metadata: run_metadata: 244 rows where devstage_curation_coarse = "Larval" and experiment.platform = "DNBSEQ"

244 rows where devstage_curation_coarse = "Larval" and experiment.platform = "DNBSEQ"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.growthprotocol	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.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
24854	24854	SRR25519420	SRX21249697	SRS18503946	SRP453374	PRJNA1002260	Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model	GSE240080	Transcriptome Analysis	We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.		pubmed:37728477	zebrafish AR42 TFA 4 3dpf	GSM7681266	source name:tail\|tissue:tail\|treatment:AR 42 treated larvae with TFA modeling\|geo loc name:missing\|collection date:missing	zebrafish AR42 TFA 4 3dpf	Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	tail	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:tail\|treatment:AR 42 treated larvae with TFA modeling	GSM7681266	GSM7681266: zebrafish AR42 TFA 4 3dpf; Danio rerio; RNA Seq	GSM7681266 r1	GSM7681266	1	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP453374		AR42_TFA_4.R1.fq.gz AR42_TFA_4.R2.fq.gz	fastq fastq	9896772900.0	32989243.0	GSM7681266 r1	0:150 1:150	A:2382403653;C:2457377213;G:2470646159;T:2586345875;N:0	150	150	2382403653	2457377213	2470646159	2586345875	0	SRX21249697	SRS18503946	SRA1687041	Chongqing medical university	Chongqing medical university	2	0.70537	0.88934	0.03159	0.04209	0.78013	0.75416	0.50713	0.45138	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-08-04	Larval	Larval	Tail	Multi-system
24855	24855	SRR25519421	SRX21249696	SRS18503945	SRP453374	PRJNA1002260	Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model	GSE240080	Transcriptome Analysis	We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.		pubmed:37728477	zebrafish AR42 TFA 3 3dpf	GSM7681265	source name:tail\|tissue:tail\|treatment:AR 42 treated larvae with TFA modeling\|geo loc name:missing\|collection date:missing	zebrafish AR42 TFA 3 3dpf	Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	tail	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:tail\|treatment:AR 42 treated larvae with TFA modeling	GSM7681265	GSM7681265: zebrafish AR42 TFA 3 3dpf; Danio rerio; RNA Seq	GSM7681265 r1	GSM7681265	1	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP453374		AR42_TFA_3.R1.fq.gz AR42_TFA_3.R2.fq.gz	fastq fastq	10265927100.0	34219757.0	GSM7681265 r1	0:150 1:150	A:2473552302;C:2548535087;G:2562873160;T:2680966551;N:0	150	150	2473552302	2548535087	2562873160	2680966551	0	SRX21249696	SRS18503945	SRA1687041	Chongqing medical university	Chongqing medical university	2	0.70516	0.88765	0.03163	0.04168	0.7782	0.75083	0.50851	0.45305	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-08-04	Larval	Larval	Tail	Multi-system
24856	24856	SRR25519422	SRX21249695	SRS18503944	SRP453374	PRJNA1002260	Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model	GSE240080	Transcriptome Analysis	We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.		pubmed:37728477	zebrafish AR42 TFA 2 3dpf	GSM7681264	source name:tail\|tissue:tail\|treatment:AR 42 treated larvae with TFA modeling\|geo loc name:missing\|collection date:missing	zebrafish AR42 TFA 2 3dpf	Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	tail	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:tail\|treatment:AR 42 treated larvae with TFA modeling	GSM7681264	GSM7681264: zebrafish AR42 TFA 2 3dpf; Danio rerio; RNA Seq	GSM7681264 r1	GSM7681264	1	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP453374		AR42_TFA_2.R2.fq.gz AR42_TFA_2.R1.fq.gz	fastq fastq	10003398900.0	33344663.0	GSM7681264 r1	0:150 1:150	A:2409580340;C:2483650756;G:2497057051;T:2613110753;N:0	150	150	2409580340	2483650756	2497057051	2613110753	0	SRX21249695	SRS18503944	SRA1687041	Chongqing medical university	Chongqing medical university	2	0.70787	0.89158	0.03203	0.04194	0.77851	0.75108	0.5072	0.45508	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-08-04	Larval	Larval	Tail	Multi-system
24857	24857	SRR25519423	SRX21249694	SRS18503943	SRP453374	PRJNA1002260	Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model	GSE240080	Transcriptome Analysis	We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.		pubmed:37728477	zebrafish AR42 TFA 1 3dpf	GSM7681263	source name:tail\|tissue:tail\|treatment:AR 42 treated larvae with TFA modeling\|geo loc name:missing\|collection date:missing	zebrafish AR42 TFA 1 3dpf	Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	tail	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:tail\|treatment:AR 42 treated larvae with TFA modeling	GSM7681263	GSM7681263: zebrafish AR42 TFA 1 3dpf; Danio rerio; RNA Seq	GSM7681263 r1	GSM7681263	1	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP453374		AR42_TFA_1.R1.fq.gz AR42_TFA_1.R2.fq.gz	fastq fastq	7420308900.0	24734363.0	GSM7681263 r1	0:150 1:150	A:1791092728;C:1841012408;G:1852583633;T:1935620131;N:0	150	150	1791092728	1841012408	1852583633	1935620131	0	SRX21249694	SRS18503943	SRA1687041	Chongqing medical university	Chongqing medical university	2	0.69668	0.87862	0.03153	0.04215	0.77463	0.74949	0.50657	0.45971	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-08-04	Larval	Larval	Tail	Multi-system
24858	24858	SRR25519424	SRX21249693	SRS18503942	SRP453374	PRJNA1002260	Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model	GSE240080	Transcriptome Analysis	We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.		pubmed:37728477	zebrafish DMSO TFA 4 3dpf	GSM7681262	source name:tail\|tissue:tail\|treatment:DMSO treated larvae with TFA modeling\|geo loc name:missing\|collection date:missing	zebrafish DMSO TFA 4 3dpf	Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	tail	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:tail\|treatment:DMSO treated larvae with TFA modeling	GSM7681262	GSM7681262: zebrafish DMSO TFA 4 3dpf; Danio rerio; RNA Seq	GSM7681262 r1	GSM7681262	1	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP453374		DMSO_TFA_4.R1.fq.gz DMSO_TFA_4.R2.fq.gz	fastq fastq	10178474100.0	33928247.0	GSM7681262 r1	0:150 1:150	A:2452172460;C:2526571372;G:2532799116;T:2666931152;N:0	150	150	2452172460	2526571372	2532799116	2666931152	0	SRX21249693	SRS18503942	SRA1687041	Chongqing medical university	Chongqing medical university	2	0.72132	0.91072	0.03161	0.04366	0.77709	0.75016	0.516	0.45312	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-08-04	Larval	Larval	Tail	Multi-system
24859	24859	SRR25519425	SRX21249692	SRS18503941	SRP453374	PRJNA1002260	Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model	GSE240080	Transcriptome Analysis	We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.		pubmed:37728477	zebrafish DMSO TFA 3 3dpf	GSM7681261	source name:tail\|tissue:tail\|treatment:DMSO treated larvae with TFA modeling\|geo loc name:missing\|collection date:missing	zebrafish DMSO TFA 3 3dpf	Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	tail	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:tail\|treatment:DMSO treated larvae with TFA modeling	GSM7681261	GSM7681261: zebrafish DMSO TFA 3 3dpf; Danio rerio; RNA Seq	GSM7681261 r1	GSM7681261	1	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP453374		DMSO_TFA_3.R1.fq.gz DMSO_TFA_3.R2.fq.gz	fastq fastq	9483201300.0	31610671.0	GSM7681261 r1	0:150 1:150	A:2282797855;C:2354211318;G:2361918927;T:2484273200;N:0	150	150	2282797855	2354211318	2361918927	2484273200	0	SRX21249692	SRS18503941	SRA1687041	Chongqing medical university	Chongqing medical university	2	0.71779	0.90757	0.03224	0.04329	0.77853	0.74862	0.51128	0.44891	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-08-04	Larval	Larval	Tail	Multi-system
24860	24860	SRR25519426	SRX21249691	SRS18503940	SRP453374	PRJNA1002260	Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model	GSE240080	Transcriptome Analysis	We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.		pubmed:37728477	zebrafish DMSO TFA 2 3dpf	GSM7681260	source name:tail\|tissue:tail\|treatment:DMSO treated larvae with TFA modeling\|geo loc name:missing\|collection date:missing	zebrafish DMSO TFA 2 3dpf	Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	tail	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:tail\|treatment:DMSO treated larvae with TFA modeling	GSM7681260	GSM7681260: zebrafish DMSO TFA 2 3dpf; Danio rerio; RNA Seq	GSM7681260 r1	GSM7681260	1	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP453374		DMSO_TFA_2.R1.fq.gz DMSO_TFA_2.R2.fq.gz	fastq fastq	9372641700.0	31242139.0	GSM7681260 r1	0:150 1:150	A:2255045813;C:2327185536;G:2333956274;T:2456454077;N:0	150	150	2255045813	2327185536	2333956274	2456454077	0	SRX21249691	SRS18503940	SRA1687041	Chongqing medical university	Chongqing medical university	2	0.71913	0.91061	0.0318	0.04251	0.7778	0.74907	0.51295	0.45006	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-08-04	Larval	Larval	Tail	Multi-system
24861	24861	SRR25519427	SRX21249690	SRS18503939	SRP453374	PRJNA1002260	Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model	GSE240080	Transcriptome Analysis	We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.		pubmed:37728477	zebrafish DMSO TFA 1 3dpf	GSM7681259	source name:tail\|tissue:tail\|treatment:DMSO treated larvae with TFA modeling\|geo loc name:missing\|collection date:missing	zebrafish DMSO TFA 1 3dpf	Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	tail	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:tail\|treatment:DMSO treated larvae with TFA modeling	GSM7681259	GSM7681259: zebrafish DMSO TFA 1 3dpf; Danio rerio; RNA Seq	GSM7681259 r1	GSM7681259	1	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP453374		DMSO_TFA_1.R1.fq.gz DMSO_TFA_1.R2.fq.gz	fastq fastq	8665981200.0	28886604.0	GSM7681259 r1	0:150 1:150	A:2086560929;C:2153111953;G:2157203992;T:2269104326;N:0	150	150	2086560929	2153111953	2157203992	2269104326	0	SRX21249690	SRS18503939	SRA1687041	Chongqing medical university	Chongqing medical university	2	0.71996	0.90816	0.03211	0.04297	0.77739	0.75097	0.5122	0.452	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-08-04	Larval	Larval	Tail	Multi-system
24862	24862	SRR25519428	SRX21249689	SRS18503938	SRP453374	PRJNA1002260	Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model	GSE240080	Transcriptome Analysis	We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.		pubmed:37728477	zebrafish AR42 4 3dpf	GSM7681258	source name:tail\|tissue:tail\|treatment:AR 42 treated larvae without xxx modeling\|geo loc name:missing\|collection date:missing	zebrafish AR42 4 3dpf	Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	tail	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:tail\|treatment:AR 42 treated larvae without xxx modeling	GSM7681258	GSM7681258: zebrafish AR42 4 3dpf; Danio rerio; RNA Seq	GSM7681258 r1	GSM7681258	1	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP453374		AR42_4.R1.fq.gz AR42_4.R2.fq.gz	fastq fastq	10199154900.0	33997183.0	GSM7681258 r1	0:150 1:150	A:2461755295;C:2524481077;G:2536143078;T:2676775450;N:0	150	150	2461755295	2524481077	2536143078	2676775450	0	SRX21249689	SRS18503938	SRA1687041	Chongqing medical university	Chongqing medical university	2	0.70676	0.89456	0.031	0.04108	0.77508	0.747	0.44642	0.47521	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-08-04	Larval	Larval	Tail	Multi-system
24863	24863	SRR25519429	SRX21249688	SRS18503937	SRP453374	PRJNA1002260	Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model	GSE240080	Transcriptome Analysis	We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.		pubmed:37728477	zebrafish AR42 3 3dpf	GSM7681257	source name:tail\|tissue:tail\|treatment:AR 42 treated larvae without xxx modeling\|geo loc name:missing\|collection date:missing	zebrafish AR42 3 3dpf	Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	tail	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:tail\|treatment:AR 42 treated larvae without xxx modeling	GSM7681257	GSM7681257: zebrafish AR42 3 3dpf; Danio rerio; RNA Seq	GSM7681257 r1	GSM7681257	1	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP453374		AR42_3.R1.fq.gz AR42_3.R2.fq.gz	fastq fastq	9953498100.0	33178327.0	GSM7681257 r1	0:150 1:150	A:2400858967;C:2463285586;G:2477369817;T:2611983730;N:0	150	150	2400858967	2463285586	2477369817	2611983730	0	SRX21249688	SRS18503937	SRA1687041	Chongqing medical university	Chongqing medical university	2	0.70865	0.89517	0.03101	0.04127	0.77325	0.74679	0.50253	0.50409	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-08-04	Larval	Larval	Tail	Multi-system
24864	24864	SRR25519430	SRX21249687	SRS18503936	SRP453374	PRJNA1002260	Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model	GSE240080	Transcriptome Analysis	We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.		pubmed:37728477	zebrafish AR42 2 3dpf	GSM7681256	source name:tail\|tissue:tail\|treatment:AR 42 treated larvae without xxx modeling\|geo loc name:missing\|collection date:missing	zebrafish AR42 2 3dpf	Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	tail	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:tail\|treatment:AR 42 treated larvae without xxx modeling	GSM7681256	GSM7681256: zebrafish AR42 2 3dpf; Danio rerio; RNA Seq	GSM7681256 r1	GSM7681256	1	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP453374		AR42_2.R1.fq.gz AR42_2.R2.fq.gz	fastq fastq	10005489000.0	33351630.0	GSM7681256 r1	0:150 1:150	A:2413672248;C:2477611702;G:2491304598;T:2622900452;N:0	150	150	2413672248	2477611702	2491304598	2622900452	0	SRX21249687	SRS18503936	SRA1687041	Chongqing medical university	Chongqing medical university	2	0.70639	0.89204	0.03035	0.04087	0.77502	0.74955	0.50558	0.50545	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-08-04	Larval	Larval	Tail	Multi-system
24865	24865	SRR25519431	SRX21249686	SRS18503935	SRP453374	PRJNA1002260	Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model	GSE240080	Transcriptome Analysis	We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.		pubmed:37728477	zebrafish AR42 1 3dpf	GSM7681255	source name:tail\|tissue:tail\|treatment:AR 42 treated larvae without xxx modeling\|geo loc name:missing\|collection date:missing	zebrafish AR42 1 3dpf	Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	tail	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:tail\|treatment:AR 42 treated larvae without xxx modeling	GSM7681255	GSM7681255: zebrafish AR42 1 3dpf; Danio rerio; RNA Seq	GSM7681255 r1	GSM7681255	1	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP453374		AR42_1.R1.fq.gz AR42_1.R2.fq.gz	fastq fastq	9698587800.0	32328626.0	GSM7681255 r1	0:150 1:150	A:2337968859;C:2400315331;G:2416067610;T:2544236000;N:0	150	150	2337968859	2400315331	2416067610	2544236000	0	SRX21249686	SRS18503935	SRA1687041	Chongqing medical university	Chongqing medical university	2	0.70903	0.89448	0.02976	0.04032	0.77583	0.74935	0.50747	0.5081	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-08-04	Larval	Larval	Tail	Multi-system
24866	24866	SRR25519432	SRX21249685	SRS18503934	SRP453374	PRJNA1002260	Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model	GSE240080	Transcriptome Analysis	We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.		pubmed:37728477	zebrafish DMSO 4 3dpf	GSM7681254	source name:tail\|tissue:tail\|treatment:DMSO treated larvae without xxx modeling\|geo loc name:missing\|collection date:missing	zebrafish DMSO 4 3dpf	Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	tail	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:tail\|treatment:DMSO treated larvae without xxx modeling	GSM7681254	GSM7681254: zebrafish DMSO 4 3dpf; Danio rerio; RNA Seq	GSM7681254 r1	GSM7681254	1	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP453374		DMSO_4.R1.fq.gz DMSO_4.R2.fq.gz	fastq fastq	9083670000.0	30278900.0	GSM7681254 r1	0:150 1:150	A:2191941100;C:2247936730;G:2258913579;T:2384878591;N:0	150	150	2191941100	2247936730	2258913579	2384878591	0	SRX21249685	SRS18503934	SRA1687041	Chongqing medical university	Chongqing medical university	2	0.71071	0.90457	0.03362	0.04688	0.77106	0.74357	0.50842	0.50975	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-08-04	Larval	Larval	Tail	Multi-system
24867	24867	SRR25519433	SRX21249684	SRS18503933	SRP453374	PRJNA1002260	Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model	GSE240080	Transcriptome Analysis	We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.		pubmed:37728477	zebrafish DMSO 3 3dpf	GSM7681253	source name:tail\|tissue:tail\|treatment:DMSO treated larvae without xxx modeling\|geo loc name:missing\|collection date:missing	zebrafish DMSO 3 3dpf	Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	tail	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:tail\|treatment:DMSO treated larvae without xxx modeling	GSM7681253	GSM7681253: zebrafish DMSO 3 3dpf; Danio rerio; RNA Seq	GSM7681253 r1	GSM7681253	1	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP453374		DMSO_3.R2.fq.gz DMSO_3.R1.fq.gz	fastq fastq	9394455000.0	31314850.0	GSM7681253 r1	0:150 1:150	A:2266296733;C:2324081714;G:2335347043;T:2468729510;N:0	150	150	2266296733	2324081714	2335347043	2468729510	0	SRX21249684	SRS18503933	SRA1687041	Chongqing medical university	Chongqing medical university	2	0.70975	0.90445	0.03329	0.04594	0.77005	0.7417	0.51188	0.5163	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-08-04	Larval	Larval	Tail	Multi-system
24868	24868	SRR25519434	SRX21249683	SRS18503932	SRP453374	PRJNA1002260	Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model	GSE240080	Transcriptome Analysis	We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.		pubmed:37728477	zebrafish DMSO 2 3dpf	GSM7681252	source name:tail\|tissue:tail\|treatment:DMSO treated larvae without xxx modeling\|geo loc name:missing\|collection date:missing	zebrafish DMSO 2 3dpf	Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	tail	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:tail\|treatment:DMSO treated larvae without xxx modeling	GSM7681252	GSM7681252: zebrafish DMSO 2 3dpf; Danio rerio; RNA Seq	GSM7681252 r1	GSM7681252	1	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP453374		DMSO_2.R1.fq.gz DMSO_2.R2.fq.gz	fastq fastq	9157453500.0	30524845.0	GSM7681252 r1	0:150 1:150	A:2209331568;C:2266614182;G:2273923578;T:2407584172;N:0	150	150	2209331568	2266614182	2273923578	2407584172	0	SRX21249683	SRS18503932	SRA1687041	Chongqing medical university	Chongqing medical university	2	0.70922	0.90538	0.03379	0.04616	0.7723	0.74213	0.50839	0.50803	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-08-04	Larval	Larval	Tail	Multi-system
24869	24869	SRR25519435	SRX21249682	SRS18503931	SRP453374	PRJNA1002260	Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model	GSE240080	Transcriptome Analysis	We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.		pubmed:37728477	zebrafish DMSO 1 3dpf	GSM7681251	source name:tail\|tissue:tail\|treatment:DMSO treated larvae without xxx modeling\|geo loc name:missing\|collection date:missing	zebrafish DMSO 1 3dpf	Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	tail	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:tail\|treatment:DMSO treated larvae without xxx modeling	GSM7681251	GSM7681251: zebrafish DMSO 1 3dpf; Danio rerio; RNA Seq	GSM7681251 r1	GSM7681251	1	RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP453374		DMSO_1.R2.fq.gz DMSO_1.R1.fq.gz	fastq fastq	8769040200.0	29230134.0	GSM7681251 r1	0:150 1:150	A:2114427483;C:2170929931;G:2179906163;T:2303776623;N:0	150	150	2114427483	2170929931	2179906163	2303776623	0	SRX21249682	SRS18503931	SRA1687041	Chongqing medical university	Chongqing medical university	2	0.71002	0.9037	0.0335	0.04604	0.77155	0.74308	0.51339	0.50801	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-08-04	Larval	Larval	Tail	Multi-system
30204	30204	SRR27715729	SRX23381950	SRS20243484	SRP485714	PRJNA1068542	The effects of HSP60 chaperone deficiency on zebrafish larvae	GSE254091	Transcriptome Analysis	To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed.		pubmed:39147275	Ko 3	GSM8033238	source name:embryo\|tissue:embryo\|cell line:5 dpf\|genotype:hspd1 / \|treatment:hspd1 knockout\|geo loc name:missing\|collection date:missing	Ko 3	Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample	embryo	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf.	tissue:embryo\|cell line:5 dpf\|genotype:hspd1 / \|treatment:hspd1 knockout	GSM8033238	GSM8033238: Ko 3; Danio rerio; RNA Seq	GSM8033238 r1	GSM8033238	1	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP485714		15_1.fq.gz 15_2.fq.gz	fastq fastq	5020450600.0	25102253.0	GSM8033238 r1	0:100 1:100	A:1371660785;C:1125396855;G:1130384333;T:1393008627;N:0	100	100	1371660785	1125396855	1130384333	1393008627	0	SRX23381950	SRS20243484	SRA1791378	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	2	0.9229	0.92453	0.12667	0.12674	0.65143	0.65232	0.48379	0.48431	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Denmark	2024-01-24	Larval	Larval	Embryo Imprecise	All anatomical structures
30205	30205	SRR27715730	SRX23381949	SRS20243483	SRP485714	PRJNA1068542	The effects of HSP60 chaperone deficiency on zebrafish larvae	GSE254091	Transcriptome Analysis	To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed.		pubmed:39147275	control 3	GSM8033237	source name:embryo\|tissue:embryo\|cell line:5 dpf\|genotype:hspd1+/+\|treatment:control\|geo loc name:missing\|collection date:missing	control 3	Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample	embryo	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf.	tissue:embryo\|cell line:5 dpf\|genotype:hspd1+/+\|treatment:control	GSM8033237	GSM8033237: control 3; Danio rerio; RNA Seq	GSM8033237 r1	GSM8033237	1	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP485714		14_1.fq.gz 14_2.fq.gz	fastq fastq	5020525200.0	25102626.0	GSM8033237 r1	0:100 1:100	A:1366975716;C:1129522599;G:1135845277;T:1388181608;N:0	100	100	1366975716	1129522599	1135845277	1388181608	0	SRX23381949	SRS20243483	SRA1791378	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	2	0.92923	0.93091	0.11899	0.11908	0.65117	0.651	0.48861	0.48085	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Denmark	2024-01-24	Larval	Larval	Embryo Imprecise	All anatomical structures
30206	30206	SRR27715731	SRX23381948	SRS20243485	SRP485714	PRJNA1068542	The effects of HSP60 chaperone deficiency on zebrafish larvae	GSE254091	Transcriptome Analysis	To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed.		pubmed:39147275	Ko 2	GSM8033236	source name:embryo\|tissue:embryo\|cell line:5 dpf\|genotype:hspd1 / \|treatment:hspd1 knockout\|geo loc name:missing\|collection date:missing	Ko 2	Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample	embryo	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf.	tissue:embryo\|cell line:5 dpf\|genotype:hspd1 / \|treatment:hspd1 knockout	GSM8033236	GSM8033236: Ko 2; Danio rerio; RNA Seq	GSM8033236 r1	GSM8033236	1	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP485714		13_1.fq.gz 13_2.fq.gz	fastq fastq	5016980000.0	25084900.0	GSM8033236 r1	0:100 1:100	A:1362095542;C:1131485761;G:1140659655;T:1382739042;N:0	100	100	1362095542	1131485761	1140659655	1382739042	0	SRX23381948	SRS20243485	SRA1791378	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	2	0.92867	0.92952	0.12009	0.11989	0.64989	0.65129	0.48735	0.48822	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Denmark	2024-01-24	Larval	Larval	Embryo Imprecise	All anatomical structures
30207	30207	SRR27715732	SRX23381947	SRS20243482	SRP485714	PRJNA1068542	The effects of HSP60 chaperone deficiency on zebrafish larvae	GSE254091	Transcriptome Analysis	To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed.		pubmed:39147275	control 2	GSM8033235	source name:embryo\|tissue:embryo\|cell line:5 dpf\|genotype:hspd1+/+\|treatment:control\|geo loc name:missing\|collection date:missing	control 2	Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample	embryo	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf.	tissue:embryo\|cell line:5 dpf\|genotype:hspd1+/+\|treatment:control	GSM8033235	GSM8033235: control 2; Danio rerio; RNA Seq	GSM8033235 r1	GSM8033235	1	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP485714		12_1.fq.gz 12_2.fq.gz	fastq fastq	5014043600.0	25070218.0	GSM8033235 r1	0:100 1:100	A:1365729811;C:1126481057;G:1137205154;T:1384627578;N:0	100	100	1365729811	1126481057	1137205154	1384627578	0	SRX23381947	SRS20243482	SRA1791378	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	2	0.92582	0.92658	0.11419	0.11406	0.65173	0.65257	0.48606	0.48533	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Denmark	2024-01-24	Larval	Larval	Embryo Imprecise	All anatomical structures
30208	30208	SRR27715733	SRX23381946	SRS20243480	SRP485714	PRJNA1068542	The effects of HSP60 chaperone deficiency on zebrafish larvae	GSE254091	Transcriptome Analysis	To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed.		pubmed:39147275	Ko 1	GSM8033234	source name:embryo\|tissue:embryo\|cell line:5 dpf\|genotype:hspd1 / \|treatment:hspd1 knockout\|geo loc name:missing\|collection date:missing	Ko 1	Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample	embryo	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf.	tissue:embryo\|cell line:5 dpf\|genotype:hspd1 / \|treatment:hspd1 knockout	GSM8033234	GSM8033234: Ko 1; Danio rerio; RNA Seq	GSM8033234 r1	GSM8033234	1	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP485714		11_1.fq.gz 11_2.fq.gz	fastq fastq	5245066800.0	26225334.0	GSM8033234 r1	0:100 1:100	A:1440549629;C:1168536590;G:1175698878;T:1460281703;N:0	100	100	1440549629	1168536590	1175698878	1460281703	0	SRX23381946	SRS20243480	SRA1791378	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	2	0.92279	0.92105	0.13454	0.13464	0.65238	0.65291	0.47828	0.48217	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Denmark	2024-01-24	Larval	Larval	Embryo Imprecise	All anatomical structures
30209	30209	SRR27715734	SRX23381945	SRS20243481	SRP485714	PRJNA1068542	The effects of HSP60 chaperone deficiency on zebrafish larvae	GSE254091	Transcriptome Analysis	To understand the effects of Hsp60 deficiency in developing vertebrates we generated CRISPR/Cas9 mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf . Overall design: Wildtype control and hspd1 / larvae at 5dpf were analyzed by RNASeq. For this purpose 3 biological replicates of groups of 5 genotyped larvae from each genotype were pooled and analyzed.		pubmed:39147275	control 1	GSM8033233	source name:embryo\|tissue:embryo\|cell line:5 dpf\|genotype:hspd1+/+\|treatment:control\|geo loc name:missing\|collection date:missing	control 1	Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC Babraham Bioinformatics. Adaptor removal and trimming of low quality ends were performed using Trim Galore with default settings Babraham Bioinformatics. Gene expression was quantified using Salmon against decoy aware reference transcriptomes Danio rerio GRCz11. Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 applying a false discovery rate FDR threshold of less than 0.05. Assembly: GRCz11 Supplementary files format and content: Comma delimited files contain raw data for each sample	embryo	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	Adult hspd1+/ zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/ knockout line was in crossed and obtained embryos were maintained at 28.5°C in E3 buffer 5 mm NaCl 0.17 mm KCl 0.33 mm CaCl2 0.33 mm MgSO4 10−5% methylene blue 2 mM HEPES pH 7.4 with daily replacements until 5 dpf.	tissue:embryo\|cell line:5 dpf\|genotype:hspd1+/+\|treatment:control	GSM8033233	GSM8033233: control 1; Danio rerio; RNA Seq	GSM8033233 r1	GSM8033233	1	The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96 well plate with 100% methanol filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol Invitrogen; #15596 018 and stored at 80°C until RNA extraction. According to the obtained genotyping results bodies of hspd1+/+ and hspd1 / larvae were pooled in groups of 5 larvae and this process was repeated for 3 mating sets resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle Kimble; #Z359971. RNA isolation was performed using TRIzol including DNase treatment with DNA free Kit Ambion AM1906 according to the manufacturer's instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate BioTek Agilent. Quality control analysis was performed with an automated 4200 TapeStation System Agilent G2991AA and RNA integrity number RIN values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer's instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap frozen in an empty 96 well plate Biorad; #12001925 on dry ice and stored at 80°C until sample preparation. Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non stranded and polyA selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP485714		10_1.fq.gz 10_2.fq.gz	fastq fastq	5460961000.0	27304805.0	GSM8033233 r1	0:100 1:100	A:1485370839;C:1228940953;G:1237868479;T:1508780729;N:0	100	100	1485370839	1228940953	1237868479	1508780729	0	SRX23381945	SRS20243481	SRA1791378	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	Research Unit for Molecular Medicine (MMF), Department of Clinical Medicine, Aarhus University and Aarhus University Hospital	2	0.92598	0.92555	0.12074	0.12035	0.65731	0.6577	0.46497	0.47306	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Denmark	2024-01-24	Larval	Larval	Embryo Imprecise	All anatomical structures
32865	32865	SRR29488925	SRX24999628	SRS21700588	SRP515253	PRJNA1126644	Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity	GSE270442	Transcriptome Analysis	Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.			DKO5	GSM8343040	source name:larvae\|tissue:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:DKO\|geo loc name:missing\|collection date:missing	DKO5	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.	larvae	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:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:DKO	GSM8343040	GSM8343040: DKO5; Danio rerio; RNA Seq	GSM8343040 r1	GSM8343040	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	SRP515253		DKO5_1.fq.gz DKO5_2.fq.gz	fastq fastq	4813408600.0	24067043.0	GSM8343040 r1	0:100 1:100	A:1302917202;C:1105312585;G:1123058369;T:1282120444;N:0	100	100	1302917202	1105312585	1123058369	1282120444	0	SRX24999628	SRS21700588	SRA1904686	ECAS	ECAS												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2024-06-21	Larval	Larval	Cell Line	Cell Line
32866	32866	SRR29488926	SRX24999627	SRS21700587	SRP515253	PRJNA1126644	Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity	GSE270442	Transcriptome Analysis	Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.			DKO4	GSM8343039	source name:larvae\|tissue:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:DKO\|geo loc name:missing\|collection date:missing	DKO4	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.	larvae	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:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:DKO	GSM8343039	GSM8343039: DKO4; Danio rerio; RNA Seq	GSM8343039 r1	GSM8343039	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	SRP515253		DKO4_1.fq.gz DKO4_2.fq.gz	fastq fastq	4825860200.0	24129301.0	GSM8343039 r1	0:100 1:100	A:1303584214;C:1108617528;G:1131675283;T:1281983175;N:0	100	100	1303584214	1108617528	1131675283	1281983175	0	SRX24999627	SRS21700587	SRA1904686	ECAS	ECAS												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2024-06-21	Larval	Larval	Cell Line	Cell Line
32867	32867	SRR29488927	SRX24999626	SRS21700586	SRP515253	PRJNA1126644	Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity	GSE270442	Transcriptome Analysis	Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.			DKO3	GSM8343038	source name:larvae\|tissue:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:DKO\|geo loc name:missing\|collection date:missing	DKO3	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.	larvae	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:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:DKO	GSM8343038	GSM8343038: DKO3; Danio rerio; RNA Seq	GSM8343038 r1	GSM8343038	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	SRP515253		DKO3_1.fq.gz DKO3_2.fq.gz	fastq fastq	4806754400.0	24033772.0	GSM8343038 r1	0:100 1:100	A:1289902978;C:1113397086;G:1131727783;T:1271726553;N:0	100	100	1289902978	1113397086	1131727783	1271726553	0	SRX24999626	SRS21700586	SRA1904686	ECAS	ECAS												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2024-06-21	Larval	Larval	Cell Line	Cell Line
32868	32868	SRR29488928	SRX24999625	SRS21700585	SRP515253	PRJNA1126644	Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity	GSE270442	Transcriptome Analysis	Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.			DKO2	GSM8343037	source name:larvae\|tissue:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:DKO\|geo loc name:missing\|collection date:missing	DKO2	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.	larvae	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:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:DKO	GSM8343037	GSM8343037: DKO2; Danio rerio; RNA Seq	GSM8343037 r1	GSM8343037	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	SRP515253		DKO2_1.fq.gz DKO2_2.fq.gz	fastq fastq	4805757800.0	24028789.0	GSM8343037 r1	0:100 1:100	A:1299804990;C:1103101159;G:1124220106;T:1278631545;N:0	100	100	1299804990	1103101159	1124220106	1278631545	0	SRX24999625	SRS21700585	SRA1904686	ECAS	ECAS												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2024-06-21	Larval	Larval	Cell Line	Cell Line
32869	32869	SRR29488929	SRX24999624	SRS21700584	SRP515253	PRJNA1126644	Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity	GSE270442	Transcriptome Analysis	Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.			DKO1	GSM8343036	source name:larvae\|tissue:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:DKO\|geo loc name:missing\|collection date:missing	DKO1	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.	larvae	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:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:DKO	GSM8343036	GSM8343036: DKO1; Danio rerio; RNA Seq	GSM8343036 r1	GSM8343036	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	SRP515253		DKO1_1.fq.gz DKO1_2.fq.gz	fastq fastq	4819172400.0	24095862.0	GSM8343036 r1	0:100 1:100	A:1296017748;C:1112321357;G:1133115185;T:1277718110;N:0	100	100	1296017748	1112321357	1133115185	1277718110	0	SRX24999624	SRS21700584	SRA1904686	ECAS	ECAS												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2024-06-21	Larval	Larval	Cell Line	Cell Line
32870	32870	SRR29488930	SRX24999623	SRS21700583	SRP515253	PRJNA1126644	Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity	GSE270442	Transcriptome Analysis	Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.			GLO1KO5	GSM8343035	source name:larvae\|tissue:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:GLO1KO\|geo loc name:missing\|collection date:missing	GLO1KO5	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.	larvae	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:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:GLO1KO	GSM8343035	GSM8343035: GLO1KO5; Danio rerio; RNA Seq	GSM8343035 r1	GSM8343035	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	SRP515253		GLO1KO5_1.fq.gz GLO1KO5_2.fq.gz	fastq fastq	4813614800.0	24068074.0	GSM8343035 r1	0:100 1:100	A:1289774342;C:1116099072;G:1136080400;T:1271660986;N:0	100	100	1289774342	1116099072	1136080400	1271660986	0	SRX24999623	SRS21700583	SRA1904686	ECAS	ECAS												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2024-06-21	Larval	Larval	Cell Line	Cell Line
32871	32871	SRR29488931	SRX24999622	SRS21700582	SRP515253	PRJNA1126644	Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity	GSE270442	Transcriptome Analysis	Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.			GLO1KO4	GSM8343034	source name:larvae\|tissue:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:GLO1KO\|geo loc name:missing\|collection date:missing	GLO1KO4	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.	larvae	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:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:GLO1KO	GSM8343034	GSM8343034: GLO1KO4; Danio rerio; RNA Seq	GSM8343034 r1	GSM8343034	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	SRP515253		GLO1KO4_1.fq.gz GLO1KO4_2.fq.gz	fastq fastq	4805954200.0	24029771.0	GSM8343034 r1	0:100 1:100	A:1288997011;C:1113616764;G:1132409574;T:1270930851;N:0	100	100	1288997011	1113616764	1132409574	1270930851	0	SRX24999622	SRS21700582	SRA1904686	ECAS	ECAS												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2024-06-21	Larval	Larval	Cell Line	Cell Line
32872	32872	SRR29488932	SRX24999621	SRS21700581	SRP515253	PRJNA1126644	Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity	GSE270442	Transcriptome Analysis	Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.			GLO1KO3	GSM8343033	source name:larvae\|tissue:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:GLO1KO\|geo loc name:missing\|collection date:missing	GLO1KO3	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.	larvae	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:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:GLO1KO	GSM8343033	GSM8343033: GLO1KO3; Danio rerio; RNA Seq	GSM8343033 r1	GSM8343033	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	SRP515253		GLO1KO3_1.fq.gz GLO1KO3_2.fq.gz	fastq fastq	4817965600.0	24089828.0	GSM8343033 r1	0:100 1:100	A:1290593290;C:1118086028;G:1134064137;T:1275222145;N:0	100	100	1290593290	1118086028	1134064137	1275222145	0	SRX24999621	SRS21700581	SRA1904686	ECAS	ECAS												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2024-06-21	Larval	Larval	Cell Line	Cell Line
32873	32873	SRR29488933	SRX24999620	SRS21700580	SRP515253	PRJNA1126644	Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity	GSE270442	Transcriptome Analysis	Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.			GLO1KO2	GSM8343032	source name:larvae\|tissue:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:GLO1KO\|geo loc name:missing\|collection date:missing	GLO1KO2	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.	larvae	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:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:GLO1KO	GSM8343032	GSM8343032: GLO1KO2; Danio rerio; RNA Seq	GSM8343032 r1	GSM8343032	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	SRP515253		GLO1KO2_1.fq.gz GLO1KO2_2.fq.gz	fastq fastq	4805999000.0	24029995.0	GSM8343032 r1	0:100 1:100	A:1293609489;C:1109265811;G:1128786421;T:1274337279;N:0	100	100	1293609489	1109265811	1128786421	1274337279	0	SRX24999620	SRS21700580	SRA1904686	ECAS	ECAS												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2024-06-21	Larval	Larval	Cell Line	Cell Line
32874	32874	SRR29488934	SRX24999619	SRS21700579	SRP515253	PRJNA1126644	Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity	GSE270442	Transcriptome Analysis	Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.			GLO1KO1	GSM8343031	source name:larvae\|tissue:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:GLO1KO\|geo loc name:missing\|collection date:missing	GLO1KO1	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.	larvae	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:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:GLO1KO	GSM8343031	GSM8343031: GLO1KO1; Danio rerio; RNA Seq	GSM8343031 r1	GSM8343031	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	SRP515253		GLO1KO1_1.fq.gz GLO1KO1_2.fq.gz	fastq fastq	4806768400.0	24033842.0	GSM8343031 r1	0:100 1:100	A:1286467027;C:1115478546;G:1135313631;T:1269509196;N:0	100	100	1286467027	1115478546	1135313631	1269509196	0	SRX24999619	SRS21700579	SRA1904686	ECAS	ECAS												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2024-06-21	Larval	Larval	Cell Line	Cell Line
32875	32875	SRR29488935	SRX24999618	SRS21700578	SRP515253	PRJNA1126644	Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity	GSE270442	Transcriptome Analysis	Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.			ALDH3A1KO5	GSM8343030	source name:larvae\|tissue:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:ALDH3A1KO\|geo loc name:missing\|collection date:missing	ALDH3A1KO5	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.	larvae	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:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:ALDH3A1KO	GSM8343030	GSM8343030: ALDH3A1KO5; Danio rerio; RNA Seq	GSM8343030 r1	GSM8343030	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	SRP515253		ALDH3A1KO5_1.fq.gz ALDH3A1KO5_2.fq.gz	fastq fastq	4811331000.0	24056655.0	GSM8343030 r1	0:100 1:100	A:1314568654;C:1091419677;G:1111494171;T:1293848498;N:0	100	100	1314568654	1091419677	1111494171	1293848498	0	SRX24999618	SRS21700578	SRA1904686	ECAS	ECAS												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2024-06-21	Larval	Larval	Cell Line	Cell Line
32876	32876	SRR29488936	SRX24999617	SRS21700577	SRP515253	PRJNA1126644	Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity	GSE270442	Transcriptome Analysis	Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.			ALDH3A1KO4	GSM8343029	source name:larvae\|tissue:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:ALDH3A1KO\|geo loc name:missing\|collection date:missing	ALDH3A1KO4	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.	larvae	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:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:ALDH3A1KO	GSM8343029	GSM8343029: ALDH3A1KO4; Danio rerio; RNA Seq	GSM8343029 r1	GSM8343029	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	SRP515253		ALDH3A1KO4_1.fq.gz ALDH3A1KO4_2.fq.gz	fastq fastq	4816993800.0	24084969.0	GSM8343029 r1	0:100 1:100	A:1320840277;C:1087361823;G:1108886472;T:1299905228;N:0	100	100	1320840277	1087361823	1108886472	1299905228	0	SRX24999617	SRS21700577	SRA1904686	ECAS	ECAS												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2024-06-21	Larval	Larval	Cell Line	Cell Line
32877	32877	SRR29488937	SRX24999616	SRS21700576	SRP515253	PRJNA1126644	Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity	GSE270442	Transcriptome Analysis	Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.			ALDH3A1KO3	GSM8343028	source name:larvae\|tissue:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:ALDH3A1KO\|geo loc name:missing\|collection date:missing	ALDH3A1KO3	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.	larvae	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:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:ALDH3A1KO	GSM8343028	GSM8343028: ALDH3A1KO3; Danio rerio; RNA Seq	GSM8343028 r1	GSM8343028	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	SRP515253		ALDH3A1KO3_1.fq.gz ALDH3A1KO3_2.fq.gz	fastq fastq	4828261200.0	24141306.0	GSM8343028 r1	0:100 1:100	A:1325980327;C:1088988247;G:1107987702;T:1305304924;N:0	100	100	1325980327	1088988247	1107987702	1305304924	0	SRX24999616	SRS21700576	SRA1904686	ECAS	ECAS												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2024-06-21	Larval	Larval	Cell Line	Cell Line
32878	32878	SRR29488938	SRX24999615	SRS21700575	SRP515253	PRJNA1126644	Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity	GSE270442	Transcriptome Analysis	Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.			ALDH3A1KO2	GSM8343027	source name:larvae\|tissue:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:ALDH3A1KO\|geo loc name:missing\|collection date:missing	ALDH3A1KO2	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.	larvae	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:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:ALDH3A1KO	GSM8343027	GSM8343027: ALDH3A1KO2; Danio rerio; RNA Seq	GSM8343027 r1	GSM8343027	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	SRP515253		ALDH3A1KO2_1.fq.gz ALDH3A1KO2_2.fq.gz	fastq fastq	4806790400.0	24033952.0	GSM8343027 r1	0:100 1:100	A:1296924744;C:1110667292;G:1117161162;T:1282037202;N:0	100	100	1296924744	1110667292	1117161162	1282037202	0	SRX24999615	SRS21700575	SRA1904686	ECAS	ECAS												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2024-06-21	Larval	Larval	Cell Line	Cell Line
32879	32879	SRR29488939	SRX24999614	SRS21700574	SRP515253	PRJNA1126644	Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity	GSE270442	Transcriptome Analysis	Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.			ALDH3A1KO1	GSM8343026	source name:larvae\|tissue:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:ALDH3A1KO\|geo loc name:missing\|collection date:missing	ALDH3A1KO1	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.	larvae	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:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:ALDH3A1KO	GSM8343026	GSM8343026: ALDH3A1KO1; Danio rerio; RNA Seq	GSM8343026 r1	GSM8343026	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	SRP515253		ALDH3A1KO1_1.fq.gz ALDH3A1KO1_2.fq.gz	fastq fastq	4801013600.0	24005068.0	GSM8343026 r1	0:100 1:100	A:1307355551;C:1094613295;G:1111765622;T:1287279132;N:0	100	100	1307355551	1094613295	1111765622	1287279132	0	SRX24999614	SRS21700574	SRA1904686	ECAS	ECAS												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2024-06-21	Larval	Larval	Cell Line	Cell Line
32880	32880	SRR29488940	SRX24999613	SRS21700573	SRP515253	PRJNA1126644	Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity	GSE270442	Transcriptome Analysis	Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.			WT5	GSM8343025	source name:larvae\|tissue:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:WT\|geo loc name:missing\|collection date:missing	WT5	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.	larvae	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:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:WT	GSM8343025	GSM8343025: WT5; Danio rerio; RNA Seq	GSM8343025 r1	GSM8343025	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	SRP515253		WT5_1.fq.gz WT5_2.fq.gz	fastq fastq	4820580400.0	24102902.0	GSM8343025 r1	0:100 1:100	A:1288306977;C:1120287477;G:1138943028;T:1273042918;N:0	100	100	1288306977	1120287477	1138943028	1273042918	0	SRX24999613	SRS21700573	SRA1904686	ECAS	ECAS												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2024-06-21	Larval	Larval	Cell Line	Cell Line
32881	32881	SRR29488941	SRX24999612	SRS21700572	SRP515253	PRJNA1126644	Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity	GSE270442	Transcriptome Analysis	Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.			WT4	GSM8343024	source name:larvae\|tissue:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:WT\|geo loc name:missing\|collection date:missing	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.	larvae	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:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:WT	GSM8343024	GSM8343024: WT4; Danio rerio; RNA Seq	GSM8343024 r1	GSM8343024	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	SRP515253		WT4_1.fq.gz WT4_2.fq.gz	fastq fastq	4821144600.0	24105723.0	GSM8343024 r1	0:100 1:100	A:1275218149;C:1133748961;G:1151831603;T:1260345887;N:0	100	100	1275218149	1133748961	1151831603	1260345887	0	SRX24999612	SRS21700572	SRA1904686	ECAS	ECAS												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2024-06-21	Larval	Larval	Cell Line	Cell Line
32882	32882	SRR29488942	SRX24999611	SRS21700571	SRP515253	PRJNA1126644	Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity	GSE270442	Transcriptome Analysis	Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.			WT3	GSM8343023	source name:larvae\|tissue:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:WT\|geo loc name:missing\|collection date:missing	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.	larvae	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:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:WT	GSM8343023	GSM8343023: WT3; Danio rerio; RNA Seq	GSM8343023 r1	GSM8343023	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	SRP515253		WT3_1.fq.gz WT3_2.fq.gz	fastq fastq	4826072600.0	24130363.0	GSM8343023 r1	0:100 1:100	A:1278424901;C:1132200743;G:1150406212;T:1265040744;N:0	100	100	1278424901	1132200743	1150406212	1265040744	0	SRX24999611	SRS21700571	SRA1904686	ECAS	ECAS												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2024-06-21	Larval	Larval	Cell Line	Cell Line
32883	32883	SRR29488943	SRX24999610	SRS21700570	SRP515253	PRJNA1126644	Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity	GSE270442	Transcriptome Analysis	Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.			WT2	GSM8343022	source name:larvae\|tissue:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:WT\|geo loc name:missing\|collection date:missing	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.	larvae	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:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:WT	GSM8343022	GSM8343022: WT2; Danio rerio; RNA Seq	GSM8343022 r1	GSM8343022	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	SRP515253		WT2_1.fq.gz WT2_2.fq.gz	fastq fastq	4801181000.0	24005905.0	GSM8343022 r1	0:100 1:100	A:1271169177;C:1127438892;G:1145437659;T:1257135272;N:0	100	100	1271169177	1127438892	1145437659	1257135272	0	SRX24999610	SRS21700570	SRA1904686	ECAS	ECAS												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2024-06-21	Larval	Larval	Cell Line	Cell Line
32884	32884	SRR29488944	SRX24999609	SRS21700569	SRP515253	PRJNA1126644	Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity	GSE270442	Transcriptome Analysis	Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.			WT1	GSM8343021	source name:larvae\|tissue:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:WT\|geo loc name:missing\|collection date:missing	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.	larvae	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:larvae\|cell line:Tgfli1:EGFP\|cell type:larvae\|genotype:WT	GSM8343021	GSM8343021: WT1; Danio rerio; RNA Seq	GSM8343021 r1	GSM8343021	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	SRP515253		WT1_1.fq.gz WT1_2.fq.gz	fastq fastq	4802502800.0	24012514.0	GSM8343021 r1	0:100 1:100	A:1263416018;C:1135581393;G:1152700487;T:1250804902;N:0	100	100	1263416018	1135581393	1152700487	1250804902	0	SRX24999609	SRS21700569	SRA1904686	ECAS	ECAS												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2024-06-21	Larval	Larval	Cell Line	Cell Line
33934	33934	SRR30947094	SRX26349630	SRS22874784	SRP537826	PRJNA1171482	TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development	GSE279246	Transcriptome Analysis	Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1…			whole heart tak1+/+ wild type replicate #3	GSM8565205	source name:Whole heart 3 dpf\|tissue:Whole heart 3 dpf\|genotype:tak1+/+\|geo loc name:missing\|collection date:missing	whole heart tak1+/+ wild type replicate #3	post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.	Whole heart 3 dpf	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.		tissue:Whole heart 3 dpf\|genotype:tak1+/+	GSM8565205	GSM8565205: whole heart tak1+/+ wild type replicate #3; Danio rerio; RNA Seq	GSM8565205 r1	GSM8565205	1	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP537826		WT_3_1.fq.gz WT_3_2.fq.gz	fastq fastq	4449566200.0	22247831.0	GSM8565205 r1	0:100 1:100	A:1179341017;C:1046638560;G:1046356098;T:1177230525;N:0	100	100	1179341017	1046638560	1046356098	1177230525	0	SRX26349630	SRS22874784	SRA1990217	Department of Cellular and Molecular Medicine, University of Copenhagen	Department of Cellular and Molecular Medicine, University of Copenhagen												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Denmark	2024-10-10	Larval	Larval	Heart	Cardiovascular System
33935	33935	SRR30947095	SRX26349629	SRS22874783	SRP537826	PRJNA1171482	TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development	GSE279246	Transcriptome Analysis	Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1…			whole heart tak1+/+ wild type replicate #2	GSM8565204	source name:Whole heart 3 dpf\|tissue:Whole heart 3 dpf\|genotype:tak1+/+\|geo loc name:missing\|collection date:missing	whole heart tak1+/+ wild type replicate #2	post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.	Whole heart 3 dpf	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.		tissue:Whole heart 3 dpf\|genotype:tak1+/+	GSM8565204	GSM8565204: whole heart tak1+/+ wild type replicate #2; Danio rerio; RNA Seq	GSM8565204 r1	GSM8565204	1	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP537826		WT_2_1.fq.gz WT_2_2.fq.gz	fastq fastq	4519627600.0	22598138.0	GSM8565204 r1	0:100 1:100	A:1207344552;C:1055139553;G:1056806709;T:1200336786;N:0	100	100	1207344552	1055139553	1056806709	1200336786	0	SRX26349629	SRS22874783	SRA1990217	Department of Cellular and Molecular Medicine, University of Copenhagen	Department of Cellular and Molecular Medicine, University of Copenhagen												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Denmark	2024-10-10	Larval	Larval	Heart	Cardiovascular System
33936	33936	SRR30947096	SRX26349628	SRS22874781	SRP537826	PRJNA1171482	TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development	GSE279246	Transcriptome Analysis	Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1…			whole heart tak1+/+ wild type replicate #1	GSM8565203	source name:Whole heart 3 dpf\|tissue:Whole heart 3 dpf\|genotype:tak1+/+\|geo loc name:missing\|collection date:missing	whole heart tak1+/+ wild type replicate #1	post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.	Whole heart 3 dpf	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.		tissue:Whole heart 3 dpf\|genotype:tak1+/+	GSM8565203	GSM8565203: whole heart tak1+/+ wild type replicate #1; Danio rerio; RNA Seq	GSM8565203 r1	GSM8565203	1	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP537826		WT_1_1.fq.gz WT_1_2.fq.gz	fastq fastq	4496601200.0	22483006.0	GSM8565203 r1	0:100 1:100	A:1201390946;C:1050348674;G:1051355386;T:1193506194;N:0	100	100	1201390946	1050348674	1051355386	1193506194	0	SRX26349628	SRS22874781	SRA1990217	Department of Cellular and Molecular Medicine, University of Copenhagen	Department of Cellular and Molecular Medicine, University of Copenhagen												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Denmark	2024-10-10	Larval	Larval	Heart	Cardiovascular System
33937	33937	SRR30947097	SRX26349627	SRS22874780	SRP537826	PRJNA1171482	TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development	GSE279246	Transcriptome Analysis	Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1…			whole heart tak1 / mutant replicate #3	GSM8565202	source name:Whole heart 3 dpf\|tissue:Whole heart 3 dpf\|genotype:tak1 / \|geo loc name:missing\|collection date:missing	whole heart tak1 / mutant replicate #3	post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.	Whole heart 3 dpf	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.		tissue:Whole heart 3 dpf\|genotype:tak1 /	GSM8565202	GSM8565202: whole heart tak1 / mutant replicate #3; Danio rerio; RNA Seq	GSM8565202 r1	GSM8565202	1	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP537826		mut_3_1.fq.gz mut_3_2.fq.gz	fastq fastq	4451759600.0	22258798.0	GSM8565202 r1	0:100 1:100	A:1167798041;C:1064608876;G:1066460994;T:1152891689;N:0	100	100	1167798041	1064608876	1066460994	1152891689	0	SRX26349627	SRS22874780	SRA1990217	Department of Cellular and Molecular Medicine, University of Copenhagen	Department of Cellular and Molecular Medicine, University of Copenhagen												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Denmark	2024-10-10	Larval	Larval	Heart	Cardiovascular System
33938	33938	SRR30947098	SRX26349626	SRS22874782	SRP537826	PRJNA1171482	TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development	GSE279246	Transcriptome Analysis	Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1…			whole heart tak1 / mutant replicate #2	GSM8565201	source name:Whole heart 3 dpf\|tissue:Whole heart 3 dpf\|genotype:tak1 / \|geo loc name:missing\|collection date:missing	whole heart tak1 / mutant replicate #2	post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.	Whole heart 3 dpf	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.		tissue:Whole heart 3 dpf\|genotype:tak1 /	GSM8565201	GSM8565201: whole heart tak1 / mutant replicate #2; Danio rerio; RNA Seq	GSM8565201 r1	GSM8565201	1	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP537826		mut_2_1.fq.gz mut_2_2.fq.gz	fastq fastq	4534495200.0	22672476.0	GSM8565201 r1										SRX26349626	SRS22874782	SRA1990217	Department of Cellular and Molecular Medicine, University of Copenhagen	Department of Cellular and Molecular Medicine, University of Copenhagen												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Denmark	2024-10-10	Larval	Larval	Heart	Cardiovascular System
33939	33939	SRR30947099	SRX26349625	SRS22874779	SRP537826	PRJNA1171482	TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development	GSE279246	Transcriptome Analysis	Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1…			whole heart tak1 / mutant replicate #1	GSM8565200	source name:Whole heart 3 dpf\|tissue:Whole heart 3 dpf\|genotype:tak1 / \|geo loc name:missing\|collection date:missing	whole heart tak1 / mutant replicate #1	post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.	Whole heart 3 dpf	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.		tissue:Whole heart 3 dpf\|genotype:tak1 /	GSM8565200	GSM8565200: whole heart tak1 / mutant replicate #1; Danio rerio; RNA Seq	GSM8565200 r1	GSM8565200	1	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP537826		mut_1_1.fq.gz mut_1_2.fq.gz	fastq fastq	4425052600.0	22125263.0	GSM8565200 r1	0:100 1:100	A:1161989932;C:1055452567;G:1055912540;T:1151697561;N:0	100	100	1161989932	1055452567	1055912540	1151697561	0	SRX26349625	SRS22874779	SRA1990217	Department of Cellular and Molecular Medicine, University of Copenhagen	Department of Cellular and Molecular Medicine, University of Copenhagen												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Denmark	2024-10-10	Larval	Larval	Heart	Cardiovascular System
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	0	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	0	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	0	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	0	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	0	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	0	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	0	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	0	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	0	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	0	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	0	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	0	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
35452	35452	SRR32815440	SRX28098911	SRS24455832	SRP572346	PRJNA1240620	The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes	PRJNA1240620	Other					T4Danio rerio	strain:T4\|age:96hpf\|collection date:2023 12 20\|geo loc name:China: Xiangyang\|sex:missing\|tissue:Tissue of juvenile fish\|replicate:T4\|BioSampleModel:Model organism or animal								T4	T4	T4	T4		RNA-Seq	METATRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP572346		T4_1.fq.gz T4_2.fq.gz	fastq fastq	6608651700.0	22028839.0	T4 1.fq.gz	0:150 1:150	A:1815401801;C:1489859310;G:1499379699;T:1804010890;N:0	150	150	1815401801	1489859310	1499379699	1804010890	0	SRX28098911	SRS24455832	SRA2098321	Wuhan University of Science and Technology\|School of Medicine	Wuhan University of Science and Technology												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2025-03-22	Larval	Larval	Undetermined	Undetermined
35453	35453	SRR32815441	SRX28098910	SRS24455831	SRP572346	PRJNA1240620	The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes	PRJNA1240620	Other					T3Danio rerio	strain:T3\|age:96hpf\|collection date:2023 12 20\|geo loc name:China: Xiangyang\|sex:missing\|tissue:Tissue of juvenile fish\|replicate:T3\|BioSampleModel:Model organism or animal								T3	T3	T3	T3		RNA-Seq	METATRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP572346		T3_1.fq.gz T3_2.fq.gz	fastq fastq	6656167200.0	22187224.0	T3 1.fq.gz	0:150 1:150	A:1840552276;C:1489247530;G:1499297584;T:1827069810;N:0	150	150	1840552276	1489247530	1499297584	1827069810	0	SRX28098910	SRS24455831	SRA2098321	Wuhan University of Science and Technology\|School of Medicine	Wuhan University of Science and Technology												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2025-03-22	Larval	Larval	Undetermined	Undetermined
35454	35454	SRR32815442	SRX28098909	SRS24455830	SRP572346	PRJNA1240620	The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes	PRJNA1240620	Other					T2Danio rerio	strain:T2\|age:96hpf\|collection date:2023 12 20\|geo loc name:China: Xiangyang\|sex:missing\|tissue:Tissue of juvenile fish\|replicate:T2\|BioSampleModel:Model organism or animal								T2	T2	T2	T2		RNA-Seq	METATRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP572346		T2_1.fq.gz T2_2.fq.gz	fastq fastq	6622204800.0	22074016.0	T2 1.fq.gz	0:150 1:150	A:1834396150;C:1480094606;G:1490046882;T:1817667162;N:0	150	150	1834396150	1480094606	1490046882	1817667162	0	SRX28098909	SRS24455830	SRA2098321	Wuhan University of Science and Technology\|School of Medicine	Wuhan University of Science and Technology												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2025-03-22	Larval	Larval	Undetermined	Undetermined
35455	35455	SRR32815443	SRX28098908	SRS24455829	SRP572346	PRJNA1240620	The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes	PRJNA1240620	Other					T1Danio rerio	strain:T1\|age:96hpf\|collection date:2023 12 20\|geo loc name:China: Xiangyang\|sex:missing\|tissue:Tissue of juvenile fish\|replicate:T1\|BioSampleModel:Model organism or animal								T1	T1	T1	T1		RNA-Seq	METATRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP572346		T1_1.fq.gz T1_2.fq.gz	fastq fastq	6626122500.0	22087075.0	T1 1.fq.gz	0:150 1:150	A:1833541012;C:1481665295;G:1491851279;T:1819064914;N:0	150	150	1833541012	1481665295	1491851279	1819064914	0	SRX28098908	SRS24455829	SRA2098321	Wuhan University of Science and Technology\|School of Medicine	Wuhan University of Science and Technology												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2025-03-22	Larval	Larval	Undetermined	Undetermined
35456	35456	SRR32815444	SRX28098907	SRS24455828	SRP572346	PRJNA1240620	The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes	PRJNA1240620	Other					Q4Danio rerio	strain:Q4\|age:96hpf\|collection date:2023 12 20\|geo loc name:China: Xiangyang\|sex:missing\|tissue:Tissue of juvenile fish\|replicate:Q4\|BioSampleModel:Model organism or animal								Q4	Q4	Q4	Q4		RNA-Seq	METATRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP572346		Q4_1.fq.gz Q4_2.fq.gz	fastq fastq	6646083600.0	22153612.0	Q4 1.fq.gz	0:150 1:150	A:1823086981;C:1499930776;G:1510718905;T:1812346938;N:0	150	150	1823086981	1499930776	1510718905	1812346938	0	SRX28098907	SRS24455828	SRA2098321	Wuhan University of Science and Technology\|School of Medicine	Wuhan University of Science and Technology												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2025-03-22	Larval	Larval	Undetermined	Undetermined
35457	35457	SRR32815445	SRX28098906	SRS24455827	SRP572346	PRJNA1240620	The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes	PRJNA1240620	Other					Q3Danio rerio	strain:Q3\|age:96hpf\|collection date:2023 12 20\|geo loc name:China: Xiangyang\|sex:missing\|tissue:Tissue of juvenile fish\|replicate:Q3\|BioSampleModel:Model organism or animal								Q3	Q3	Q3	Q3		RNA-Seq	METATRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP572346		Q3_1.fq.gz Q3_2.fq.gz	fastq fastq	6683275200.0	22277584.0	Q3 1.fq.gz	0:150 1:150	A:1838068171;C:1503920885;G:1514577234;T:1826708910;N:0	150	150	1838068171	1503920885	1514577234	1826708910	0	SRX28098906	SRS24455827	SRA2098321	Wuhan University of Science and Technology\|School of Medicine	Wuhan University of Science and Technology												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2025-03-22	Larval	Larval	Undetermined	Undetermined
35458	35458	SRR32815446	SRX28098905	SRS24455826	SRP572346	PRJNA1240620	The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes	PRJNA1240620	Other					Q2Danio rerio	strain:Q2\|age:96hpf\|collection date:2023 12 20\|geo loc name:China: Xiangyang\|sex:missing\|tissue:Tissue of juvenile fish\|replicate:Q2\|BioSampleModel:Model organism or animal								Q2	Q2	Q2	Q2		RNA-Seq	METATRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP572346		Q2_1.fq.gz Q2_2.fq.gz	fastq fastq	6612253800.0	22040846.0	Q2 1.fq.gz	0:150 1:150	A:1821750297;C:1484945478;G:1495582042;T:1809975983;N:0	150	150	1821750297	1484945478	1495582042	1809975983	0	SRX28098905	SRS24455826	SRA2098321	Wuhan University of Science and Technology\|School of Medicine	Wuhan University of Science and Technology												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2025-03-22	Larval	Larval	Undetermined	Undetermined
35459	35459	SRR32815447	SRX28098904	SRS24455825	SRP572346	PRJNA1240620	The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes	PRJNA1240620	Other					Q1Danio rerio	strain:Q1\|age:96hpf\|collection date:2023 12 20\|geo loc name:China: Xiangyang\|sex:missing\|tissue:Tissue of juvenile fish\|replicate:Q1\|BioSampleModel:Model organism or animal								Q1	Q1	Q1	Q1		RNA-Seq	METATRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP572346		Q1_1.fq.gz Q1_2.fq.gz	fastq fastq	6725919900.0	22419733.0	Q1 1.fq.gz	0:150 1:150	A:1845653740;C:1518697545;G:1530630124;T:1830938491;N:0	150	150	1845653740	1518697545	1530630124	1830938491	0	SRX28098904	SRS24455825	SRA2098321	Wuhan University of Science and Technology\|School of Medicine	Wuhan University of Science and Technology												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2025-03-22	Larval	Larval	Undetermined	Undetermined
36214	36214	SRR33581822	SRX28811683	SRS25048556	SRP585544	PRJNA1263423	Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis	PRJNA1263423	Other					Rg1 L3	strain:Not collected\|isolate:Rg1 L3\|cultivar:Not collected\|ecotype:Not collected\|age:8 dpf stage:Larvae\|collection date:2024 06 03\|geo loc name:Not collected\|sex:Not collected\|tissue:Larvae\|tmp:9\|BioSampleModel:Model organism or animal								RNA seq of Zebrafish: Treatment	Rg1 L3	Rg1 L3	Treatment		WGS	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP585544		D4_1.fq.gz D4_2.fq.gz	fastq fastq	6696495000.0	22321650.0	D4 1.fq.gz	0:150 1:150	A:1846856660;C:1513002602;G:1504866522;T:1831769216;N:0	150	150	1846856660	1513002602	1504866522	1831769216	0	SRX28811683	SRS25048556	SRA2130283	Hubei University of Medicine\|Graduate school	Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2025-05-15	Larval	Larval	Undetermined	Undetermined
36215	36215	SRR33581823	SRX28811682	SRS25048555	SRP585544	PRJNA1263423	Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis	PRJNA1263423	Other					Rg1 L7	strain:Not collected\|isolate:Rg1 L7\|cultivar:Not collected\|ecotype:Not collected\|age:8 dpf stage:Larvae\|collection date:2024 06 03\|geo loc name:Not collected\|sex:Not collected\|tissue:Larvae\|tmp:8\|BioSampleModel:Model organism or animal								RNA seq of Zebrafish: Treatment	Rg1 L7	Rg1 L7	Treatment		WGS	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP585544		D2_1.fq.gz D2_2.fq.gz	fastq fastq	6666041700.0	22220139.0	D2 1.fq.gz	0:150 1:150	A:1845276816;C:1500512488;G:1492917547;T:1827334849;N:0	150	150	1845276816	1500512488	1492917547	1827334849	0	SRX28811682	SRS25048555	SRA2130283	Hubei University of Medicine\|Graduate school	Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2025-05-15	Larval	Larval	Undetermined	Undetermined
36216	36216	SRR33581824	SRX28811681	SRS25048554	SRP585544	PRJNA1263423	Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis	PRJNA1263423	Other					Rg1 L5	strain:Not collected\|isolate:Rg1 L5\|cultivar:Not collected\|ecotype:Not collected\|age:8 dpf stage:Larvae\|collection date:2024 06 03\|geo loc name:Not collected\|sex:Not collected\|tissue:Larvae\|tmp:7\|BioSampleModel:Model organism or animal								RNA seq of Zebrafish: Treatment	Rg1 L5	Rg1 L5	Treatment		WGS	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP585544		D1_1.fq.gz D1_2.fq.gz	fastq fastq	6698296200.0	22327654.0	D1 1.fq.gz	0:150 1:150	A:1843962508;C:1518208646;G:1509450148;T:1826674898;N:0	150	150	1843962508	1518208646	1509450148	1826674898	0	SRX28811681	SRS25048554	SRA2130283	Hubei University of Medicine\|Graduate school	Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2025-05-15	Larval	Larval	Undetermined	Undetermined
36217	36217	SRR33581825	SRX28811680	SRS25048553	SRP585544	PRJNA1263423	Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis	PRJNA1263423	Other					PN L7	strain:Not collected\|isolate:PN L7\|cultivar:Not collected\|ecotype:Not collected\|age:8 dpf stage:Larvae\|collection date:2024 06 03\|geo loc name:Not collected\|sex:Not collected\|tissue:Larvae\|tmp:6\|BioSampleModel:Model organism or animal								RNA seq of Zebrafish: Model	PN L7	PN L7	Model		WGS	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP585544		B3_1.fq.gz B3_2.fq.gz	fastq fastq	6611023200.0	22036744.0	B3 1.fq.gz	0:150 1:150	A:1823488173;C:1492231000;G:1485521400;T:1809782627;N:0	150	150	1823488173	1492231000	1485521400	1809782627	0	SRX28811680	SRS25048553	SRA2130283	Hubei University of Medicine\|Graduate school	Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2025-05-15	Larval	Larval	Undetermined	Undetermined
36218	36218	SRR33581826	SRX28811679	SRS25048552	SRP585544	PRJNA1263423	Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis	PRJNA1263423	Other					PN L2	strain:Not collected\|isolate:PN L2\|cultivar:Not collected\|ecotype:Not collected\|age:8 dpf stage:Larvae\|collection date:2024 06 03\|geo loc name:Not collected\|sex:Not collected\|tissue:Larvae\|tmp:5\|BioSampleModel:Model organism or animal								RNA seq of Zebrafish: Model	PN L2	PN L2	Model		WGS	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP585544		B2_1.fq.gz B2_2.fq.gz	fastq fastq	6673419600.0	22244732.0	B2 1.fq.gz	0:150 1:150	A:1853555661;C:1496204062;G:1487686506;T:1835973371;N:0	150	150	1853555661	1496204062	1487686506	1835973371	0	SRX28811679	SRS25048552	SRA2130283	Hubei University of Medicine\|Graduate school	Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2025-05-15	Larval	Larval	Undetermined	Undetermined
36219	36219	SRR33581827	SRX28811678	SRS25048551	SRP585544	PRJNA1263423	Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis	PRJNA1263423	Other					PN L4	strain:Not collected\|isolate:PN L4\|cultivar:Not collected\|ecotype:Not collected\|age:8 dpf stage:Larvae\|collection date:2024 06 03\|geo loc name:Not collected\|sex:Not collected\|tissue:Larvae\|tmp:4\|BioSampleModel:Model organism or animal								RNA seq of Zebrafish: Model	PN L4	PN L4	Model		WGS	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP585544		B1_1.fq.gz B1_2.fq.gz	fastq fastq	6654915300.0	22183051.0	B1 1.fq.gz	0:150 1:150	A:1864666474;C:1477163584;G:1469026869;T:1844058373;N:0	150	150	1864666474	1477163584	1469026869	1844058373	0	SRX28811678	SRS25048551	SRA2130283	Hubei University of Medicine\|Graduate school	Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2025-05-15	Larval	Larval	Undetermined	Undetermined
36220	36220	SRR33581828	SRX28811677	SRS25048550	SRP585544	PRJNA1263423	Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis	PRJNA1263423	Other					Con L1	strain:Not collected\|isolate:Con L1\|cultivar:Not collected\|ecotype:Not collected\|age:8 dpf stage:Larvae\|collection date:2024 06 03\|geo loc name:Not collected\|sex:Not collected\|tissue:Larvae\|tmp:3\|BioSampleModel:Model organism or animal								RNA seq of Zebrafish: Control	Con L1	Con L1	Control		WGS	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP585544		A3_1.fq.gz A3_2.fq.gz	fastq fastq	6805948200.0	22686494.0	A3 1.fq.gz	0:150 1:150	A:1865806598;C:1548653255;G:1540767459;T:1850720888;N:0	150	150	1865806598	1548653255	1540767459	1850720888	0	SRX28811677	SRS25048550	SRA2130283	Hubei University of Medicine\|Graduate school	Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2025-05-15	Larval	Larval	Undetermined	Undetermined
36221	36221	SRR33581829	SRX28811676	SRS25048549	SRP585544	PRJNA1263423	Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis	PRJNA1263423	Other					Con Lb	strain:Not collected\|isolate:Con Lb\|cultivar:Not collected\|ecotype:Not collected\|age:8 dpf stage:Larvae\|collection date:2024 06 03\|geo loc name:Not collected\|sex:Not collected\|tissue:Larvae\|tmp:2\|BioSampleModel:Model organism or animal								RNA seq of Zebrafish: Control	Con Lb	Con Lb	Control		WGS	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP585544		A2_1.fq.gz A2_2.fq.gz	fastq fastq	6807123600.0	22690412.0	A2 1.fq.gz	0:150 1:150	A:1868554012;C:1546467202;G:1539322143;T:1852780243;N:0	150	150	1868554012	1546467202	1539322143	1852780243	0	SRX28811676	SRS25048549	SRA2130283	Hubei University of Medicine\|Graduate school	Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2025-05-15	Larval	Larval	Undetermined	Undetermined
36222	36222	SRR33581830	SRX28811675	SRS25048548	SRP585544	PRJNA1263423	Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis	PRJNA1263423	Other					Con La	strain:Not collected\|isolate:Con La\|cultivar:Not collected\|ecotype:Not collected\|age:8 dpf stage:Larvae\|collection date:2024 06 03\|geo loc name:Not collected\|sex:Not collected\|tissue:Larvae\|tmp:1\|BioSampleModel:Model organism or animal								RNA seq of Zebrafish: Control	Con La	Con La			WGS	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP585544		A1_1.fq.gz A1_2.fq.gz	fastq fastq	6782914200.0	22609714.0	A1 1.fq.gz	0:150 1:150	A:1857557307;C:1544915899;G:1537431564;T:1843009430;N:0	150	150	1857557307	1544915899	1537431564	1843009430	0	SRX28811675	SRS25048548	SRA2130283	Hubei University of Medicine\|Graduate school	Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2025-05-15	Larval	Larval	Undetermined	Undetermined
64514	64514	SRR17137062	SRX13321492	SRS11229253	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 72hpf COL104	GSM5718328	source name:Zebrafish 72hpf sample3\|strain:AB\|age:72 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 72hpf COL104	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5718328	GSM5718328: Microwell seq datasets of Zebrafish 72hpf COL104; Danio rerio; RNA Seq	GSM5718328		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL104.bam	10X Genomics bam file	90497447328.0	520100272.0	GSM5718328 r1	0:24 1:150	A:26568037621;C:19526761960;G:20762820842;T:23593883403;N:45943502	24	150	26568037621	19526761960	20762820842	23593883403	45943502	SRX13321492	SRS11229253	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00219	0.7651	0.00205	0.0914	0.99981	0.79953	0.5	0.51979	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2021-12-05	Larval	Larval	Whole Organism	All anatomical structures
64515	64515	SRR17137061	SRX13321491	SRS11229252	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 72hpf COL103	GSM5718327	source name:Zebrafish 72hpf sample3\|strain:AB\|age:72 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 72hpf COL103	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5718327	GSM5718327: Microwell seq datasets of Zebrafish 72hpf COL103; Danio rerio; RNA Seq	GSM5718327		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL103.bam	bam	97437769842.0	559987183.0	GSM5718327 r1	0:24 1:150	A:28425257606;C:21026057575;G:22210354179;T:25724166722;N:51933760	24	150	28425257606	21026057575	22210354179	25724166722	51933760	SRX13321491	SRS11229252	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00232	0.76296	0.00214	0.09247	0.99975	0.7963	0.58333	0.50975	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-05	Larval	Larval	Whole Organism	All anatomical structures
64516	64516	SRR17137060	SRX13321490	SRS11229251	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 72hpf COL102	GSM5718326	source name:Zebrafish 72hpf sample3\|strain:AB\|age:72 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 72hpf COL102	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5718326	GSM5718326: Microwell seq datasets of Zebrafish 72hpf COL102; Danio rerio; RNA Seq	GSM5718326		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL102.bam	bam	99647119878.0	572684597.0	GSM5718326 r1	0:24 1:150	A:29163675513;C:21410312143;G:22841561495;T:26179135838;N:52434889	24	150	29163675513	21410312143	22841561495	26179135838	52434889	SRX13321490	SRS11229251	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00211	0.75462	0.00197	0.08783	0.99979	0.79614	0.6	0.48777	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-05	Larval	Larval	Whole Organism	All anatomical structures
64517	64517	SRR17137059	SRX13321489	SRS11229250	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 72hpf COL101	GSM5718325	source name:Zebrafish 72hpf sample3\|strain:AB\|age:72 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 72hpf COL101	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5718325	GSM5718325: Microwell seq datasets of Zebrafish 72hpf COL101; Danio rerio; RNA Seq	GSM5718325		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL101.bam	bam	103850532360.0	596842140.0	GSM5718325 r1	0:24 1:150	A:30253504994;C:22208170461;G:23486370057;T:27846281411;N:56205437	24	150	30253504994	22208170461	23486370057	27846281411	56205437	SRX13321489	SRS11229250	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00248	0.76955	0.00238	0.09242	0.99985	0.78549	0.0	0.48332	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-05	Larval	Larval	Whole Organism	All anatomical structures
64518	64518	SRR17137058	SRX13321488	SRS11229249	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 72hpf COL100	GSM5718324	source name:Zebrafish 72hpf sample3\|strain:AB\|age:72 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 72hpf COL100	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5718324	GSM5718324: Microwell seq datasets of Zebrafish 72hpf COL100; Danio rerio; RNA Seq	GSM5718324		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL100.bam	bam	79732033224.0	458230076.0	GSM5718324 r1	0:24 1:150	A:23142121477;C:17273443279;G:18152994838;T:21124595570;N:38878060	24	150	23142121477	17273443279	18152994838	21124595570	38878060	SRX13321488	SRS11229249	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.0019	0.78954	0.00176	0.1	0.99977	0.79302	0.45454	0.53183	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-05	Larval	Larval	Whole Organism	All anatomical structures
64519	64519	SRR17137057	SRX13321487	SRS11229248	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 72hpf COL99	GSM5718323	source name:Zebrafish 72hpf sample3\|strain:AB\|age:72 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 72hpf COL99	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5718323	GSM5718323: Microwell seq datasets of Zebrafish 72hpf COL99; Danio rerio; RNA Seq	GSM5718323		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL99.bam	bam	57905355774.0	332789401.0	GSM5718323 r1	0:24 1:150	A:16732054497;C:12484254815;G:13099812159;T:15561038953;N:28195350	24	150	16732054497	12484254815	13099812159	15561038953	28195350	SRX13321487	SRS11229248	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.0023	0.79516	0.00213	0.10777	0.99977	0.79413	0.5	0.52425	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-05	Larval	Larval	Whole Organism	All anatomical structures
64520	64520	SRR17137056	SRX13321486	SRS11229247	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 72hpf COL98	GSM5718322	source name:Zebrafish 72hpf sample3\|strain:AB\|age:72 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 72hpf COL98	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5718322	GSM5718322: Microwell seq datasets of Zebrafish 72hpf COL98; Danio rerio; RNA Seq	GSM5718322		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL98.bam	bam	133922399388.0	769668962.0	GSM5718322 r1	0:24 1:150	A:39157671234;C:28685783001;G:30222645162;T:35787052837;N:69247154	24	150	39157671234	28685783001	30222645162	35787052837	69247154	SRX13321486	SRS11229247	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00205	0.77779	0.00189	0.10045	0.99977	0.7903	0.36363	0.52076	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-05	Larval	Larval	Whole Organism	All anatomical structures
64521	64521	SRR17137055	SRX13321485	SRS11229246	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 72hpf COL97	GSM5718321	source name:Zebrafish 72hpf sample3\|strain:AB\|age:72 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 72hpf COL97	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample3	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5718321	GSM5718321: Microwell seq datasets of Zebrafish 72hpf COL97; Danio rerio; RNA Seq	GSM5718321		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL97.bam	bam	102882979782.0	591281493.0	GSM5718321 r1	0:24 1:150	A:30066107926;C:21991309044;G:23041144876;T:27728508333;N:55909603	24	150	30066107926	21991309044	23041144876	27728508333	55909603	SRX13321485	SRS11229246	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00231	0.78387	0.00216	0.09479	0.99977	0.78638	0.63636	0.48401	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-05	Larval	Larval	Whole Organism	All anatomical structures
64522	64522	SRR17075126	SRX13263481	SRS11185248	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL92	GSM5709061	source name:Zebrafish 72hpf sample2\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL92	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample2	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5709061	GSM5709061: Micorwell seq datasets of Zebrafish 72hpf COL92; Danio rerio; RNA Seq	GSM5709061		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL92.bam	bam	93305697882.0	536239643.0	GSM5709061 r1	0:24 1:150	A:27107741517;C:19830183542;G:20994123402;T:25327971257;N:45678164	24	150	27107741517	19830183542	20994123402	25327971257	45678164	SRX13263481	SRS11185248	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00194	0.78236	0.00179	0.10164	0.99975	0.78618	0.75	0.48898	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-30	Larval	Larval	Whole Organism	All anatomical structures
64523	64523	SRR17075125	SRX13263480	SRS11185247	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL91	GSM5709060	source name:Zebrafish 72hpf sample2\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL91	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample2	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5709060	GSM5709060: Micorwell seq datasets of Zebrafish 72hpf COL91; Danio rerio; RNA Seq	GSM5709060		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL91.bam	bam	96227810904.0	553033396.0	GSM5709060 r1	0:24 1:150	A:27923073482;C:20564137902;G:21719882675;T:25970776374;N:49940471	24	150	27923073482	20564137902	21719882675	25970776374	49940471	SRX13263480	SRS11185247	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.0019	0.78115	0.00184	0.10758	0.99989	0.78725	0.4	0.49305	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-30	Larval	Larval	Whole Organism	All anatomical structures
64524	64524	SRR17075124	SRX13263479	SRS11185246	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL90	GSM5709059	source name:Zebrafish 72hpf sample2\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL90	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample2	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5709059	GSM5709059: Micorwell seq datasets of Zebrafish 72hpf COL90; Danio rerio; RNA Seq	GSM5709059		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL90.bam	bam	101004540858.0	580485867.0	GSM5709059 r1	0:24 1:150	A:29424345909;C:21610893920;G:22734702528;T:27180463498;N:54135003	24	150	29424345909	21610893920	22734702528	27180463498	54135003	SRX13263479	SRS11185246	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00188	0.78353	0.00176	0.10575	0.99981	0.78699	0.55555	0.50829	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-30	Larval	Larval	Whole Organism	All anatomical structures
64525	64525	SRR17075123	SRX13263478	SRS11185245	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL89	GSM5709058	source name:Zebrafish 72hpf sample2\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL89	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample2	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5709058	GSM5709058: Micorwell seq datasets of Zebrafish 72hpf COL89; Danio rerio; RNA Seq	GSM5709058		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL89.bam	bam	103228879080.0	593269420.0	GSM5709058 r1	0:24 1:150	A:30122538038;C:21933106979;G:23172314020;T:27949125385;N:51794658	24	150	30122538038	21933106979	23172314020	27949125385	51794658	SRX13263478	SRS11185245	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00229	0.78058	0.00208	0.11813	0.99967	0.78642	0.4375	0.51666	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-30	Larval	Larval	Whole Organism	All anatomical structures
64526	64526	SRR17075130	SRX13263477	SRS11185244	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL96	GSM5709065	source name:Zebrafish 72hpf sample2\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL96	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample2	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5709065	GSM5709065: Micorwell seq datasets of Zebrafish 72hpf COL96; Danio rerio; RNA Seq	GSM5709065		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL96.bam	bam	72161390838.0	414720637.0	GSM5709065 r1	0:24 1:150	A:20858972054;C:15631755598;G:16378791674;T:19256108785;N:35762727	24	150	20858972054	15631755598	16378791674	19256108785	35762727	SRX13263477	SRS11185244	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.0024	0.78585	0.00221	0.10389	0.99971	0.79099	0.64285	0.51929	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-30	Larval	Larval	Whole Organism	All anatomical structures
64527	64527	SRR17075129	SRX13263476	SRS11185243	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL95	GSM5709064	source name:Zebrafish 72hpf sample2\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL95	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample2	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5709064	GSM5709064: Micorwell seq datasets of Zebrafish 72hpf COL95; Danio rerio; RNA Seq	GSM5709064		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL95.bam	bam	116725350900.0	670835350.0	GSM5709064 r1	0:24 1:150	A:33766055210;C:25258192198;G:26422558801;T:31219012086;N:59532605	24	150	33766055210	25258192198	26422558801	31219012086	59532605	SRX13263476	SRS11185243	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00223	0.78242	0.00205	0.10222	0.99973	0.7948	0.76923	0.51107	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-30	Larval	Larval	Whole Organism	All anatomical structures
64528	64528	SRR17075128	SRX13263475	SRS11185241	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL94	GSM5709063	source name:Zebrafish 72hpf sample2\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL94	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample2	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5709063	GSM5709063: Micorwell seq datasets of Zebrafish 72hpf COL94; Danio rerio; RNA Seq	GSM5709063		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL94.bam	bam	115204393758.0	662094217.0	GSM5709063 r1	0:24 1:150	A:33385976074;C:24728619684;G:25999313932;T:31027995525;N:62488543	24	150	33385976074	24728619684	25999313932	31027995525	62488543	SRX13263475	SRS11185241	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00227	0.78471	0.00206	0.10458	0.99967	0.78591	0.4375	0.50275	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-30	Larval	Larval	Whole Organism	All anatomical structures
64529	64529	SRR17075127	SRX13263474	SRS11185242	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL93	GSM5709062	source name:Zebrafish 72hpf sample2\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL93	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample2	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5709062	GSM5709062: Micorwell seq datasets of Zebrafish 72hpf COL93; Danio rerio; RNA Seq	GSM5709062		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_72hpf_COL93.bam	bam	109890007632.0	631551768.0	GSM5709062 r1	0:24 1:150	A:31784495967;C:23590735781;G:24835459995;T:29625393694;N:53922195	24	150	31784495967	23590735781	24835459995	29625393694	53922195	SRX13263474	SRS11185242	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00221	0.77545	0.002	0.11238	0.99969	0.78879	0.4375	0.50979	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-30	Larval	Larval	Whole Organism	All anatomical structures
64530	64530	SRR17010806	SRX13200959	SRS11127611	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL88	GSM5699934	source name:Zebrafish 72hpf sample1\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL88	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5699934	GSM5699934: Micorwell seq datasets of Zebrafish 72hpf COL88; Danio rerio; RNA Seq	GSM5699934		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:Danio rerio reference genome GRCz11\|intentional duplicate	Zebrafish_72hpf_COL88.bam	bam	105325546890.0	605319235.0	GSM5699934 r1	0:24 1:150	A:30618141170;C:22639431941;G:23832910711;T:28175599693;N:59463375	24	150	30618141170	22639431941	23832910711	28175599693	59463375	SRX13200959	SRS11127611	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00204	0.77653	0.00184	0.1038	0.99969	0.78896	0.4	0.49664	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-22	Larval	Larval	Whole Organism	All anatomical structures
64531	64531	SRR17010805	SRX13200958	SRS11127610	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL87	GSM5699933	source name:Zebrafish 72hpf sample1\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL87	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5699933	GSM5699933: Micorwell seq datasets of Zebrafish 72hpf COL87; Danio rerio; RNA Seq	GSM5699933		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:Danio rerio reference genome GRCz11\|intentional duplicate	Zebrafish_72hpf_COL87.bam	bam	104410657848.0	600061252.0	GSM5699933 r1	0:24 1:150	A:30448105235;C:22372529466;G:23651054417;T:27884763811;N:54204919	24	150	30448105235	22372529466	23651054417	27884763811	54204919	SRX13200958	SRS11127610	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00239	0.76912	0.00221	0.11084	0.99971	0.78847	0.5	0.51741	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-22	Larval	Larval	Whole Organism	All anatomical structures
64532	64532	SRR17010804	SRX13200957	SRS11127609	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL86	GSM5699932	source name:Zebrafish 72hpf sample1\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL86	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5699932	GSM5699932: Micorwell seq datasets of Zebrafish 72hpf COL86; Danio rerio; RNA Seq	GSM5699932		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:Danio rerio reference genome GRCz11\|intentional duplicate	Zebrafish_72hpf_COL86.bam	bam	85539017526.0	491603549.0	GSM5699932 r1	0:24 1:150	A:24891444353;C:18382714837;G:19465935988;T:22755762595;N:43159753	24	150	24891444353	18382714837	19465935988	22755762595	43159753	SRX13200957	SRS11127609	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00186	0.7737	0.00168	0.10503	0.99973	0.78553	0.35714	0.52806	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-22	Larval	Larval	Whole Organism	All anatomical structures
64533	64533	SRR17010803	SRX13200956	SRS11127608	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL85	GSM5699931	source name:Zebrafish 72hpf sample1\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL85	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5699931	GSM5699931: Micorwell seq datasets of Zebrafish 72hpf COL85; Danio rerio; RNA Seq	GSM5699931		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:Danio rerio reference genome GRCz11\|intentional duplicate	Zebrafish_72hpf_COL85.bam	bam	96579499182.0	555054593.0	GSM5699931 r1	0:24 1:150	A:28258999810;C:20566647022;G:21776511096;T:25928948228;N:48393026	24	150	28258999810	20566647022	21776511096	25928948228	48393026	SRX13200956	SRS11127608	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00215	0.77075	0.00203	0.09684	0.99981	0.78348	0.44444	0.50291	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-22	Larval	Larval	Whole Organism	All anatomical structures
64534	64534	SRR17010802	SRX13200955	SRS11127607	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL84	GSM5699930	source name:Zebrafish 72hpf sample1\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL84	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5699930	GSM5699930: Micorwell seq datasets of Zebrafish 72hpf COL84; Danio rerio; RNA Seq	GSM5699930		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:Danio rerio reference genome GRCz11\|intentional duplicate	Zebrafish_72hpf_COL84.bam	bam	95402087292.0	548287858.0	GSM5699930 r1	0:24 1:150	A:27920812951;C:20371734068;G:21595614980;T:25463535654;N:50389639	24	150	27920812951	20371734068	21595614980	25463535654	50389639	SRX13200955	SRS11127607	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00199	0.76291	0.00186	0.09597	0.99981	0.79001	0.3	0.50069	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-22	Larval	Larval	Whole Organism	All anatomical structures
64535	64535	SRR17010801	SRX13200954	SRS11127606	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL83	GSM5699929	source name:Zebrafish 72hpf sample1\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL83	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5699929	GSM5699929: Micorwell seq datasets of Zebrafish 72hpf COL83; Danio rerio; RNA Seq	GSM5699929		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:Danio rerio reference genome GRCz11\|intentional duplicate	Zebrafish_72hpf_COL83.bam	bam	94589605254.0	543618421.0	GSM5699929 r1	0:24 1:150	A:27596905697;C:20243328527;G:21378738112;T:25321573995;N:49058923	24	150	27596905697	20243328527	21378738112	25321573995	49058923	SRX13200954	SRS11127606	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00216	0.77625	0.00202	0.09982	0.99979	0.78831	0.36363	0.51012	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-22	Larval	Larval	Whole Organism	All anatomical structures
64536	64536	SRR17010800	SRX13200953	SRS11127605	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Micorwell seq datasets of Zebrafish 72hpf COL82	GSM5699928	source name:Zebrafish 72hpf sample1\|strain:AB\|age:72 hours\|tissue:whole organism	Micorwell seq datasets of Zebrafish 72hpf COL82	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 72hpf sample1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:72 hours\|tissue:whole organism	GSM5699928	GSM5699928: Micorwell seq datasets of Zebrafish 72hpf COL82; Danio rerio; RNA Seq	GSM5699928		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:Danio rerio reference genome GRCz11\|intentional duplicate	Zebrafish_72hpf_COL82.bam	bam	89062661598.0	511854377.0	GSM5699928 r1	0:24 1:150	A:26102790989;C:19094974289;G:20282271482;T:23541508213;N:41116625	24	150	26102790989	19094974289	20282271482	23541508213	41116625	SRX13200953	SRS11127605	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00227	0.76728	0.00206	0.10248	0.99969	0.79196	0.29411	0.53203	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-11-22	Larval	Larval	Whole Organism	All anatomical structures

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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");;