metadata: run_metadata: 12 rows where experiment.platform = "DNBSEQ", technology = "unknown" and tissue_curation

12 rows where experiment.platform = "DNBSEQ", technology = "unknown" and tissue_curation_coarse = "Sensory System"

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.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
34658	34658	SRR32162987	SRX27508420	SRS23927742	SRP560539	PRJNA1216901	Impaired detoxification of Acrolein interrupted ocular vascular integrity and kidney structure in akr7a3 / zebrafish via enhancing Arachidonic acid/leukotriene metabolism	GSE288313	Transcriptome Analysis	Acrolein ACR is an endogenous reactive unsaturated aldehyde that can be detoxified by the aldo keto reductase AKR enzyme system. The accumulation of ACR is associated with several health issues including inflammation oxidative stress and cardiovascular diseases. In this study an akr7a3 mutant zebrafish with the Tgfli1: EGFP signature was generated to investigate the effect of ACR on vascular integrity. Elevated ACR levels were observed in akr7a3 / zebrafish larvae and adults. Subsequent experiments demonstrated that increased ACR induced an enlargement of the hyaloid and retinal vasculature as well as alterations in the larvae pronephron and adult kidney. Transcriptome and metabolomics analyses followed by validation experiments revealed that the upregulation of arachidonic acid metabolism and leukotriene production are responsible for the observed vascular and organ changes. In conclusion our data suggests that the loss of akr7a3 in zebrafish impairs the detoxification of ACR which subsequently disrupts vascular integrity and normal kidney structure by promoting an inflammatory response. Overall design: akr7a3 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations transcriptome and metabolomics in Tgfli1:EGFP zebrafish.	pubmed:40258306	zf akr7a3 hom9	GSM8764271	source name:eye\|tissue:eye\|genotype:akr7a3 / \|geo loc name:missing\|collection date:missing	zf akr7a3 hom9	Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.	eye	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	tissue:eye\|genotype:akr7a3 /	GSM8764271	GSM8764271: zf akr7a3 hom9; Danio rerio; RNA Seq	GSM8764271 r1	GSM8764271	1	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP560539	h9_1.fq.gz h9_2.fq.gz	fastq fastq	4830034200.0	24150171.0	GSM8764271 r1	0:100 1:100	A:1314740521;C:1098654357;G:1108546731;T:1308092591;N:0	100	100	1314740521	1098654357	1108546731	1308092591	SRX27508420	SRS23927742	SRA2064109	Medical Faculty Mannheim	Medical Faculty Mannheim	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2025-01-29	Undetermined	Larval	Eye	Sensory System
34659	34659	SRR32162988	SRX27508419	SRS23927741	SRP560539	PRJNA1216901	Impaired detoxification of Acrolein interrupted ocular vascular integrity and kidney structure in akr7a3 / zebrafish via enhancing Arachidonic acid/leukotriene metabolism	GSE288313	Transcriptome Analysis	Acrolein ACR is an endogenous reactive unsaturated aldehyde that can be detoxified by the aldo keto reductase AKR enzyme system. The accumulation of ACR is associated with several health issues including inflammation oxidative stress and cardiovascular diseases. In this study an akr7a3 mutant zebrafish with the Tgfli1: EGFP signature was generated to investigate the effect of ACR on vascular integrity. Elevated ACR levels were observed in akr7a3 / zebrafish larvae and adults. Subsequent experiments demonstrated that increased ACR induced an enlargement of the hyaloid and retinal vasculature as well as alterations in the larvae pronephron and adult kidney. Transcriptome and metabolomics analyses followed by validation experiments revealed that the upregulation of arachidonic acid metabolism and leukotriene production are responsible for the observed vascular and organ changes. In conclusion our data suggests that the loss of akr7a3 in zebrafish impairs the detoxification of ACR which subsequently disrupts vascular integrity and normal kidney structure by promoting an inflammatory response. Overall design: akr7a3 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations transcriptome and metabolomics in Tgfli1:EGFP zebrafish.	pubmed:40258306	zf akr7a3 hom8	GSM8764270	source name:eye\|tissue:eye\|genotype:akr7a3 / \|geo loc name:missing\|collection date:missing	zf akr7a3 hom8	Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.	eye	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	tissue:eye\|genotype:akr7a3 /	GSM8764270	GSM8764270: zf akr7a3 hom8; Danio rerio; RNA Seq	GSM8764270 r1	GSM8764270	1	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP560539	h8_1.fq.gz h8_2.fq.gz	fastq fastq	4842768400.0	24213842.0	GSM8764270 r1	0:100 1:100	A:1306148372;C:1113721147;G:1128251057;T:1294647824;N:0	100	100	1306148372	1113721147	1128251057	1294647824	SRX27508419	SRS23927741	SRA2064109	Medical Faculty Mannheim	Medical Faculty Mannheim	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2025-01-29	Undetermined	Larval	Eye	Sensory System
34660	34660	SRR32162989	SRX27508418	SRS23927740	SRP560539	PRJNA1216901	Impaired detoxification of Acrolein interrupted ocular vascular integrity and kidney structure in akr7a3 / zebrafish via enhancing Arachidonic acid/leukotriene metabolism	GSE288313	Transcriptome Analysis	Acrolein ACR is an endogenous reactive unsaturated aldehyde that can be detoxified by the aldo keto reductase AKR enzyme system. The accumulation of ACR is associated with several health issues including inflammation oxidative stress and cardiovascular diseases. In this study an akr7a3 mutant zebrafish with the Tgfli1: EGFP signature was generated to investigate the effect of ACR on vascular integrity. Elevated ACR levels were observed in akr7a3 / zebrafish larvae and adults. Subsequent experiments demonstrated that increased ACR induced an enlargement of the hyaloid and retinal vasculature as well as alterations in the larvae pronephron and adult kidney. Transcriptome and metabolomics analyses followed by validation experiments revealed that the upregulation of arachidonic acid metabolism and leukotriene production are responsible for the observed vascular and organ changes. In conclusion our data suggests that the loss of akr7a3 in zebrafish impairs the detoxification of ACR which subsequently disrupts vascular integrity and normal kidney structure by promoting an inflammatory response. Overall design: akr7a3 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations transcriptome and metabolomics in Tgfli1:EGFP zebrafish.	pubmed:40258306	zf akr7a3 hom7	GSM8764269	source name:eye\|tissue:eye\|genotype:akr7a3 / \|geo loc name:missing\|collection date:missing	zf akr7a3 hom7	Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.	eye	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	tissue:eye\|genotype:akr7a3 /	GSM8764269	GSM8764269: zf akr7a3 hom7; Danio rerio; RNA Seq	GSM8764269 r1	GSM8764269	1	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP560539	h7_1.fq.gz h7_2.fq.gz	fastq fastq	4830723600.0	24153618.0	GSM8764269 r1	0:100 1:100	A:1309010576;C:1102003245;G:1117775599;T:1301934180;N:0	100	100	1309010576	1102003245	1117775599	1301934180	SRX27508418	SRS23927740	SRA2064109	Medical Faculty Mannheim	Medical Faculty Mannheim	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2025-01-29	Undetermined	Larval	Eye	Sensory System
34661	34661	SRR32162990	SRX27508417	SRS23927739	SRP560539	PRJNA1216901	Impaired detoxification of Acrolein interrupted ocular vascular integrity and kidney structure in akr7a3 / zebrafish via enhancing Arachidonic acid/leukotriene metabolism	GSE288313	Transcriptome Analysis	Acrolein ACR is an endogenous reactive unsaturated aldehyde that can be detoxified by the aldo keto reductase AKR enzyme system. The accumulation of ACR is associated with several health issues including inflammation oxidative stress and cardiovascular diseases. In this study an akr7a3 mutant zebrafish with the Tgfli1: EGFP signature was generated to investigate the effect of ACR on vascular integrity. Elevated ACR levels were observed in akr7a3 / zebrafish larvae and adults. Subsequent experiments demonstrated that increased ACR induced an enlargement of the hyaloid and retinal vasculature as well as alterations in the larvae pronephron and adult kidney. Transcriptome and metabolomics analyses followed by validation experiments revealed that the upregulation of arachidonic acid metabolism and leukotriene production are responsible for the observed vascular and organ changes. In conclusion our data suggests that the loss of akr7a3 in zebrafish impairs the detoxification of ACR which subsequently disrupts vascular integrity and normal kidney structure by promoting an inflammatory response. Overall design: akr7a3 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations transcriptome and metabolomics in Tgfli1:EGFP zebrafish.	pubmed:40258306	zf akr7a3 hom5	GSM8764268	source name:eye\|tissue:eye\|genotype:akr7a3 / \|geo loc name:missing\|collection date:missing	zf akr7a3 hom5	Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.	eye	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	tissue:eye\|genotype:akr7a3 /	GSM8764268	GSM8764268: zf akr7a3 hom5; Danio rerio; RNA Seq	GSM8764268 r1	GSM8764268	1	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP560539	h5_1.fq.gz h5_2.fq.gz	fastq fastq	4841344600.0	24206723.0	GSM8764268 r1	0:100 1:100	A:1293979155;C:1123490462;G:1137125262;T:1286749721;N:0	100	100	1293979155	1123490462	1137125262	1286749721	SRX27508417	SRS23927739	SRA2064109	Medical Faculty Mannheim	Medical Faculty Mannheim	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2025-01-29	Undetermined	Larval	Eye	Sensory System
34662	34662	SRR32162991	SRX27508416	SRS23927738	SRP560539	PRJNA1216901	Impaired detoxification of Acrolein interrupted ocular vascular integrity and kidney structure in akr7a3 / zebrafish via enhancing Arachidonic acid/leukotriene metabolism	GSE288313	Transcriptome Analysis	Acrolein ACR is an endogenous reactive unsaturated aldehyde that can be detoxified by the aldo keto reductase AKR enzyme system. The accumulation of ACR is associated with several health issues including inflammation oxidative stress and cardiovascular diseases. In this study an akr7a3 mutant zebrafish with the Tgfli1: EGFP signature was generated to investigate the effect of ACR on vascular integrity. Elevated ACR levels were observed in akr7a3 / zebrafish larvae and adults. Subsequent experiments demonstrated that increased ACR induced an enlargement of the hyaloid and retinal vasculature as well as alterations in the larvae pronephron and adult kidney. Transcriptome and metabolomics analyses followed by validation experiments revealed that the upregulation of arachidonic acid metabolism and leukotriene production are responsible for the observed vascular and organ changes. In conclusion our data suggests that the loss of akr7a3 in zebrafish impairs the detoxification of ACR which subsequently disrupts vascular integrity and normal kidney structure by promoting an inflammatory response. Overall design: akr7a3 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations transcriptome and metabolomics in Tgfli1:EGFP zebrafish.	pubmed:40258306	zf akr7a3 hom4	GSM8764267	source name:eye\|tissue:eye\|genotype:akr7a3 / \|geo loc name:missing\|collection date:missing	zf akr7a3 hom4	Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.	eye	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	tissue:eye\|genotype:akr7a3 /	GSM8764267	GSM8764267: zf akr7a3 hom4; Danio rerio; RNA Seq	GSM8764267 r1	GSM8764267	1	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP560539	h4_1.fq.gz h4_2.fq.gz	fastq fastq	4833039200.0	24165196.0	GSM8764267 r1	0:100 1:100	A:1300759651;C:1113327310;G:1126592364;T:1292359875;N:0	100	100	1300759651	1113327310	1126592364	1292359875	SRX27508416	SRS23927738	SRA2064109	Medical Faculty Mannheim	Medical Faculty Mannheim	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2025-01-29	Undetermined	Larval	Eye	Sensory System
34663	34663	SRR32162992	SRX27508415	SRS23927737	SRP560539	PRJNA1216901	Impaired detoxification of Acrolein interrupted ocular vascular integrity and kidney structure in akr7a3 / zebrafish via enhancing Arachidonic acid/leukotriene metabolism	GSE288313	Transcriptome Analysis	Acrolein ACR is an endogenous reactive unsaturated aldehyde that can be detoxified by the aldo keto reductase AKR enzyme system. The accumulation of ACR is associated with several health issues including inflammation oxidative stress and cardiovascular diseases. In this study an akr7a3 mutant zebrafish with the Tgfli1: EGFP signature was generated to investigate the effect of ACR on vascular integrity. Elevated ACR levels were observed in akr7a3 / zebrafish larvae and adults. Subsequent experiments demonstrated that increased ACR induced an enlargement of the hyaloid and retinal vasculature as well as alterations in the larvae pronephron and adult kidney. Transcriptome and metabolomics analyses followed by validation experiments revealed that the upregulation of arachidonic acid metabolism and leukotriene production are responsible for the observed vascular and organ changes. In conclusion our data suggests that the loss of akr7a3 in zebrafish impairs the detoxification of ACR which subsequently disrupts vascular integrity and normal kidney structure by promoting an inflammatory response. Overall design: akr7a3 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations transcriptome and metabolomics in Tgfli1:EGFP zebrafish.	pubmed:40258306	zf akr7a3 hom1	GSM8764266	source name:eye\|tissue:eye\|genotype:akr7a3 / \|geo loc name:missing\|collection date:missing	zf akr7a3 hom1	Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.	eye	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	tissue:eye\|genotype:akr7a3 /	GSM8764266	GSM8764266: zf akr7a3 hom1; Danio rerio; RNA Seq	GSM8764266 r1	GSM8764266	1	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP560539	h1_1.fq.gz h1_2.fq.gz	fastq fastq	4824827000.0	24124135.0	GSM8764266 r1	0:100 1:100	A:1310983476;C:1097644236;G:1110687755;T:1305511533;N:0	100	100	1310983476	1097644236	1110687755	1305511533	SRX27508415	SRS23927737	SRA2064109	Medical Faculty Mannheim	Medical Faculty Mannheim	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2025-01-29	Undetermined	Larval	Eye	Sensory System
34664	34664	SRR32162993	SRX27508414	SRS23927736	SRP560539	PRJNA1216901	Impaired detoxification of Acrolein interrupted ocular vascular integrity and kidney structure in akr7a3 / zebrafish via enhancing Arachidonic acid/leukotriene metabolism	GSE288313	Transcriptome Analysis	Acrolein ACR is an endogenous reactive unsaturated aldehyde that can be detoxified by the aldo keto reductase AKR enzyme system. The accumulation of ACR is associated with several health issues including inflammation oxidative stress and cardiovascular diseases. In this study an akr7a3 mutant zebrafish with the Tgfli1: EGFP signature was generated to investigate the effect of ACR on vascular integrity. Elevated ACR levels were observed in akr7a3 / zebrafish larvae and adults. Subsequent experiments demonstrated that increased ACR induced an enlargement of the hyaloid and retinal vasculature as well as alterations in the larvae pronephron and adult kidney. Transcriptome and metabolomics analyses followed by validation experiments revealed that the upregulation of arachidonic acid metabolism and leukotriene production are responsible for the observed vascular and organ changes. In conclusion our data suggests that the loss of akr7a3 in zebrafish impairs the detoxification of ACR which subsequently disrupts vascular integrity and normal kidney structure by promoting an inflammatory response. Overall design: akr7a3 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations transcriptome and metabolomics in Tgfli1:EGFP zebrafish.	pubmed:40258306	zf akr7a3 wt7	GSM8764265	source name:eye\|tissue:eye\|genotype:akr7a3+/+\|geo loc name:missing\|collection date:missing	zf akr7a3 wt7	Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.	eye	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	tissue:eye\|genotype:akr7a3+/+	GSM8764265	GSM8764265: zf akr7a3 wt7; Danio rerio; RNA Seq	GSM8764265 r1	GSM8764265	1	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP560539	wt7_1.fq.gz wt7_2.fq.gz	fastq fastq	4814413600.0	24072068.0	GSM8764265 r1	0:100 1:100	A:1283581046;C:1120298358;G:1134358560;T:1276175636;N:0	100	100	1283581046	1120298358	1134358560	1276175636	SRX27508414	SRS23927736	SRA2064109	Medical Faculty Mannheim	Medical Faculty Mannheim	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2025-01-29	Undetermined	Larval	Eye	Sensory System
34665	34665	SRR32162994	SRX27508413	SRS23927735	SRP560539	PRJNA1216901	Impaired detoxification of Acrolein interrupted ocular vascular integrity and kidney structure in akr7a3 / zebrafish via enhancing Arachidonic acid/leukotriene metabolism	GSE288313	Transcriptome Analysis	Acrolein ACR is an endogenous reactive unsaturated aldehyde that can be detoxified by the aldo keto reductase AKR enzyme system. The accumulation of ACR is associated with several health issues including inflammation oxidative stress and cardiovascular diseases. In this study an akr7a3 mutant zebrafish with the Tgfli1: EGFP signature was generated to investigate the effect of ACR on vascular integrity. Elevated ACR levels were observed in akr7a3 / zebrafish larvae and adults. Subsequent experiments demonstrated that increased ACR induced an enlargement of the hyaloid and retinal vasculature as well as alterations in the larvae pronephron and adult kidney. Transcriptome and metabolomics analyses followed by validation experiments revealed that the upregulation of arachidonic acid metabolism and leukotriene production are responsible for the observed vascular and organ changes. In conclusion our data suggests that the loss of akr7a3 in zebrafish impairs the detoxification of ACR which subsequently disrupts vascular integrity and normal kidney structure by promoting an inflammatory response. Overall design: akr7a3 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations transcriptome and metabolomics in Tgfli1:EGFP zebrafish.	pubmed:40258306	zf akr7a3 wt6	GSM8764264	source name:eye\|tissue:eye\|genotype:akr7a3+/+\|geo loc name:missing\|collection date:missing	zf akr7a3 wt6	Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.	eye	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	tissue:eye\|genotype:akr7a3+/+	GSM8764264	GSM8764264: zf akr7a3 wt6; Danio rerio; RNA Seq	GSM8764264 r1	GSM8764264	1	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP560539	wt6_1.fq.gz wt6_2.fq.gz	fastq fastq	4811652400.0	24058262.0	GSM8764264 r1	0:100 1:100	A:1296911532;C:1104236297;G:1119774441;T:1290730130;N:0	100	100	1296911532	1104236297	1119774441	1290730130	SRX27508413	SRS23927735	SRA2064109	Medical Faculty Mannheim	Medical Faculty Mannheim	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2025-01-29	Undetermined	Larval	Eye	Sensory System
34666	34666	SRR32162995	SRX27508412	SRS23927734	SRP560539	PRJNA1216901	Impaired detoxification of Acrolein interrupted ocular vascular integrity and kidney structure in akr7a3 / zebrafish via enhancing Arachidonic acid/leukotriene metabolism	GSE288313	Transcriptome Analysis	Acrolein ACR is an endogenous reactive unsaturated aldehyde that can be detoxified by the aldo keto reductase AKR enzyme system. The accumulation of ACR is associated with several health issues including inflammation oxidative stress and cardiovascular diseases. In this study an akr7a3 mutant zebrafish with the Tgfli1: EGFP signature was generated to investigate the effect of ACR on vascular integrity. Elevated ACR levels were observed in akr7a3 / zebrafish larvae and adults. Subsequent experiments demonstrated that increased ACR induced an enlargement of the hyaloid and retinal vasculature as well as alterations in the larvae pronephron and adult kidney. Transcriptome and metabolomics analyses followed by validation experiments revealed that the upregulation of arachidonic acid metabolism and leukotriene production are responsible for the observed vascular and organ changes. In conclusion our data suggests that the loss of akr7a3 in zebrafish impairs the detoxification of ACR which subsequently disrupts vascular integrity and normal kidney structure by promoting an inflammatory response. Overall design: akr7a3 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations transcriptome and metabolomics in Tgfli1:EGFP zebrafish.	pubmed:40258306	zf akr7a3 wt4	GSM8764263	source name:eye\|tissue:eye\|genotype:akr7a3+/+\|geo loc name:missing\|collection date:missing	zf akr7a3 wt4	Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.	eye	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	tissue:eye\|genotype:akr7a3+/+	GSM8764263	GSM8764263: zf akr7a3 wt4; Danio rerio; RNA Seq	GSM8764263 r1	GSM8764263	1	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP560539	wt4_1.fq.gz wt4_2.fq.gz	fastq fastq	4807384800.0	24036924.0	GSM8764263 r1	0:100 1:100	A:1287001771;C:1113056126;G:1126875295;T:1280451608;N:0	100	100	1287001771	1113056126	1126875295	1280451608	SRX27508412	SRS23927734	SRA2064109	Medical Faculty Mannheim	Medical Faculty Mannheim	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2025-01-29	Undetermined	Larval	Eye	Sensory System
34667	34667	SRR32162996	SRX27508411	SRS23927733	SRP560539	PRJNA1216901	Impaired detoxification of Acrolein interrupted ocular vascular integrity and kidney structure in akr7a3 / zebrafish via enhancing Arachidonic acid/leukotriene metabolism	GSE288313	Transcriptome Analysis	Acrolein ACR is an endogenous reactive unsaturated aldehyde that can be detoxified by the aldo keto reductase AKR enzyme system. The accumulation of ACR is associated with several health issues including inflammation oxidative stress and cardiovascular diseases. In this study an akr7a3 mutant zebrafish with the Tgfli1: EGFP signature was generated to investigate the effect of ACR on vascular integrity. Elevated ACR levels were observed in akr7a3 / zebrafish larvae and adults. Subsequent experiments demonstrated that increased ACR induced an enlargement of the hyaloid and retinal vasculature as well as alterations in the larvae pronephron and adult kidney. Transcriptome and metabolomics analyses followed by validation experiments revealed that the upregulation of arachidonic acid metabolism and leukotriene production are responsible for the observed vascular and organ changes. In conclusion our data suggests that the loss of akr7a3 in zebrafish impairs the detoxification of ACR which subsequently disrupts vascular integrity and normal kidney structure by promoting an inflammatory response. Overall design: akr7a3 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations transcriptome and metabolomics in Tgfli1:EGFP zebrafish.	pubmed:40258306	zf akr7a3 wt3	GSM8764262	source name:eye\|tissue:eye\|genotype:akr7a3+/+\|geo loc name:missing\|collection date:missing	zf akr7a3 wt3	Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.	eye	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	tissue:eye\|genotype:akr7a3+/+	GSM8764262	GSM8764262: zf akr7a3 wt3; Danio rerio; RNA Seq	GSM8764262 r1	GSM8764262	1	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP560539	wt3_1.fq.gz wt3_2.fq.gz	fastq fastq	4811145200.0	24055726.0	GSM8764262 r1	0:100 1:100	A:1281465119;C:1119986171;G:1134517584;T:1275176326;N:0	100	100	1281465119	1119986171	1134517584	1275176326	SRX27508411	SRS23927733	SRA2064109	Medical Faculty Mannheim	Medical Faculty Mannheim	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2025-01-29	Undetermined	Larval	Eye	Sensory System
34668	34668	SRR32162997	SRX27508410	SRS23927732	SRP560539	PRJNA1216901	Impaired detoxification of Acrolein interrupted ocular vascular integrity and kidney structure in akr7a3 / zebrafish via enhancing Arachidonic acid/leukotriene metabolism	GSE288313	Transcriptome Analysis	Acrolein ACR is an endogenous reactive unsaturated aldehyde that can be detoxified by the aldo keto reductase AKR enzyme system. The accumulation of ACR is associated with several health issues including inflammation oxidative stress and cardiovascular diseases. In this study an akr7a3 mutant zebrafish with the Tgfli1: EGFP signature was generated to investigate the effect of ACR on vascular integrity. Elevated ACR levels were observed in akr7a3 / zebrafish larvae and adults. Subsequent experiments demonstrated that increased ACR induced an enlargement of the hyaloid and retinal vasculature as well as alterations in the larvae pronephron and adult kidney. Transcriptome and metabolomics analyses followed by validation experiments revealed that the upregulation of arachidonic acid metabolism and leukotriene production are responsible for the observed vascular and organ changes. In conclusion our data suggests that the loss of akr7a3 in zebrafish impairs the detoxification of ACR which subsequently disrupts vascular integrity and normal kidney structure by promoting an inflammatory response. Overall design: akr7a3 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations transcriptome and metabolomics in Tgfli1:EGFP zebrafish.	pubmed:40258306	zf akr7a3 wt2	GSM8764261	source name:eye\|tissue:eye\|genotype:akr7a3+/+\|geo loc name:missing\|collection date:missing	zf akr7a3 wt2	Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.	eye	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	tissue:eye\|genotype:akr7a3+/+	GSM8764261	GSM8764261: zf akr7a3 wt2; Danio rerio; RNA Seq	GSM8764261 r1	GSM8764261	1	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP560539	wt2_1.fq.gz wt2_2.fq.gz	fastq fastq	4828531200.0	24142656.0	GSM8764261 r1	0:100 1:100	A:1298620554;C:1114914030;G:1129292015;T:1285704601;N:0	100	100	1298620554	1114914030	1129292015	1285704601	SRX27508410	SRS23927732	SRA2064109	Medical Faculty Mannheim	Medical Faculty Mannheim	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2025-01-29	Undetermined	Larval	Eye	Sensory System
34669	34669	SRR32162998	SRX27508409	SRS23927731	SRP560539	PRJNA1216901	Impaired detoxification of Acrolein interrupted ocular vascular integrity and kidney structure in akr7a3 / zebrafish via enhancing Arachidonic acid/leukotriene metabolism	GSE288313	Transcriptome Analysis	Acrolein ACR is an endogenous reactive unsaturated aldehyde that can be detoxified by the aldo keto reductase AKR enzyme system. The accumulation of ACR is associated with several health issues including inflammation oxidative stress and cardiovascular diseases. In this study an akr7a3 mutant zebrafish with the Tgfli1: EGFP signature was generated to investigate the effect of ACR on vascular integrity. Elevated ACR levels were observed in akr7a3 / zebrafish larvae and adults. Subsequent experiments demonstrated that increased ACR induced an enlargement of the hyaloid and retinal vasculature as well as alterations in the larvae pronephron and adult kidney. Transcriptome and metabolomics analyses followed by validation experiments revealed that the upregulation of arachidonic acid metabolism and leukotriene production are responsible for the observed vascular and organ changes. In conclusion our data suggests that the loss of akr7a3 in zebrafish impairs the detoxification of ACR which subsequently disrupts vascular integrity and normal kidney structure by promoting an inflammatory response. Overall design: akr7a3 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations transcriptome and metabolomics in Tgfli1:EGFP zebrafish.	pubmed:40258306	zf akr7a3 wt1	GSM8764260	source name:eye\|tissue:eye\|genotype:akr7a3+/+\|geo loc name:missing\|collection date:missing	zf akr7a3 wt1	Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.	eye	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	tissue:eye\|genotype:akr7a3+/+	GSM8764260	GSM8764260: zf akr7a3 wt1; Danio rerio; RNA Seq	GSM8764260 r1	GSM8764260	1	Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP560539	wt1_1.fq.gz wt1_2.fq.gz	fastq fastq	4825299200.0	24126496.0	GSM8764260 r1	0:100 1:100	A:1304417841;C:1107129239;G:1120658736;T:1293093384;N:0	100	100	1304417841	1107129239	1120658736	1293093384	SRX27508409	SRS23927731	SRA2064109	Medical Faculty Mannheim	Medical Faculty Mannheim	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2025-01-29	Undetermined	Larval	Eye	Sensory System

Advanced export

JSON shape: default, array, newline-delimited

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");;