:2269535412;G:2326632146;T:2459796830;N:3135244,125,125,,,2520690618,2269535412,2326632146,2459796830,3135244,SRX2619905,SRS2029868,SRA543390,GEO,"Molecular Medicine and Pathology, University of Auckland",2,0.96456,0.96615,0.08928,0.09003,0.68373,0.6856,0.46544,0.46416,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-03-08,Multi-stage,Multi-stage,Kidney,Renal System
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,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,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,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,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,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,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,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
49087,SRR7664345,SRX4524952,SRS3643046,SRP156914,PRJNA485334,Characterization of the immune response to Mycobacterium marinum infection in zebrafish [mutant 463],GSE118350,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. In addition  we carried out a medium scale forward genetic screen to identify genes underlying defense mechanisms against M. marinum infection in zebrafish. Our aim was to gain more information about the genetic mechanisms important in the immune defense against human tuberculosis. In this screen  we identified a mutant zebrafish line with impaired resistance to a low dose M. marinum infection. In this line  the transcriptome analysis at 14 days post infection revealed decreased expression of a gene homologous to human UNC119 which has been shown to have a role in T cell activation. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in zebrafish. 4 samples were analyzed  four biological replicates in each group.,,pubmed:31626817,,mutant463 inf rep4,GSM3325717,,tissue:zebrafish kidney|strain:mutant463,mutant463 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.,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. The mutant zebrafish line was produced with the gene breaking transposon based mutagenesis using the RP2 construct.,strain:mutant463,GSM3325717,GSM3325717: mutant463 inf rep4; Danio rerio; RNA Seq,GSM3325717,,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:GSM3325717,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP156914,,,F1_463_4_1.fq.gz F1_463_4_2.fq.gz,fastq fastq,7892745600.0,26309152.0,GSM3325717 r1,0:150 1:150,A:2102605709;C:1854325558;G:1849161474;T:2085489415;N:1163444,150,150,,,2102605709,1854325558,1849161474,2085489415,1163444,SRX4524952,SRS3643046,SRA756218,GEO,University of Tampere,2,0.9279,0.91721,0.05059,0.0497,0.7302,0.73448,0.51354,0.51569,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,Finland,2018-08-09,Multi-stage,Multi-stage,Kidney,Renal System
49088,SRR7664344,SRX4524951,SRS3643047,SRP156914,PRJNA485334,Characterization of the immune response to Mycobacterium marinum infection in zebrafish [mutant 463],GSE118350,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. In addition  we carried out a medium scale forward genetic screen to identify genes underlying defense mechanisms against M. marinum infection in zebrafish. Our aim was to gain more information about the genetic mechanisms important in the immune defense against human tuberculosis. In this screen  we identified a mutant zebrafish line with impaired resistance to a low dose M. marinum infection. In this line  the transcriptome analysis at 14 days post infection revealed decreased expression of a gene homologous to human UNC119 which has been shown to have a role in T cell activation. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in zebrafish. 4 samples were analyzed  four biological replicates in each group.,,pubmed:31626817,,mutant463 inf rep3,GSM3325716,,tissue:zebrafish kidney|strain:mutant463,mutant463 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.,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. The mutant zebrafish line was produced with the gene breaking transposon based mutagenesis using the RP2 construct.,strain:mutant463,GSM3325716,GSM3325716: mutant463 inf rep3; Danio rerio; RNA Seq,GSM3325716,,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:GSM3325716,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP156914,,,F1_463_3_1.fq.gz F1_463_3_2.fq.gz,fastq fastq,8128128900.0,27093763.0,GSM3325716 r1,0:150 1:150,A:2183432859;C:1890349432;G:1885512767;T:2167999703;N:834139,150,150,,,2183432859,1890349432,1885512767,2167999703,834139,SRX4524951,SRS3643047,SRA756218,GEO,University of Tampere,2,0.92534,0.91699,0.0575,0.05751,0.72368,0.72675,0.53219,0.53162,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,Finland,2018-08-09,Multi-stage,Multi-stage,Kidney,Renal System
49089,SRR7664343,SRX4524950,SRS3643045,SRP156914,PRJNA485334,Characterization of the immune response to Mycobacterium marinum infection in zebrafish [mutant 463],GSE118350,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. In addition  we carried out a medium scale forward genetic screen to identify genes underlying defense mechanisms against M. marinum infection in zebrafish. Our aim was to gain more information about the genetic mechanisms important in the immune defense against human tuberculosis. In this screen  we identified a mutant zebrafish line with impaired resistance to a low dose M. marinum infection. In this line  the transcriptome analysis at 14 days post infection revealed decreased expression of a gene homologous to human UNC119 which has been shown to have a role in T cell activation. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in zebrafish. 4 samples were analyzed  four biological replicates in each group.,,pubmed:31626817,,mutant463 inf rep2,GSM3325715,,tissue:zebrafish kidney|strain:mutant463,mutant463 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.,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. The mutant zebrafish line was produced with the gene breaking transposon based mutagenesis using the RP2 construct.,strain:mutant463,GSM3325715,GSM3325715: mutant463 inf rep2; Danio rerio; RNA Seq,GSM3325715,,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:GSM3325715,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP156914,,,F1_463_2_1.fq.gz F1_463_2_2.fq.gz,fastq fastq,8481546900.0,28271823.0,GSM3325715 r1,0:150 1:150,A:2274428903;C:1976862267;G:1971746746;T:2257250093;N:1258891,150,150,,,2274428903,1976862267,1971746746,2257250093,1258891,SRX4524950,SRS3643045,SRA756218,GEO,University of Tampere,2,0.9244,0.91499,0.05718,0.05626,0.72941,0.73379,0.53004,0.53034,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,Finland,2018-08-09,Multi-stage,Multi-stage,Kidney,Renal System
49090,SRR7664342,SRX4524949,SRS3643043,SRP156914,PRJNA485334,Characterization of the immune response to Mycobacterium marinum infection in zebrafish [mutant 463],GSE118350,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. In addition  we carried out a medium scale forward genetic screen to identify genes underlying defense mechanisms against M. marinum infection in zebrafish. Our aim was to gain more information about the genetic mechanisms important in the immune defense against human tuberculosis. In this screen  we identified a mutant zebrafish line with impaired resistance to a low dose M. marinum infection. In this line  the transcriptome analysis at 14 days post infection revealed decreased expression of a gene homologous to human UNC119 which has been shown to have a role in T cell activation. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in zebrafish. 4 samples were analyzed  four biological replicates in each group.,,pubmed:31626817,,mutant463 inf rep1,GSM3325714,,tissue:zebrafish kidney|strain:mutant463,mutant463 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.,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. The mutant zebrafish line was produced with the gene breaking transposon based mutagenesis using the RP2 construct.,strain:mutant463,GSM3325714,GSM3325714: mutant463 inf rep1; Danio rerio; RNA Seq,GSM3325714,,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:GSM3325714,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP156914,,,F1_463_1_2.fq.gz F1_463_1_1.fq.gz,fastq fastq,7430278200.0,24767594.0,GSM3325714 r1,0:150 1:150,A:1981941438;C:1739863325;G:1736512377;T:1970856840;N:1104220,150,150,,,1981941438,1739863325,1736512377,1970856840,1104220,SRX4524949,SRS3643043,SRA756218,GEO,University of Tampere,2,0.91811,0.90734,0.04866,0.04819,0.70512,0.70966,0.50962,0.50717,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,Finland,2018-08-09,Multi-stage,Multi-stage,Kidney,Renal System
63833,SRR14077612,SRX10451897,SRS8583182,SRP312298,PRJNA717672,Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2],GSE169689,Transcriptome Analysis,Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 /  siblings  2.5 mpf  pool of 3 kidneys/replicate.,parent bioproject:PRJNA663961,pubmed:34492681,,WT kidney3 [runx1],GSM5212431,,source name:adult kidney|genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month,WT kidney3 [runx1],RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts,adult kidney,,Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in  80C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2,,genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month,GSM5212431,GSM5212431: WT kidney3 [runx1]; Danio rerio; RNA Seq,GSM5212431,,1,Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in  80C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2,GEO Accession:GSM5212431,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP312298,,,141031_OPTIMUS_C5M4FANXX.5.8142700.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.5.8142700.2.cln.fq.gz,fastq fastq,5620598490.0,22731446.0,GSM5212431 r1,0:123.63 1:123.63,A:1519385372;C:1283859179;G:1297145256;T:1520155478;N:53205,123,123,,,1519385372,1283859179,1297145256,1520155478,53205,SRX10451897,SRS8583182,SRA1210911,GEO,NHGRI,2,0.94209,0.94365,0.1093,0.10867,0.7655,0.76471,0.52137,0.52991,57,57,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2021-03-26,Multi-stage,Multi-stage,Kidney,Renal System
63834,SRR14077613,SRX10451897,SRS8583182,SRP312298,PRJNA717672,Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2],GSE169689,Transcriptome Analysis,Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 /  siblings  2.5 mpf  pool of 3 kidneys/replicate.,parent bioproject:PRJNA663961,pubmed:34492681,,WT kidney3 [runx1],GSM5212431,,source name:adult kidney|genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month,WT kidney3 [runx1],RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts,adult kidney,,Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in  80C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2,,genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month,GSM5212431,GSM5212431: WT kidney3 [runx1]; Danio rerio; RNA Seq,GSM5212431,,1,Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in  80C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2,GEO Accession:GSM5212431,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP312298,,,141031_OPTIMUS_C5M4FANXX.4.8142700.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.4.8142700.2.cln.fq.gz,fastq fastq,5653835646.0,22866105.0,GSM5212431 r2,0:123.63 1:123.63,A:1528563748;C:1291263140;G:1304651524;T:1529275913;N:81321,123,123,,,1528563748,1291263140,1304651524,1529275913,81321,SRX10451897,SRS8583182,SRA1210911,GEO,NHGRI,2,0.94227,0.9433,0.10809,0.1082,0.7654,0.76629,0.46698,0.51583,120,120,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2021-03-26,Multi-stage,Multi-stage,Kidney,Renal System
63835,SRR14077610,SRX10451896,SRS8583181,SRP312298,PRJNA717672,Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2],GSE169689,Transcriptome Analysis,Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 /  siblings  2.5 mpf  pool of 3 kidneys/replicate.,parent bioproject:PRJNA663961,pubmed:34492681,,WT kidney2 [runx1],GSM5212430,,source name:adult kidney|genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month,WT kidney2 [runx1],RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts,adult kidney,,Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in  80C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2,,genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month,GSM5212430,GSM5212430: WT kidney2 [runx1]; Danio rerio; RNA Seq,GSM5212430,,1,Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in  80C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2,GEO Accession:GSM5212430,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP312298,,,141031_OPTIMUS_C5M4FANXX.4.8142702.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.4.8142702.2.cln.fq.gz,fastq fastq,5711423980.0,23122476.0,GSM5212430 r1,0:123.50 1:123.50,A:1541001316;C:1305691699;G:1320208515;T:1544438912;N:83538,123,123,,,1541001316,1305691699,1320208515,1544438912,83538,SRX10451896,SRS8583181,SRA1210911,GEO,NHGRI,2,0.95092,0.95171,0.07601,0.07547,0.73584,0.73665,0.45011,0.45353,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2021-03-26,Multi-stage,Multi-stage,Kidney,Renal System
63836,SRR14077611,SRX10451896,SRS8583181,SRP312298,PRJNA717672,Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2],GSE169689,Transcriptome Analysis,Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 /  siblings  2.5 mpf  pool of 3 kidneys/replicate.,parent bioproject:PRJNA663961,pubmed:34492681,,WT kidney2 [runx1],GSM5212430,,source name:adult kidney|genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month,WT kidney2 [runx1],RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts,adult kidney,,Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in  80C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2,,genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month,GSM5212430,GSM5212430: WT kidney2 [runx1]; Danio rerio; RNA Seq,GSM5212430,,1,Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in  80C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2,GEO Accession:GSM5212430,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP312298,,,141031_OPTIMUS_C5M4FANXX.5.8142702.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.5.8142702.2.cln.fq.gz,fastq fastq,5674131430.0,22971228.0,GSM5212430 r2,0:123.51 1:123.51,A:1530898067;C:1297222710;G:1311658561;T:1534297201;N:54891,123,123,,,1530898067,1297222710,1311658561,1534297201,54891,SRX10451896,SRS8583181,SRA1210911,GEO,NHGRI,2,0.95066,0.95158,0.07593,0.07608,0.73263,0.7343,0.44607,0.44584,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2021-03-26,Multi-stage,Multi-stage,Kidney,Renal System
63837,SRR14077608,SRX10451895,SRS8583180,SRP312298,PRJNA717672,Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2],GSE169689,Transcriptome Analysis,Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 /  siblings  2.5 mpf  pool of 3 kidneys/replicate.,parent bioproject:PRJNA663961,pubmed:34492681,,WT kidney1 [runx1],GSM5212429,,source name:adult kidney|genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month,WT kidney1 [runx1],RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts,adult kidney,,Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in  80C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2,,genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month,GSM5212429,GSM5212429: WT kidney1 [runx1]; Danio rerio; RNA Seq,GSM5212429,,1,Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in  80C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2,GEO Accession:GSM5212429,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP312298,,,141031_OPTIMUS_C5M4FANXX.5.8142698.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.5.8142698.2.cln.fq.gz,fastq fastq,6048097920.0,24370362.0,GSM5212429 r1,0:124.09 1:124.09,A:1630531156;C:1385676653;G:1399270262;T:1632562524;N:57325,124,124,,,1630531156,1385676653,1399270262,1632562524,57325,SRX10451895,SRS8583180,SRA1210911,GEO,NHGRI,2,0.94669,0.94821,0.09654,0.09706,0.73537,0.73606,0.49615,0.49775,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2021-03-26,Multi-stage,Multi-stage,Kidney,Renal System
63838,SRR14077609,SRX10451895,SRS8583180,SRP312298,PRJNA717672,Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2],GSE169689,Transcriptome Analysis,Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 /  siblings  2.5 mpf  pool of 3 kidneys/replicate.,parent bioproject:PRJNA663961,pubmed:34492681,,WT kidney1 [runx1],GSM5212429,,source name:adult kidney|genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month,WT kidney1 [runx1],RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts,adult kidney,,Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in  80C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2,,genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month,GSM5212429,GSM5212429: WT kidney1 [runx1]; Danio rerio; RNA Seq,GSM5212429,,1,Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in  80C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2,GEO Accession:GSM5212429,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP312298,,,141031_OPTIMUS_C5M4FANXX.4.8142698.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.4.8142698.2.cln.fq.gz,fastq fastq,6086298924.0,24523879.0,GSM5212429 r2,0:124.09 1:124.09,A:1640963544;C:1394293929;G:1408031161;T:1642922398;N:87892,124,124,,,1640963544,1394293929,1408031161,1642922398,87892,SRX10451895,SRS8583180,SRA1210911,GEO,NHGRI,2,0.94597,0.94665,0.09708,0.09725,0.73744,0.73839,0.49464,0.49315,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2021-03-26,Multi-stage,Multi-stage,Kidney,Renal System
63839,SRR14077616,SRX10451894,SRS8583179,SRP312298,PRJNA717672,Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2],GSE169689,Transcriptome Analysis,Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 /  siblings  2.5 mpf  pool of 3 kidneys/replicate.,parent bioproject:PRJNA663961,pubmed:34492681,,runx1 /  kidney6 [runx1],GSM5212433,,source name:adult kidney|genotype:runx1 /  del8  hg96|strain:EK|tissue:kidney|biopsy time:2.5 month,runx1 /  kidney6 [runx1],RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts,adult kidney,,Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in  80C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2,,genotype:runx1 /  del8  hg96|strain:EK|tissue:kidney|biopsy time:2.5 month,GSM5212433,GSM5212433: runx1 /  kidney6 [runx1]; Danio rerio; RNA Seq,GSM5212433,,1,Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in  80C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2,GEO Accession:GSM5212433,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP312298,,,141031_OPTIMUS_C5M4FANXX.4.8142704.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.4.8142704.2.cln.fq.gz,fastq fastq,5830417310.0,23547116.0,GSM5212433 r1,0:123.80 1:123.80,A:1528065414;C:1374560308;G:1389503409;T:1538204560;N:83619,123,123,,,1528065414,1374560308,1389503409,1538204560,83619,SRX10451894,SRS8583179,SRA1210911,GEO,NHGRI,2,0.94227,0.9443,0.0312,0.03106,0.7305,0.73198,0.4564,0.45229,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2021-03-26,Multi-stage,Multi-stage,Kidney,Renal System
63840,SRR14077617,SRX10451894,SRS8583179,SRP312298,PRJNA717672,Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2],GSE169689,Transcriptome Analysis,Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 /  siblings  2.5 mpf  pool of 3 kidneys/replicate.,parent bioproject:PRJNA663961,pubmed:34492681,,runx1 /  kidney6 [runx1],GSM5212433,,source name:adult kidney|genotype:runx1 /  del8  hg96|strain:EK|tissue:kidney|biopsy time:2.5 month,runx1 /  kidney6 [runx1],RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts,adult kidney,,Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in  80C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2,,genotype:runx1 /  del8  hg96|strain:EK|tissue:kidney|biopsy time:2.5 month,GSM5212433,GSM5212433: runx1 /  kidney6 [runx1]; Danio rerio; RNA Seq,GSM5212433,,1,Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in  80C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2,GEO Accession:GSM5212433,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP312298,,,141031_OPTIMUS_C5M4FANXX.5.8142704.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.5.8142704.2.cln.fq.gz,fastq fastq,5801368354.0,23428774.0,GSM5212433 r2,0:123.81 1:123.81,A:1520440154;C:1367723047;G:1382629888;T:1530520601;N:54664,123,123,,,1520440154,1367723047,1382629888,1530520601,54664,SRX10451894,SRS8583179,SRA1210911,GEO,NHGRI,2,0.94318,0.94442,0.03018,0.0303,0.72835,0.72906,0.44351,0.44657,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2021-03-26,Multi-stage,Multi-stage,Kidney,Renal System
63841,SRR14077614,SRX10451893,SRS8583178,SRP312298,PRJNA717672,Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2],GSE169689,Transcriptome Analysis,Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 /  siblings  2.5 mpf  pool of 3 kidneys/replicate.,parent bioproject:PRJNA663961,pubmed:34492681,,runx1 /  kidney5 [runx1],GSM5212432,,source name:adult kidney|genotype:runx1 /  del8  hg96|strain:EK|tissue:kidney|biopsy time:2.5 month,runx1 /  kidney5 [runx1],RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts,adult kidney,,Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in  80C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2,,genotype:runx1 /  del8  hg96|strain:EK|tissue:kidney|biopsy time:2.5 month,GSM5212432,GSM5212432: runx1 /  kidney5 [runx1]; Danio rerio; RNA Seq,GSM5212432,,1,Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in  80C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2,GEO Accession:GSM5212432,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP312298,,,141031_OPTIMUS_C5M4FANXX.5.8142695.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.5.8142695.2.cln.fq.gz,fastq fastq,5768438696.0,23423221.0,GSM5212432 r1,0:123.14 1:123.14,A:1566209291;C:1310337702;G:1323216779;T:1568619957;N:54967,123,123,,,1566209291,1310337702,1323216779,1568619957,54967,SRX10451893,SRS8583178,SRA1210911,GEO,NHGRI,2,0.94778,0.94948,0.0935,0.09399,0.72157,0.72299,0.49608,0.49634,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2021-03-26,Multi-stage,Multi-stage,Kidney,Renal System
63842,SRR14077615,SRX10451893,SRS8583178,SRP312298,PRJNA717672,Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2],GSE169689,Transcriptome Analysis,Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 /  siblings  2.5 mpf  pool of 3 kidneys/replicate.,parent bioproject:PRJNA663961,pubmed:34492681,,runx1 /  kidney5 [runx1],GSM5212432,,source name:adult kidney|genotype:runx1 /  del8  hg96|strain:EK|tissue:kidney|biopsy time:2.5 month,runx1 /  kidney5 [runx1],RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts,adult kidney,,Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in  80C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2,,genotype:runx1 /  del8  hg96|strain:EK|tissue:kidney|biopsy time:2.5 month,GSM5212432,GSM5212432: runx1 /  kidney5 [runx1]; Danio rerio; RNA Seq,GSM5212432,,1,Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish  pool of 3 kidneys/replicate and immediately collected in Trizol #15596018  Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in  80C  RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research  #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2,GEO Accession:GSM5212432,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP312298,,,141031_OPTIMUS_C5M4FANXX.4.8142695.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.4.8142695.2.cln.fq.gz,fastq fastq,5808145902.0,23584233.0,GSM5212432 r2,0:123.14 1:123.14,A:1576938864;C:1319376550;G:1332344310;T:1579402358;N:83820,123,123,,,1576938864,1319376550,1332344310,1579402358,83820,SRX10451893,SRS8583178,SRA1210911,GEO,NHGRI,2,0.94737,0.94902,0.09296,0.09311,0.72228,0.7236,0.49544,0.48947,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2021-03-26,Multi-stage,Multi-stage,Kidney,Renal System
67062,SRR17048184,SRX13237924,SRS11162468,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,Mut Inf 7 [210019 24 Mut Inf 42 s24 S235],GSM5704997,,source name:Mut Inf kidney|treatment:M. marinum infection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,Mut Inf 7 [210019 24 Mut Inf 42 s24 S235],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,Mut Inf kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:M. marinum infection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704997,GSM5704997: Mut Inf 7 [210019 24 Mut Inf 42 s24 S235]; Danio rerio; RNA Seq,GSM5704997,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704997,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_24_Mut_Inf_42_s24_S235_L004_R1_001.fastq.gz 210019_24_Mut_Inf_42_s24_S235_L004_R2_001.fastq.gz,fastq fastq,7032894927.0,35884038.0,GSM5704997 r1,0:97.96 1:98.03,A:1731100028;C:1788276798;G:1809972002;T:1694957455;N:8588644,97,98,,,1731100028,1788276798,1809972002,1694957455,8588644,SRX13237924,SRS11162468,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.95915,0.96169,0.11158,0.10796,0.80955,0.80827,0.66594,0.66734,100,99,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67063,SRR17048183,SRX13237923,SRS11162467,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,Mut Inf 6 [210019 23 Mut Inf 40 s23 S234],GSM5704996,,source name:Mut Inf kidney|treatment:M. marinum infection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,Mut Inf 6 [210019 23 Mut Inf 40 s23 S234],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,Mut Inf kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:M. marinum infection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704996,GSM5704996: Mut Inf 6 [210019 23 Mut Inf 40 s23 S234]; Danio rerio; RNA Seq,GSM5704996,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704996,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_23_Mut_Inf_40_s23_S234_L004_R1_001.fastq.gz 210019_23_Mut_Inf_40_s23_S234_L004_R2_001.fastq.gz,fastq fastq,5863554559.0,30352906.0,GSM5704996 r1,0:96.52 1:96.66,A:1426131519;C:1483378471;G:1506857016;T:1396909564;N:50277989,96,96,,,1426131519,1483378471,1506857016,1396909564,50277989,SRX13237923,SRS11162467,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.95854,0.95918,0.12378,0.12045,0.8171,0.81631,0.64334,0.68212,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67064,SRR17048182,SRX13237922,SRS11162466,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,Mut Inf 5 [210019 22 Mut Inf 39 s22 S233],GSM5704995,,source name:Mut Inf kidney|treatment:M. marinum infection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,Mut Inf 5 [210019 22 Mut Inf 39 s22 S233],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,Mut Inf kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:M. marinum infection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704995,GSM5704995: Mut Inf 5 [210019 22 Mut Inf 39 s22 S233]; Danio rerio; RNA Seq,GSM5704995,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704995,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_22_Mut_Inf_39_s22_S233_L004_R1_001.fastq.gz 210019_22_Mut_Inf_39_s22_S233_L004_R2_001.fastq.gz,fastq fastq,6574444328.0,33467850.0,GSM5704995 r1,0:98.20 1:98.24,A:1646588277;C:1641744576;G:1664107413;T:1614615584;N:7388478,98,98,,,1646588277,1641744576,1664107413,1614615584,7388478,SRX13237922,SRS11162466,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.95384,0.95827,0.10707,0.10445,0.80752,0.80507,0.63725,0.59647,100,98,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67065,SRR17048181,SRX13237921,SRS11162465,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,Mut Inf 4 [210019 21 Mut Inf 38 s21 S232],GSM5704994,,source name:Mut Inf kidney|treatment:M. marinum infection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,Mut Inf 4 [210019 21 Mut Inf 38 s21 S232],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,Mut Inf kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:M. marinum infection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704994,GSM5704994: Mut Inf 4 [210019 21 Mut Inf 38 s21 S232]; Danio rerio; RNA Seq,GSM5704994,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704994,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_21_Mut_Inf_38_s21_S232_L004_R1_001.fastq.gz 210019_21_Mut_Inf_38_s21_S232_L004_R2_001.fastq.gz,fastq fastq,7220864595.0,36751167.0,GSM5704994 r1,0:98.20 1:98.28,A:1710142182;C:1905627574;G:1926351728;T:1672025400;N:6717711,98,98,,,1710142182,1905627574,1926351728,1672025400,6717711,SRX13237921,SRS11162465,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.96396,0.9651,0.11474,0.11004,0.82763,0.82781,0.67982,0.65505,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67066,SRR17048180,SRX13237920,SRS11162464,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,Mut Inf 3 [210019 20 Mut Inf 36 s20 S231],GSM5704993,,source name:Mut Inf kidney|treatment:M. marinum infection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,Mut Inf 3 [210019 20 Mut Inf 36 s20 S231],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,Mut Inf kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:M. marinum infection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704993,GSM5704993: Mut Inf 3 [210019 20 Mut Inf 36 s20 S231]; Danio rerio; RNA Seq,GSM5704993,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704993,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_20_Mut_Inf_36_s20_S231_L004_R1_001.fastq.gz 210019_20_Mut_Inf_36_s20_S231_L004_R2_001.fastq.gz,fastq fastq,6906529169.0,35214335.0,GSM5704993 r1,0:98.01 1:98.12,A:1647670645;C:1800519104;G:1830091985;T:1613290370;N:14957065,98,98,,,1647670645,1800519104,1830091985,1613290370,14957065,SRX13237920,SRS11162464,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.96372,0.96513,0.11777,0.11299,0.82919,0.82806,0.67879,0.67604,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67067,SRR17048179,SRX13237919,SRS11162463,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,Mut Inf 2 [210019 19 Mut Inf 35 s19 S229],GSM5704992,,source name:Mut Inf kidney|treatment:M. marinum infection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,Mut Inf 2 [210019 19 Mut Inf 35 s19 S229],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,Mut Inf kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:M. marinum infection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704992,GSM5704992: Mut Inf 2 [210019 19 Mut Inf 35 s19 S229]; Danio rerio; RNA Seq,GSM5704992,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704992,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_19_Mut_Inf_35_s19_S229_L004_R1_001.fastq.gz 210019_19_Mut_Inf_35_s19_S229_L004_R2_001.fastq.gz,fastq fastq,6202812892.0,31926759.0,GSM5704992 r1,0:97.03 1:97.25,A:1305223750;C:1781448011;G:1805043786;T:1276130122;N:34967223,97,97,,,1305223750,1781448011,1805043786,1276130122,34967223,SRX13237919,SRS11162463,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.97834,0.97823,0.17022,0.16369,0.89936,0.89883,0.69906,0.71507,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67068,SRR17048178,SRX13237918,SRS11162462,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,Mut Inf 1 [210019 18 Mut Inf 34 s18 S228],GSM5704991,,source name:Mut Inf kidney|treatment:M. marinum infection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,Mut Inf 1 [210019 18 Mut Inf 34 s18 S228],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,Mut Inf kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:M. marinum infection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704991,GSM5704991: Mut Inf 1 [210019 18 Mut Inf 34 s18 S228]; Danio rerio; RNA Seq,GSM5704991,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704991,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_18_Mut_Inf_34_s18_S228_L004_R1_001.fastq.gz 210019_18_Mut_Inf_34_s18_S228_L004_R2_001.fastq.gz,fastq fastq,7176224174.0,36624544.0,GSM5704991 r1,0:97.91 1:98.03,A:1630206113;C:1958821210;G:1981523742;T:1591801475;N:13871634,97,98,,,1630206113,1958821210,1981523742,1591801475,13871634,SRX13237918,SRS11162462,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.96446,0.96675,0.13739,0.13416,0.85094,0.85169,0.71748,0.69482,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67069,SRR17048177,SRX13237917,SRS11162461,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,WT Inf 9 [210019 17 WT Inf 33 s17 S227],GSM5704990,,source name:WT Inf kidney|treatment:M. marinum infection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,WT Inf 9 [210019 17 WT Inf 33 s17 S227],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,WT Inf kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:M. marinum infection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704990,GSM5704990: WT Inf 9 [210019 17 WT Inf 33 s17 S227]; Danio rerio; RNA Seq,GSM5704990,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704990,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_17_WT_Inf_33_s17_S227_L004_R1_001.fastq.gz 210019_17_WT_Inf_33_s17_S227_L004_R2_001.fastq.gz,fastq fastq,8309947546.0,42701790.0,GSM5704990 r1,0:97.23 1:97.37,A:1924099226;C:2216239212;G:2244211909;T:1884512106;N:40885093,97,97,,,1924099226,2216239212,2244211909,1884512106,40885093,SRX13237917,SRS11162461,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.96027,0.96149,0.14046,0.13556,0.84737,0.84739,0.71707,0.71705,99,99,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67070,SRR17048176,SRX13237916,SRS11162460,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,WT Inf 8 [210019 16 WT Inf 32 s16 S226],GSM5704989,,source name:WT Inf kidney|treatment:M. marinum infection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,WT Inf 8 [210019 16 WT Inf 32 s16 S226],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,WT Inf kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:M. marinum infection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704989,GSM5704989: WT Inf 8 [210019 16 WT Inf 32 s16 S226]; Danio rerio; RNA Seq,GSM5704989,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704989,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_16_WT_Inf_32_s16_S226_L004_R1_001.fastq.gz 210019_16_WT_Inf_32_s16_S226_L004_R2_001.fastq.gz,fastq fastq,6327666844.0,32146843.0,GSM5704989 r1,0:98.36 1:98.48,A:1394311711;C:1775337555;G:1785618112;T:1369084417;N:3315049,98,98,,,1394311711,1775337555,1785618112,1369084417,3315049,SRX13237916,SRS11162460,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.97598,0.97499,0.16157,0.15612,0.85827,0.85855,0.65722,0.67877,80,80,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67071,SRR17048175,SRX13237915,SRS11162459,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,WT Inf 7 [210019 15 WT Inf 31 s15 S225],GSM5704988,,source name:WT Inf kidney|treatment:M. marinum infection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,WT Inf 7 [210019 15 WT Inf 31 s15 S225],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,WT Inf kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:M. marinum infection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704988,GSM5704988: WT Inf 7 [210019 15 WT Inf 31 s15 S225]; Danio rerio; RNA Seq,GSM5704988,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_15_WT_Inf_31_s15_S225_L004_R1_001.fastq.gz 210019_15_WT_Inf_31_s15_S225_L004_R2_001.fastq.gz,fastq fastq,7195652752.0,36740405.0,GSM5704988 r1,0:97.89 1:97.97,A:1741246591;C:1859016659;G:1883433506;T:1702485351;N:9470645,97,97,,,1741246591,1859016659,1883433506,1702485351,9470645,SRX13237915,SRS11162459,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.96048,0.96135,0.12193,0.11965,0.80803,0.8088,0.65183,0.66177,100,99,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67072,SRR17048174,SRX13237914,SRS11162458,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,WT Inf 6 [210019 14 WT Inf 30 s14 S224],GSM5704987,,source name:WT Inf kidney|treatment:M. marinum infection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,WT Inf 6 [210019 14 WT Inf 30 s14 S224],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,WT Inf kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:M. marinum infection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704987,GSM5704987: WT Inf 6 [210019 14 WT Inf 30 s14 S224]; Danio rerio; RNA Seq,GSM5704987,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_14_WT_Inf_30_s14_S224_L004_R1_001.fastq.gz 210019_14_WT_Inf_30_s14_S224_L004_R2_001.fastq.gz,fastq fastq,7120004131.0,37004277.0,GSM5704987 r1,0:96.12 1:96.29,A:1629580191;C:1902194793;G:1928687837;T:1595379526;N:64161784,96,96,,,1629580191,1902194793,1928687837,1595379526,64161784,SRX13237914,SRS11162458,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.96472,0.96479,0.14463,0.13941,0.84721,0.84585,0.69563,0.70266,100,99,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67073,SRR17048173,SRX13237913,SRS11162457,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,WT Inf 5 [210019 13 WT Inf 29 s13 S223],GSM5704986,,source name:WT Inf kidney|treatment:M. marinum infection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,WT Inf 5 [210019 13 WT Inf 29 s13 S223],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,WT Inf kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:M. marinum infection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704986,GSM5704986: WT Inf 5 [210019 13 WT Inf 29 s13 S223]; Danio rerio; RNA Seq,GSM5704986,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704986,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_13_WT_Inf_29_s13_S223_L004_R1_001.fastq.gz 210019_13_WT_Inf_29_s13_S223_L004_R2_001.fastq.gz,fastq fastq,6322574219.0,32279299.0,GSM5704986 r1,0:97.90 1:97.97,A:1436669704;C:1722356836;G:1747757742;T:1408253804;N:7536133,97,97,,,1436669704,1722356836,1747757742,1408253804,7536133,SRX13237913,SRS11162457,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.97077,0.97332,0.13238,0.13033,0.85443,0.85218,0.693,0.69343,99,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67074,SRR17048172,SRX13237912,SRS11162456,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,WT Inf 4 [210019 12 WT Inf 28 s12 S222],GSM5704985,,source name:WT Inf kidney|treatment:M. marinum infection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,WT Inf 4 [210019 12 WT Inf 28 s12 S222],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,WT Inf kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:M. marinum infection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704985,GSM5704985: WT Inf 4 [210019 12 WT Inf 28 s12 S222]; Danio rerio; RNA Seq,GSM5704985,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704985,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_12_WT_Inf_28_s12_S222_L004_R1_001.fastq.gz 210019_12_WT_Inf_28_s12_S222_L004_R2_001.fastq.gz,fastq fastq,6389903560.0,32591111.0,GSM5704985 r1,0:97.94 1:98.12,A:1344520108;C:1841137590;G:1865653521;T:1317665992;N:20926349,97,98,,,1344520108,1841137590,1865653521,1317665992,20926349,SRX13237912,SRS11162456,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.9761,0.97677,0.15931,0.1527,0.88519,0.88357,0.74257,0.74513,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67075,SRR17048171,SRX13237911,SRS11162455,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,WT Inf 3 [210019 11 WT Inf 27 s11 S221],GSM5704984,,source name:WT Inf kidney|treatment:M. marinum infection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,WT Inf 3 [210019 11 WT Inf 27 s11 S221],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,WT Inf kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:M. marinum infection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704984,GSM5704984: WT Inf 3 [210019 11 WT Inf 27 s11 S221]; Danio rerio; RNA Seq,GSM5704984,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704984,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_11_WT_Inf_27_s11_S221_L004_R1_001.fastq.gz 210019_11_WT_Inf_27_s11_S221_L004_R2_001.fastq.gz,fastq fastq,6372761015.0,32624797.0,GSM5704984 r1,0:97.61 1:97.72,A:1515622605;C:1670260418;G:1696355893;T:1479653826;N:10868273,97,97,,,1515622605,1670260418,1696355893,1479653826,10868273,SRX13237911,SRS11162455,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.9636,0.96364,0.12937,0.12511,0.83502,0.83404,0.69038,0.69115,99,98,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67076,SRR17048170,SRX13237910,SRS11162454,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,WT Inf 2 [210019 10 WT Inf 25 s10 S220],GSM5704983,,source name:WT Inf kidney|treatment:M. marinum infection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,WT Inf 2 [210019 10 WT Inf 25 s10 S220],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,WT Inf kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:M. marinum infection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704983,GSM5704983: WT Inf 2 [210019 10 WT Inf 25 s10 S220]; Danio rerio; RNA Seq,GSM5704983,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704983,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_10_WT_Inf_25_s10_S220_L004_R1_001.fastq.gz 210019_10_WT_Inf_25_s10_S220_L004_R2_001.fastq.gz,fastq fastq,6738448918.0,34636902.0,GSM5704983 r1,0:97.20 1:97.35,A:1598257679;C:1755413287;G:1785926499;T:1562700391;N:36151062,97,97,,,1598257679,1755413287,1785926499,1562700391,36151062,SRX13237910,SRS11162454,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.96199,0.96174,0.1339,0.12921,0.82085,0.82112,0.69046,0.69066,99,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67077,SRR17048169,SRX13237909,SRS11162453,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,WT Inf 1 [210019 9 WT Inf 21 s9 S242],GSM5704982,,source name:WT Inf kidney|treatment:M. marinum infection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,WT Inf 1 [210019 9 WT Inf 21 s9 S242],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,WT Inf kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:M. marinum infection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704982,GSM5704982: WT Inf 1 [210019 9 WT Inf 21 s9 S242]; Danio rerio; RNA Seq,GSM5704982,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704982,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_9_WT_Inf_21_s9_S242_L004_R1_001.fastq.gz 210019_9_WT_Inf_21_s9_S242_L004_R2_001.fastq.gz,fastq fastq,6725971675.0,34305800.0,GSM5704982 r1,0:97.98 1:98.08,A:1544859518;C:1817702891;G:1841225564;T:1513968839;N:8214863,97,98,,,1544859518,1817702891,1841225564,1513968839,8214863,SRX13237909,SRS11162453,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.96738,0.96753,0.13517,0.12949,0.81404,0.81262,0.69003,0.67769,100,99,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67078,SRR17048168,SRX13237908,SRS11162452,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,Mut PBS 5 [210019 8 Mut PBS 18 s8 S241],GSM5704981,,source name:Mut PBS kidney|treatment:PBS injection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,Mut PBS 5 [210019 8 Mut PBS 18 s8 S241],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,Mut PBS kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:PBS injection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704981,GSM5704981: Mut PBS 5 [210019 8 Mut PBS 18 s8 S241]; Danio rerio; RNA Seq,GSM5704981,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704981,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_8_Mut_PBS_18_s8_S241_L004_R1_001.fastq.gz 210019_8_Mut_PBS_18_s8_S241_L004_R2_001.fastq.gz,fastq fastq,7244053201.0,37116137.0,GSM5704981 r1,0:97.53 1:97.64,A:1674038518;C:1949255777;G:1971571204;T:1637104124;N:12083578,97,97,,,1674038518,1949255777,1971571204,1637104124,12083578,SRX13237908,SRS11162452,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.93659,0.93806,0.12604,0.12088,0.83913,0.83847,0.665,0.67683,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67079,SRR17048167,SRX13237907,SRS11162451,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,Mut PBS 4 [210019 7 Mut PBS 15 s7 S240],GSM5704980,,source name:Mut PBS kidney|treatment:PBS injection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,Mut PBS 4 [210019 7 Mut PBS 15 s7 S240],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,Mut PBS kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:PBS injection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704980,GSM5704980: Mut PBS 4 [210019 7 Mut PBS 15 s7 S240]; Danio rerio; RNA Seq,GSM5704980,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704980,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_7_Mut_PBS_15_s7_S240_L004_R1_001.fastq.gz 210019_7_Mut_PBS_15_s7_S240_L004_R2_001.fastq.gz,fastq fastq,7095741785.0,36351682.0,GSM5704980 r1,0:97.54 1:97.65,A:1691573777;C:1851818254;G:1874503667;T:1659108487;N:18737600,97,97,,,1691573777,1851818254,1874503667,1659108487,18737600,SRX13237907,SRS11162451,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.95754,0.95819,0.1222,0.11761,0.79813,0.79862,0.64348,0.63591,99,99,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67080,SRR17048166,SRX13237906,SRS11162450,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,Mut PBS 3 [210019 6 Mut PBS 13 s6 S239],GSM5704979,,source name:Mut PBS kidney|treatment:PBS injection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,Mut PBS 3 [210019 6 Mut PBS 13 s6 S239],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,Mut PBS kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:PBS injection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704979,GSM5704979: Mut PBS 3 [210019 6 Mut PBS 13 s6 S239]; Danio rerio; RNA Seq,GSM5704979,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704979,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_6_Mut_PBS_13_s6_S239_L004_R1_001.fastq.gz 210019_6_Mut_PBS_13_s6_S239_L004_R2_001.fastq.gz,fastq fastq,8086865343.0,41144069.0,GSM5704979 r1,0:98.24 1:98.31,A:1952783620;C:2095843140;G:2122633202;T:1911709092;N:3896289,98,98,,,1952783620,2095843140,2122633202,1911709092,3896289,SRX13237906,SRS11162450,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.94739,0.95116,0.1127,0.10748,0.78723,0.78646,0.63093,0.6311,100,99,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67081,SRR17048165,SRX13237905,SRS11162449,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,Mut PBS 2 [210019 5 Mut PBS 12 s5 S238],GSM5704978,,source name:Mut PBS kidney|treatment:PBS injection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,Mut PBS 2 [210019 5 Mut PBS 12 s5 S238],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,Mut PBS kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:PBS injection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704978,GSM5704978: Mut PBS 2 [210019 5 Mut PBS 12 s5 S238]; Danio rerio; RNA Seq,GSM5704978,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704978,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_5_Mut_PBS_12_s5_S238_L004_R1_001.fastq.gz 210019_5_Mut_PBS_12_s5_S238_L004_R2_001.fastq.gz,fastq fastq,8370707075.0,42641353.0,GSM5704978 r1,0:98.12 1:98.18,A:2095935238;C:2089769498;G:2131685116;T:2046719520;N:6597703,98,98,,,2095935238,2089769498,2131685116,2046719520,6597703,SRX13237905,SRS11162449,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.9417,0.94773,0.09662,0.0923,0.74641,0.74657,0.60254,0.60452,100,99,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67082,SRR17048164,SRX13237904,SRS11162448,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,Mut PBS 1 [210019 4 Mut PBS 11 s4 S237],GSM5704977,,source name:Mut PBS kidney|treatment:PBS injection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,Mut PBS 1 [210019 4 Mut PBS 11 s4 S237],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,Mut PBS kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:PBS injection|genotype:pycard  /  mutant|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704977,GSM5704977: Mut PBS 1 [210019 4 Mut PBS 11 s4 S237]; Danio rerio; RNA Seq,GSM5704977,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704977,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_4_Mut_PBS_11_s4_S237_L004_R1_001.fastq.gz 210019_4_Mut_PBS_11_s4_S237_L004_R2_001.fastq.gz,fastq fastq,6177189221.0,31723967.0,GSM5704977 r1,0:97.31 1:97.40,A:1428096002;C:1655739047;G:1673690266;T:1399599791;N:20064115,97,97,,,1428096002,1655739047,1673690266,1399599791,20064115,SRX13237904,SRS11162448,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.96137,0.96365,0.13218,0.12708,0.8159,0.81237,0.67312,0.67761,98,99,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67083,SRR17048163,SRX13237903,SRS11162447,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,WT PBS 3 [210019 3 WT PBS s3 S236],GSM5704976,,source name:WT PBS kidney|treatment:PBS injection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,WT PBS 3 [210019 3 WT PBS s3 S236],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,WT PBS kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:PBS injection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704976,GSM5704976: WT PBS 3 [210019 3 WT PBS s3 S236]; Danio rerio; RNA Seq,GSM5704976,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704976,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_3_WT_PBS_s3_S236_L004_R1_001.fastq.gz 210019_3_WT_PBS_s3_S236_L004_R2_001.fastq.gz,fastq fastq,6855235510.0,34904895.0,GSM5704976 r1,0:98.17 1:98.23,A:1639414895;C:1787943435;G:1817354145;T:1603361188;N:7161847,98,98,,,1639414895,1787943435,1817354145,1603361188,7161847,SRX13237903,SRS11162447,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.95527,0.95969,0.09781,0.095,0.78817,0.78642,0.60505,0.60571,99,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67084,SRR17048162,SRX13237902,SRS11162446,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,WT PBS 2 [210019 2 WT PBS s2 S230],GSM5704975,,source name:WT PBS kidney|treatment:PBS injection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,WT PBS 2 [210019 2 WT PBS s2 S230],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,WT PBS kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:PBS injection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704975,GSM5704975: WT PBS 2 [210019 2 WT PBS s2 S230]; Danio rerio; RNA Seq,GSM5704975,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704975,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_2_WT_PBS_s2_S230_L004_R1_001.fastq.gz 210019_2_WT_PBS_s2_S230_L004_R2_001.fastq.gz,fastq fastq,7809546361.0,40252636.0,GSM5704975 r1,0:96.92 1:97.09,A:1914065031;C:1976055838;G:2012980285;T:1867887126;N:38558081,96,97,,,1914065031,1976055838,2012980285,1867887126,38558081,SRX13237902,SRS11162446,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.96064,0.9607,0.10259,0.09876,0.78218,0.78206,0.60954,0.61811,99,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System
67085,SRR17048161,SRX13237901,SRS11162445,SRP348087,PRJNA783915,RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection,GSE189627,Transcriptome Analysis,Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis  as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up  or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection  from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up  and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed  from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected  mutant PBS injected  WT M. marinum infected  mutant M. marinum infected.,,pubmed:39916610,,WT PBS 1 [210019 1 WT PBS s1 S219],GSM5704974,,source name:WT PBS kidney|treatment:PBS injection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,WT PBS 1 [210019 1 WT PBS s1 S219],Automatic adapter trimming  Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts  .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx,WT PBS kidney,9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish  treated with identical protocol  were used as controls.,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,The zebrafish were maintained according to the standard protocols.,treatment:PBS injection|genotype:wild type|disease state:low dose  4 wpi|tissue:Zebrafish kidney,GSM5704974,GSM5704974: WT PBS 1 [210019 1 WT PBS s1 S219]; Danio rerio; RNA Seq,GSM5704974,,1,Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.,GEO Accession:GSM5704974,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP348087,,loader:fastq load.py,210019_1_WT_PBS_s1_S219_L004_R1_001.fastq.gz 210019_1_WT_PBS_s1_S219_L004_R2_001.fastq.gz,fastq fastq,8142302267.0,41575988.0,GSM5704974 r1,0:97.88 1:97.96,A:2012479910;C:2052978488;G:2091066834;T:1968113350;N:17663685,97,97,,,2012479910,2052978488,2091066834,1968113350,17663685,SRX13237901,SRS11162445,SRA1335306,GEO,"Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center",2,0.95967,0.96113,0.10178,0.0974,0.77942,0.77881,0.61188,0.56724,89,89,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Finland,2021-11-26,Multi-stage,Multi-stage,Kidney,Renal System