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 33164,SRR29809736,SRX25309007,SRS21984115,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 20mM STS 5,GSM8393514,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 20mM STS 5,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS,GSM8393514,GSM8393514: pdx1 morpholino + 20mM STS 5; Danio rerio; RNA Seq,GSM8393514 r1,GSM8393514,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,6_2.fq.gz 6_1.fq.gz,fastq fastq,4827420200.0,24137101.0,GSM8393514 r1,0:100 1:100,A:1278807278;C:1130198430;G:1150325506;T:1268088986;N:0,100,100,,,1278807278,1130198430,1150325506,1268088986,0,SRX25309007,SRS21984115,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.9409,0.94542,0.08059,0.07981,0.69021,0.68887,0.47275,0.47095,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33165,SRR29809737,SRX25309006,SRS21984114,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 20mM STS 4,GSM8393513,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 20mM STS 4,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS,GSM8393513,GSM8393513: pdx1 morpholino + 20mM STS 4; Danio rerio; RNA Seq,GSM8393513 r1,GSM8393513,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,30_2.fq.gz 30_1.fq.gz,fastq fastq,4240862400.0,21204312.0,GSM8393513 r1,0:100 1:100,A:1146088921;C:972830110;G:990127288;T:1131816081;N:0,100,100,,,1146088921,972830110,990127288,1131816081,0,SRX25309006,SRS21984114,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.93888,0.9444,0.08826,0.08671,0.70431,0.70212,0.48083,0.48199,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33166,SRR29809738,SRX25309005,SRS21984113,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 20mM STS 3,GSM8393512,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 20mM STS 3,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS,GSM8393512,GSM8393512: pdx1 morpholino + 20mM STS 3; Danio rerio; RNA Seq,GSM8393512 r1,GSM8393512,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,24_2.fq.gz 24_1.fq.gz,fastq fastq,4822516400.0,24112582.0,GSM8393512 r1,0:100 1:100,A:1276866727;C:1130641795;G:1148897951;T:1266109927;N:0,100,100,,,1276866727,1130641795,1148897951,1266109927,0,SRX25309005,SRS21984113,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94126,0.94446,0.07837,0.07762,0.6911,0.69037,0.46251,0.4642,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33167,SRR29809739,SRX25309004,SRS21984112,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 20mM STS 2,GSM8393511,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 20mM STS 2,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS,GSM8393511,GSM8393511: pdx1 morpholino + 20mM STS 2; Danio rerio; RNA Seq,GSM8393511 r1,GSM8393511,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,18_2.fq.gz 18_1.fq.gz,fastq fastq,4820332000.0,24101660.0,GSM8393511 r1,0:100 1:100,A:1306037553;C:1103383630;G:1122255994;T:1288654823;N:0,100,100,,,1306037553,1103383630,1122255994,1288654823,0,SRX25309004,SRS21984112,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94035,0.9445,0.08468,0.08417,0.71106,0.70897,0.47897,0.47969,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33168,SRR29809740,SRX25309003,SRS21984111,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 20mM STS 1,GSM8393510,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 20mM STS 1,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS,GSM8393510,GSM8393510: pdx1 morpholino + 20mM STS 1; Danio rerio; RNA Seq,GSM8393510 r1,GSM8393510,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,12_1.fq.gz 12_2.fq.gz,fastq fastq,4825742600.0,24128713.0,GSM8393510 r1,0:100 1:100,A:1264457552;C:1145133600;G:1160084092;T:1256067356;N:0,100,100,,,1264457552,1145133600,1160084092,1256067356,0,SRX25309003,SRS21984111,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94613,0.9501,0.06915,0.06812,0.68941,0.68852,0.45659,0.45507,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33169,SRR29809741,SRX25309002,SRS21984110,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 15mM STS 5,GSM8393509,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 15mM STS 5,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS,GSM8393509,GSM8393509: pdx1 morpholino + 15mM STS 5; Danio rerio; RNA Seq,GSM8393509 r1,GSM8393509,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,5_2.fq.gz 5_1.fq.gz,fastq fastq,4816068800.0,24080344.0,GSM8393509 r1,0:100 1:100,A:1278638535;C:1126555210;G:1141985166;T:1268889889;N:0,100,100,,,1278638535,1126555210,1141985166,1268889889,0,SRX25309002,SRS21984110,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.9414,0.94516,0.08012,0.07915,0.69284,0.69185,0.46526,0.46882,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33170,SRR29809742,SRX25309001,SRS21984109,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 15mM STS 4,GSM8393508,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 15mM STS 4,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS,GSM8393508,GSM8393508: pdx1 morpholino + 15mM STS 4; Danio rerio; RNA Seq,GSM8393508 r1,GSM8393508,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,29_2.fq.gz 29_1.fq.gz,fastq fastq,4386218400.0,21931092.0,GSM8393508 r1,0:100 1:100,A:1181773341;C:1011246416;G:1025789654;T:1167408989;N:0,100,100,,,1181773341,1011246416,1025789654,1167408989,0,SRX25309001,SRS21984109,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94168,0.94587,0.08215,0.08003,0.69682,0.69544,0.47251,0.47607,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33171,SRR29809743,SRX25309000,SRS21984108,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 15mM STS 3,GSM8393507,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 15mM STS 3,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS,GSM8393507,GSM8393507: pdx1 morpholino + 15mM STS 3; Danio rerio; RNA Seq,GSM8393507 r1,GSM8393507,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,23_2.fq.gz 23_1.fq.gz,fastq fastq,4808808800.0,24044044.0,GSM8393507 r1,0:100 1:100,A:1269564907;C:1132101674;G:1149286214;T:1257856005;N:0,100,100,,,1269564907,1132101674,1149286214,1257856005,0,SRX25309000,SRS21984108,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.9434,0.94774,0.07109,0.0703,0.69264,0.69183,0.45908,0.46455,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33172,SRR29809744,SRX25308999,SRS21984107,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 15mM STS 2,GSM8393506,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 15mM STS 2,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS,GSM8393506,GSM8393506: pdx1 morpholino + 15mM STS 2; Danio rerio; RNA Seq,GSM8393506 r1,GSM8393506,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,17_1.fq.gz 17_2.fq.gz,fastq fastq,4805883400.0,24029417.0,GSM8393506 r1,0:100 1:100,A:1299291748;C:1102517917;G:1122450422;T:1281623313;N:0,100,100,,,1299291748,1102517917,1122450422,1281623313,0,SRX25308999,SRS21984107,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94253,0.9461,0.08371,0.08155,0.70589,0.70423,0.4853,0.47925,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33173,SRR29809745,SRX25308998,SRS21984106,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 15mM STS 1,GSM8393505,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 15mM STS 1,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS,GSM8393505,GSM8393505: pdx1 morpholino + 15mM STS 1; Danio rerio; RNA Seq,GSM8393505 r1,GSM8393505,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,11_1.fq.gz 11_2.fq.gz,fastq fastq,4812111600.0,24060558.0,GSM8393505 r1,0:100 1:100,A:1269803704;C:1133657948;G:1150461915;T:1258188033;N:0,100,100,,,1269803704,1133657948,1150461915,1258188033,0,SRX25308998,SRS21984106,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94311,0.94708,0.07444,0.07235,0.69266,0.69158,0.46689,0.46584,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33174,SRR29809746,SRX25308997,SRS21984105,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 0mM STS 5,GSM8393504,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 0mM STS 5,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS,GSM8393504,GSM8393504: pdx1 morpholino + 0mM STS 5; Danio rerio; RNA Seq,GSM8393504 r1,GSM8393504,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,4_2.fq.gz 4_1.fq.gz,fastq fastq,4804978800.0,24024894.0,GSM8393504 r1,0:100 1:100,A:1266882676;C:1131396187;G:1149418875;T:1257281062;N:0,100,100,,,1266882676,1131396187,1149418875,1257281062,0,SRX25308997,SRS21984105,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94345,0.94707,0.07428,0.0741,0.6898,0.68856,0.4653,0.46918,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33175,SRR29809747,SRX25308996,SRS21984104,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 0mM STS 4,GSM8393503,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 0mM STS 4,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS,GSM8393503,GSM8393503: pdx1 morpholino + 0mM STS 4; Danio rerio; RNA Seq,GSM8393503 r1,GSM8393503,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,28_1.fq.gz 28_2.fq.gz,fastq fastq,4464066400.0,22320332.0,GSM8393503 r1,0:100 1:100,A:1209155509;C:1023407835;G:1040239673;T:1191263383;N:0,100,100,,,1209155509,1023407835,1040239673,1191263383,0,SRX25308996,SRS21984104,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.934,0.93723,0.08814,0.08601,0.69834,0.69798,0.47533,0.47611,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33176,SRR29809748,SRX25308995,SRS21984103,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 0mM STS 3,GSM8393502,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 0mM STS 3,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS,GSM8393502,GSM8393502: pdx1 morpholino + 0mM STS 3; Danio rerio; RNA Seq,GSM8393502 r1,GSM8393502,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,22_1.fq.gz 22_2.fq.gz,fastq fastq,4613819800.0,23069099.0,GSM8393502 r1,0:100 1:100,A:1218890904;C:1084874278;G:1104087523;T:1205967095;N:0,100,100,,,1218890904,1084874278,1104087523,1205967095,0,SRX25308995,SRS21984103,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.9426,0.94852,0.07601,0.07487,0.69197,0.69075,0.45872,0.45856,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33177,SRR29809749,SRX25308994,SRS21984102,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 0mM STS 2,GSM8393501,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 0mM STS 2,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS,GSM8393501,GSM8393501: pdx1 morpholino + 0mM STS 2; Danio rerio; RNA Seq,GSM8393501 r1,GSM8393501,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,16_1.fq.gz 16_2.fq.gz,fastq fastq,4818005000.0,24090025.0,GSM8393501 r1,0:100 1:100,A:1291680744;C:1114433015;G:1134463270;T:1277427971;N:0,100,100,,,1291680744,1114433015,1134463270,1277427971,0,SRX25308994,SRS21984102,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.93988,0.94257,0.08614,0.08554,0.69376,0.69367,0.47178,0.47111,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33178,SRR29809750,SRX25308993,SRS21984101,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,pdx1 morpholino + 0mM STS 1,GSM8393500,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS|geo loc name:missing|collection date:missing,pdx1 morpholino + 0mM STS 1,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS,GSM8393500,GSM8393500: pdx1 morpholino + 0mM STS 1; Danio rerio; RNA Seq,GSM8393500 r1,GSM8393500,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,10_2.fq.gz 10_1.fq.gz,fastq fastq,4827935800.0,24139679.0,GSM8393500 r1,0:100 1:100,A:1267823750;C:1143323623;G:1156194469;T:1260593958;N:0,100,100,,,1267823750,1143323623,1156194469,1260593958,0,SRX25308993,SRS21984101,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94483,0.94829,0.07178,0.07025,0.69077,0.69025,0.46181,0.45982,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33179,SRR29809751,SRX25308992,SRS21984100,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 20mM STS 5,GSM8393499,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 20mM STS 5,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS,GSM8393499,GSM8393499: Control morpholino + 20mM STS 5; Danio rerio; RNA Seq,GSM8393499 r1,GSM8393499,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,9_1.fq.gz 9_2.fq.gz,fastq fastq,4822379000.0,24111895.0,GSM8393499 r1,0:100 1:100,A:1262977318;C:1145277730;G:1159167028;T:1254956924;N:0,100,100,,,1262977318,1145277730,1159167028,1254956924,0,SRX25308992,SRS21984100,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94642,0.94964,0.06863,0.0674,0.69288,0.69252,0.4574,0.44372,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33180,SRR29809752,SRX25308991,SRS21984099,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 20mM STS 4,GSM8393498,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 20mM STS 4,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS,GSM8393498,GSM8393498: Control morpholino + 20mM STS 4; Danio rerio; RNA Seq,GSM8393498 r1,GSM8393498,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,3_1.fq.gz 3_2.fq.gz,fastq fastq,4803150200.0,24015751.0,GSM8393498 r1,0:100 1:100,A:1253239300;C:1144350399;G:1158671984;T:1246888517;N:0,100,100,,,1253239300,1144350399,1158671984,1246888517,0,SRX25308991,SRS21984099,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94606,0.95015,0.06543,0.06441,0.68676,0.68611,0.44857,0.44396,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33181,SRR29809753,SRX25308990,SRS21984098,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 20mM STS 3,GSM8393497,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 20mM STS 3,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS,GSM8393497,GSM8393497: Control morpholino + 20mM STS 3; Danio rerio; RNA Seq,GSM8393497 r1,GSM8393497,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,27_1.fq.gz 27_2.fq.gz,fastq fastq,4277827200.0,21389136.0,GSM8393497 r1,0:100 1:100,A:1142589086;C:997230367;G:1005771965;T:1132235782;N:0,100,100,,,1142589086,997230367,1005771965,1132235782,0,SRX25308990,SRS21984098,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94201,0.94596,0.07754,0.07484,0.69794,0.69617,0.46286,0.45985,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33182,SRR29809754,SRX25308989,SRS21984097,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 20mM STS 2,GSM8393496,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 20mM STS 2,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS,GSM8393496,GSM8393496: Control morpholino + 20mM STS 2; Danio rerio; RNA Seq,GSM8393496 r1,GSM8393496,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,21_2.fq.gz 21_1.fq.gz,fastq fastq,4019456600.0,20097283.0,GSM8393496 r1,0:100 1:100,A:1053249649;C:953992221;G:968100759;T:1044113971;N:0,100,100,,,1053249649,953992221,968100759,1044113971,0,SRX25308989,SRS21984097,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94377,0.95125,0.06861,0.06745,0.68676,0.68523,0.45049,0.45168,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33183,SRR29809755,SRX25308988,SRS21984096,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 20mM STS 1,GSM8393495,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 20mM STS 1,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS,GSM8393495,GSM8393495: Control morpholino + 20mM STS 1; Danio rerio; RNA Seq,GSM8393495 r1,GSM8393495,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,15_1.fq.gz 15_2.fq.gz,fastq fastq,4829679200.0,24148396.0,GSM8393495 r1,0:100 1:100,A:1292193191;C:1119414896;G:1140502241;T:1277568872;N:0,100,100,,,1292193191,1119414896,1140502241,1277568872,0,SRX25308988,SRS21984096,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.9423,0.9467,0.07958,0.07808,0.69763,0.69658,0.46406,0.46623,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33184,SRR29809756,SRX25308987,SRS21984095,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 15mM STS 5,GSM8393494,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 15mM STS 5,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS,GSM8393494,GSM8393494: Control morpholino + 15mM STS 5; Danio rerio; RNA Seq,GSM8393494 r1,GSM8393494,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,8_2.fq.gz 8_1.fq.gz,fastq fastq,4803709800.0,24018549.0,GSM8393494 r1,0:100 1:100,A:1253733589;C:1143748058;G:1158768340;T:1247459813;N:0,100,100,,,1253733589,1143748058,1158768340,1247459813,0,SRX25308987,SRS21984095,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94718,0.94926,0.06582,0.06461,0.68791,0.68738,0.44759,0.44517,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33185,SRR29809757,SRX25308986,SRS21984094,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 15mM STS 4,GSM8393493,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 15mM STS 4,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS,GSM8393493,GSM8393493: Control morpholino + 15mM STS 4; Danio rerio; RNA Seq,GSM8393493 r1,GSM8393493,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,26_1.fq.gz 26_2.fq.gz,fastq fastq,4816718000.0,24083590.0,GSM8393493 r1,0:100 1:100,A:1278966223;C:1129131703;G:1144234415;T:1264385659;N:0,100,100,,,1278966223,1129131703,1144234415,1264385659,0,SRX25308986,SRS21984094,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94278,0.94713,0.07235,0.0704,0.69895,0.698,0.4536,0.45416,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33186,SRR29809758,SRX25308985,SRS21984093,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 15mM STS 3,GSM8393492,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 15mM STS 3,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS,GSM8393492,GSM8393492: Control morpholino + 15mM STS 3; Danio rerio; RNA Seq,GSM8393492 r1,GSM8393492,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,20_2.fq.gz 20_1.fq.gz,fastq fastq,4825880400.0,24129402.0,GSM8393492 r1,0:100 1:100,A:1263053657;C:1147908238;G:1161094243;T:1253824262;N:0,100,100,,,1263053657,1147908238,1161094243,1253824262,0,SRX25308985,SRS21984093,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94642,0.95164,0.06472,0.06312,0.69035,0.68909,0.44854,0.44216,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33187,SRR29809759,SRX25308984,SRS21984092,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 15mM STS 2,GSM8393491,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 15mM STS 2,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS,GSM8393491,GSM8393491: Control morpholino + 15mM STS 2; Danio rerio; RNA Seq,GSM8393491 r1,GSM8393491,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,2_1.fq.gz 2_2.fq.gz,fastq fastq,4805985200.0,24029926.0,GSM8393491 r1,0:100 1:100,A:1255841114;C:1143278337;G:1157783615;T:1249082134;N:0,100,100,,,1255841114,1143278337,1157783615,1249082134,0,SRX25308984,SRS21984092,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94666,0.94794,0.06553,0.06456,0.69181,0.69175,0.4359,0.44559,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33188,SRR29809760,SRX25308983,SRS21984091,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 15mM STS 1,GSM8393490,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 15mM STS 1,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS,GSM8393490,GSM8393490: Control morpholino + 15mM STS 1; Danio rerio; RNA Seq,GSM8393490 r1,GSM8393490,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,14_1.fq.gz 14_2.fq.gz,fastq fastq,4553465000.0,22767325.0,GSM8393490 r1,0:100 1:100,A:1209891078;C:1063666819;G:1082075995;T:1197831108;N:0,100,100,,,1209891078,1063666819,1082075995,1197831108,0,SRX25308983,SRS21984091,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.9432,0.94661,0.07696,0.07599,0.69763,0.69721,0.46463,0.46425,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33189,SRR29809761,SRX25308982,SRS21984090,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 0mM STS 5,GSM8393489,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 0mM STS 5,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS,GSM8393489,GSM8393489: Control morpholino + 0mM STS 5; Danio rerio; RNA Seq,GSM8393489 r1,GSM8393489,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,7_1.fq.gz 7_2.fq.gz,fastq fastq,4813770200.0,24068851.0,GSM8393489 r1,0:100 1:100,A:1251918123;C:1151936172;G:1164458418;T:1245457487;N:0,100,100,,,1251918123,1151936172,1164458418,1245457487,0,SRX25308982,SRS21984090,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.95021,0.95271,0.06538,0.06376,0.69171,0.68996,0.44317,0.4435,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33190,SRR29809762,SRX25308981,SRS21984089,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 0mM STS 4,GSM8393488,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 0mM STS 4,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS,GSM8393488,GSM8393488: Control morpholino + 0mM STS 4; Danio rerio; RNA Seq,GSM8393488 r1,GSM8393488,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,25_1.fq.gz 25_2.fq.gz,fastq fastq,4810346800.0,24051734.0,GSM8393488 r1,0:100 1:100,A:1275301780;C:1127999390;G:1144547869;T:1262497761;N:0,100,100,,,1275301780,1127999390,1144547869,1262497761,0,SRX25308981,SRS21984089,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94519,0.94834,0.06949,0.06803,0.69552,0.69524,0.44741,0.45052,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33191,SRR29809763,SRX25308980,SRS21984088,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 0mM STS 3,GSM8393487,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 0mM STS 3,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS,GSM8393487,GSM8393487: Control morpholino + 0mM STS 3; Danio rerio; RNA Seq,GSM8393487 r1,GSM8393487,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,19_1.fq.gz 19_2.fq.gz,fastq fastq,4811704200.0,24058521.0,GSM8393487 r1,0:100 1:100,A:1257129134;C:1146835083;G:1160663520;T:1247076463;N:0,100,100,,,1257129134,1146835083,1160663520,1247076463,0,SRX25308980,SRS21984088,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94691,0.95082,0.06344,0.06212,0.69014,0.69059,0.45386,0.43864,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33192,SRR29809764,SRX25308979,SRS21984087,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 0mM STS 2,GSM8393486,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 0mM STS 2,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS,GSM8393486,GSM8393486: Control morpholino + 0mM STS 2; Danio rerio; RNA Seq,GSM8393486 r1,GSM8393486,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,13_1.fq.gz 13_2.fq.gz,fastq fastq,4616178800.0,23080894.0,GSM8393486 r1,0:100 1:100,A:1225429879;C:1079094541;G:1096304865;T:1215349515;N:0,100,100,,,1225429879,1079094541,1096304865,1215349515,0,SRX25308979,SRS21984087,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94498,0.9498,0.07635,0.075,0.69319,0.6927,0.46598,0.466,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure 33193,SRR29809765,SRX25308978,SRS21984086,SRP519612,PRJNA1135151,The effect of sodium thiosulfate on hyperglycemic zebrafish larvae,GSE272119,Transcriptome Analysis,We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.,,pubmed:39264236,,Control morpholino + 0mM STS 1,GSM8393485,,source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS|geo loc name:missing|collection date:missing,Control morpholino + 0mM STS 1,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17,larvae,,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS,GSM8393485,GSM8393485: Control morpholino + 0mM STS 1; Danio rerio; RNA Seq,GSM8393485 r1,GSM8393485,1,RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP519612,,,1_1.fq.gz 1_2.fq.gz,fastq fastq,4823953400.0,24119767.0,GSM8393485 r1,0:100 1:100,A:1270954678;C:1137736456;G:1155516940;T:1259745326;N:0,100,100,,,1270954678,1137736456,1155516940,1259745326,0,SRX25308978,SRS21984086,SRA1923353,"ZMF, University Heidelberg","ZMF, University Heidelberg",2,0.94325,0.94699,0.06928,0.06864,0.69372,0.69307,0.44844,0.45647,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2024-07-12,Multi-stage,Multi-stage,Trunk,Surface Structure