metadata: run_metadata: 30 rows where experiment.library_selection = "cDNA", experiment.platform = "BGISEQ" and tissue_curation

30 rows where experiment.library_selection = "cDNA", experiment.platform = "BGISEQ" and tissue_curation_coarse = "Surface Structure"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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.Acount	run.Ccount	run.Gcount	run.Tcount	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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
33164	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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

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