metadata: run_metadata: 639 rows where experiment.library_layout = "PAIRED", experiment.library_strategy = "RNA-Seq" and experiment.platform = "BGISEQ"

639 rows where experiment.library_layout = "PAIRED", experiment.library_strategy = "RNA-Seq" and experiment.platform = "BGISEQ"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.description	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.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
28093	28093	SRR26196850	SRX21908248	SRS18993956	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.	pubmed:38868197		elipsa mutant clutch 4	GSM7808262	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa mutant clutch 4	Standard processing by BGI.p HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM7808262	GSM7808262: elipsa mutant clutch 4; Danio rerio; RNA Seq	GSM7808262 r1	GSM7808262	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504	ElipsaMUT4_1.fq.gz ElipsaMUT4_2.fq.gz	fastq fastq	4536153000.0	22680765.0	GSM7808262 r1	0:100 1:100	A:1194964224;C:1059904764;G:1074108947;T:1207175065;N:0	100	100	1194964224	1059904764	1074108947	1207175065	0	SRX21908248	SRS18993956	SRA1721841	NTNU	NTNU	2	0.93991	0.94735	0.10392	0.10318	0.66434	0.66344	0.48911	0.49311	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28094	28094	SRR26196851	SRX21908247	SRS18993955	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.	pubmed:38868197		elipsa mutant clutch 3	GSM7808261	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa mutant clutch 3	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM7808261	GSM7808261: elipsa mutant clutch 3; Danio rerio; RNA Seq	GSM7808261 r1	GSM7808261	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504	ElipsaMUT3_1.fq.gz ElipsaMUT3_2.fq.gz	fastq fastq	4547581600.0	22737908.0	GSM7808261 r1	0:100 1:100	A:1183476304;C:1077021222;G:1092963681;T:1194120393;N:0	100	100	1183476304	1077021222	1092963681	1194120393	0	SRX21908247	SRS18993955	SRA1721841	NTNU	NTNU	2	0.95029	0.95874	0.09085	0.09059	0.66856	0.66722	0.48534	0.48545	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28095	28095	SRR26196852	SRX21908246	SRS18993954	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.	pubmed:38868197		elipsa mutant clutch 2	GSM7808260	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa mutant clutch 2	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM7808260	GSM7808260: elipsa mutant clutch 2; Danio rerio; RNA Seq	GSM7808260 r1	GSM7808260	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504	ElipsaMUT2_1.fq.gz ElipsaMUT2_2.fq.gz	fastq fastq	4544444600.0	22722223.0	GSM7808260 r1	0:100 1:100	A:1186329827;C:1072965608;G:1087757513;T:1197391652;N:0	100	100	1186329827	1072965608	1087757513	1197391652	0	SRX21908246	SRS18993954	SRA1721841	NTNU	NTNU	2	0.94545	0.95403	0.09705	0.09653	0.66576	0.66466	0.47893	0.47882	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28096	28096	SRR26196853	SRX21908245	SRS18993953	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.	pubmed:38868197		elipsa mutant clutch 1	GSM7808259	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa mutant clutch 1	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM7808259	GSM7808259: elipsa mutant clutch 1; Danio rerio; RNA Seq	GSM7808259 r1	GSM7808259	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504	ElipsaMUT1_1.fq.gz ElipsaMUT1_2.fq.gz	fastq fastq	4561346400.0	22806732.0	GSM7808259 r1	0:100 1:100	A:1192227498;C:1073309826;G:1091718946;T:1204090130;N:0	100	100	1192227498	1073309826	1091718946	1204090130	0	SRX21908245	SRS18993953	SRA1721841	NTNU	NTNU	2	0.94079	0.94928	0.09838	0.09859	0.67093	0.66975	0.47837	0.4824	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28097	28097	SRR26196854	SRX21908244	SRS18993950	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.	pubmed:38868197		elipsa control clutch 4	GSM7808258	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa control clutch 4	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM7808258	GSM7808258: elipsa control clutch 4; Danio rerio; RNA Seq	GSM7808258 r1	GSM7808258	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504	ElipsaCTRL4_1.fq.gz ElipsaCTRL4_2.fq.gz	fastq fastq	4534543600.0	22672718.0	GSM7808258 r1	0:100 1:100	A:1195456125;C:1060510332;G:1073683545;T:1204893598;N:0	100	100	1195456125	1060510332	1073683545	1204893598	0	SRX21908244	SRS18993950	SRA1721841	NTNU	NTNU	2	0.94686	0.95523	0.0948	0.09459	0.66259	0.66093	0.49251	0.49154	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28098	28098	SRR26196855	SRX21908243	SRS18993952	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.	pubmed:38868197		elipsa control clutch 3	GSM7808257	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa control clutch 3	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM7808257	GSM7808257: elipsa control clutch 3; Danio rerio; RNA Seq	GSM7808257 r1	GSM7808257	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504	ElipsaCTRL3_1.fq.gz ElipsaCTRL3_2.fq.gz	fastq fastq	4546464800.0	22732324.0	GSM7808257 r1	0:100 1:100	A:1192169234;C:1070218166;G:1081895902;T:1202181498;N:0	100	100	1192169234	1070218166	1081895902	1202181498	0	SRX21908243	SRS18993952	SRA1721841	NTNU	NTNU	2	0.94937	0.95815	0.09867	0.09825	0.66574	0.66478	0.49056	0.48959	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28099	28099	SRR26196856	SRX21908242	SRS18993951	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.	pubmed:38868197		elipsa control clutch 2	GSM7808256	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa control clutch 2	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM7808256	GSM7808256: elipsa control clutch 2; Danio rerio; RNA Seq	GSM7808256 r1	GSM7808256	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504	ElipsaCTRL2_1.fq.gz ElipsaCTRL2_2.fq.gz	fastq fastq	4557679200.0	22788396.0	GSM7808256 r1	0:100 1:100	A:1184954651;C:1080955864;G:1098377272;T:1193391413;N:0	100	100	1184954651	1080955864	1098377272	1193391413	0	SRX21908242	SRS18993951	SRA1721841	NTNU	NTNU	2	0.94378	0.95076	0.0855	0.0847	0.66604	0.66342	0.48858	0.48404	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28100	28100	SRR26196857	SRX21908241	SRS18993949	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.	pubmed:38868197		elipsa control clutch 1	GSM7808255	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa control clutch 1	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM7808255	GSM7808255: elipsa control clutch 1; Danio rerio; RNA Seq	GSM7808255 r1	GSM7808255	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504	ElipsaCTRL1_1.fq.gz ElipsaCTRL1_2.fq.gz	fastq fastq	4566618600.0	22833093.0	GSM7808255 r1	0:100 1:100	A:1193092402;C:1076659586;G:1094193492;T:1202673120;N:0	100	100	1193092402	1076659586	1094193492	1202673120	0	SRX21908241	SRS18993949	SRA1721841	NTNU	NTNU	2	0.94269	0.94899	0.09816	0.09712	0.66991	0.66925	0.47671	0.46995	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28794	28794	SRR26685983	SRX22385777	SRS19431939	SRP470412	PRJNA1036238	RNAseq of Wild Type and pikfyve?8 zebrafish.	GSE247110	Transcriptome Analysis	Purpose: Phosphoinositide kinase FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish.			pikfyve3	GSM7883488	source name:genotype\|tissue:genotype\|genotype:pikfyve delta8\|geo loc name:missing\|collection date:missing	pikfyve3	Data filtering The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5% postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification Bowtie2[2] was applied to align the clean reads to the gene set in which known and novel coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample	genotype		The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing		tissue:genotype\|genotype:pikfyve delta8	GSM7883488	GSM7883488: pikfyve3; Danio rerio; RNA Seq	GSM7883488 r1	GSM7883488	1	The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP470412	pikfyve3_1.fq.gz pikfyve3_2.fq.gz	fastq fastq	6618846900.0	22062823.0	GSM7883488 r1	0:150 1:150	A:1763884594;C:1537497822;G:1533232898;T:1784136042;N:95544	150	150	1763884594	1537497822	1533232898	1784136042	95544	SRX22385777	SRS19431939	SRA1746433	The Second Clinical Medical College, Jinan University	The Second Clinical Medical College, Jinan University	2	0.93396	0.92718	0.09419	0.09305	0.66348	0.66496	0.48704	0.4839	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-11-06	Undetermined	Undetermined	Undetermined	Undetermined
28795	28795	SRR26685984	SRX22385776	SRS19431938	SRP470412	PRJNA1036238	RNAseq of Wild Type and pikfyve?8 zebrafish.	GSE247110	Transcriptome Analysis	Purpose: Phosphoinositide kinase FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish.			pikfyve2	GSM7883487	source name:genotype\|tissue:genotype\|genotype:pikfyve delta8\|geo loc name:missing\|collection date:missing	pikfyve2	Data filtering The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5% postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification Bowtie2[2] was applied to align the clean reads to the gene set in which known and novel coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample	genotype		The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing		tissue:genotype\|genotype:pikfyve delta8	GSM7883487	GSM7883487: pikfyve2; Danio rerio; RNA Seq	GSM7883487 r1	GSM7883487	1	The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP470412	pikfyve2_1.fq.gz pikfyve2_2.fq.gz	fastq fastq	6640406100.0	22134687.0	GSM7883487 r1	0:150 1:150	A:1765647548;C:1547424271;G:1541609810;T:1785639698;N:84773	150	150	1765647548	1547424271	1541609810	1785639698	84773	SRX22385776	SRS19431938	SRA1746433	The Second Clinical Medical College, Jinan University	The Second Clinical Medical College, Jinan University	2	0.93535	0.92946	0.08654	0.08582	0.67127	0.67298	0.48517	0.48183	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-11-06	Undetermined	Undetermined	Undetermined	Undetermined
28796	28796	SRR26685985	SRX22385775	SRS19431937	SRP470412	PRJNA1036238	RNAseq of Wild Type and pikfyve?8 zebrafish.	GSE247110	Transcriptome Analysis	Purpose: Phosphoinositide kinase FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish.			pikfyve1	GSM7883486	source name:genotype\|tissue:genotype\|genotype:pikfyve delta8\|geo loc name:missing\|collection date:missing	pikfyve1	Data filtering The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5% postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification Bowtie2[2] was applied to align the clean reads to the gene set in which known and novel coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample	genotype		The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing		tissue:genotype\|genotype:pikfyve delta8	GSM7883486	GSM7883486: pikfyve1; Danio rerio; RNA Seq	GSM7883486 r1	GSM7883486	1	The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP470412	pikfyve1_1.fq.gz pikfyve1_2.fq.gz	fastq fastq	6629613600.0	22098712.0	GSM7883486 r1	0:150 1:150	A:1765377736;C:1543131511;G:1535515864;T:1785505926;N:82563	150	150	1765377736	1543131511	1535515864	1785505926	82563	SRX22385775	SRS19431937	SRA1746433	The Second Clinical Medical College, Jinan University	The Second Clinical Medical College, Jinan University	2	0.93638	0.92994	0.08782	0.08654	0.67138	0.67119	0.47859	0.47753	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-11-06	Undetermined	Undetermined	Undetermined	Undetermined
28797	28797	SRR26685986	SRX22385774	SRS19431936	SRP470412	PRJNA1036238	RNAseq of Wild Type and pikfyve?8 zebrafish.	GSE247110	Transcriptome Analysis	Purpose: Phosphoinositide kinase FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish.			WT3	GSM7883485	source name:genotype\|tissue:genotype\|genotype:Wile Type\|geo loc name:missing\|collection date:missing	WT3	Data filtering The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5% postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification Bowtie2[2] was applied to align the clean reads to the gene set in which known and novel coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample	genotype		The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing		tissue:genotype\|genotype:Wile Type	GSM7883485	GSM7883485: WT3; Danio rerio; RNA Seq	GSM7883485 r1	GSM7883485	1	The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP470412	WT3_2.fq.gz WT3_1.fq.gz	fastq fastq	6654357000.0	22181190.0	GSM7883485 r1	0:150 1:150	A:1778694761;C:1540249434;G:1534346559;T:1801052542;N:13704	150	150	1778694761	1540249434	1534346559	1801052542	13704	SRX22385774	SRS19431936	SRA1746433	The Second Clinical Medical College, Jinan University	The Second Clinical Medical College, Jinan University	2	0.93688	0.92644	0.09182	0.09071	0.66229	0.66434	0.48313	0.48263	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-11-06	Undetermined	Undetermined	Undetermined	Undetermined
28798	28798	SRR26685987	SRX22385773	SRS19431935	SRP470412	PRJNA1036238	RNAseq of Wild Type and pikfyve?8 zebrafish.	GSE247110	Transcriptome Analysis	Purpose: Phosphoinositide kinase FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish.			WT2	GSM7883484	source name:genotype\|tissue:genotype\|genotype:Wile Type\|geo loc name:missing\|collection date:missing	WT2	Data filtering The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5% postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification Bowtie2[2] was applied to align the clean reads to the gene set in which known and novel coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample	genotype		The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing		tissue:genotype\|genotype:Wile Type	GSM7883484	GSM7883484: WT2; Danio rerio; RNA Seq	GSM7883484 r1	GSM7883484	1	The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP470412	WT2_1.fq.gz WT2_2.fq.gz	fastq fastq	6661129500.0	22203765.0	GSM7883484 r1	0:150 1:150	A:1774160269;C:1545605554;G:1545211257;T:1796139014;N:13406	150	150	1774160269	1545605554	1545211257	1796139014	13406	SRX22385773	SRS19431935	SRA1746433	The Second Clinical Medical College, Jinan University	The Second Clinical Medical College, Jinan University	2	0.93696	0.9278	0.08665	0.08477	0.66322	0.66498	0.48376	0.48557	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-11-06	Undetermined	Undetermined	Undetermined	Undetermined
28799	28799	SRR26685988	SRX22385772	SRS19431934	SRP470412	PRJNA1036238	RNAseq of Wild Type and pikfyve?8 zebrafish.	GSE247110	Transcriptome Analysis	Purpose: Phosphoinositide kinase FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish.			WT1	GSM7883483	source name:genotype\|tissue:genotype\|genotype:Wile Type\|geo loc name:missing\|collection date:missing	WT1	Data filtering The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5% postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification Bowtie2[2] was applied to align the clean reads to the gene set in which known and novel coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample	genotype		The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing		tissue:genotype\|genotype:Wile Type	GSM7883483	GSM7883483: WT1; Danio rerio; RNA Seq	GSM7883483 r1	GSM7883483	1	The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP470412	WT1_2.fq.gz WT1_1.fq.gz	fastq fastq	6648386700.0	22161289.0	GSM7883483 r1	0:150 1:150	A:1780975057;C:1536473791;G:1530388485;T:1800462718;N:86649	150	150	1780975057	1536473791	1530388485	1800462718	86649	SRX22385772	SRS19431934	SRA1746433	The Second Clinical Medical College, Jinan University	The Second Clinical Medical College, Jinan University	2	0.93595	0.92974	0.09487	0.09314	0.65969	0.66005	0.48731	0.4845	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-11-06	Undetermined	Undetermined	Undetermined	Undetermined
30075	30075	SRR27700027	SRX23366859	SRS20229171	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.	pubmed:39798091		Smh mutant clutch 4	GSM8031712	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh mutant clutch 4	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM8031712	GSM8031712: Smh mutant clutch 4; Danio rerio; RNA Seq	GSM8031712 r1	GSM8031712	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459	SmhMUT4_1.fq.gz SmhMUT4_2.fq.gz	fastq fastq	4550057400.0	22750287.0	GSM8031712 r1	0:100 1:100	A:1198976754;C:1064190197;G:1077491671;T:1209398778;N:0	100	100	1198976754	1064190197	1077491671	1209398778	0	SRX23366859	SRS20229171	SRA1790727	NTNU	NTNU	2	0.94285	0.95266	0.101	0.10096	0.66145	0.65989	0.48209	0.47768	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30076	30076	SRR27700028	SRX23366858	SRS20229175	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.	pubmed:39798091		Smh mutant clutch 3	GSM8031711	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh mutant clutch 3	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM8031711	GSM8031711: Smh mutant clutch 3; Danio rerio; RNA Seq	GSM8031711 r1	GSM8031711	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459	SmhMUT3_1.fq.gz SmhMUT3_2.fq.gz	fastq fastq	4545452600.0	22727263.0	GSM8031711 r1	0:100 1:100	A:1188958937;C:1071903723;G:1087032258;T:1197557682;N:0	100	100	1188958937	1071903723	1087032258	1197557682	0	SRX23366858	SRS20229175	SRA1790727	NTNU	NTNU	2	0.94501	0.95409	0.09005	0.08947	0.66149	0.66062	0.46824	0.48019	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30077	30077	SRR27700029	SRX23366857	SRS20229173	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.	pubmed:39798091		Smh mutant clutch 2	GSM8031710	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh mutant clutch 2	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM8031710	GSM8031710: Smh mutant clutch 2; Danio rerio; RNA Seq	GSM8031710 r1	GSM8031710	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459	SmhMUT2_1.fq.gz SmhMUT2_2.fq.gz	fastq fastq	4548042000.0	22740210.0	GSM8031710 r1	0:100 1:100	A:1184618587;C:1077947166;G:1089628929;T:1195847318;N:0	100	100	1184618587	1077947166	1089628929	1195847318	0	SRX23366857	SRS20229173	SRA1790727	NTNU	NTNU	2	0.94502	0.95416	0.09209	0.092	0.66407	0.66214	0.48538	0.48509	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30078	30078	SRR27700030	SRX23366856	SRS20229174	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.	pubmed:39798091		Smh mutant clutch 1	GSM8031709	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh mutant clutch 1	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM8031709	GSM8031709: Smh mutant clutch 1; Danio rerio; RNA Seq	GSM8031709 r1	GSM8031709	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459	SmhMUT1_1.fq.gz SmhMUT1_2.fq.gz	fastq fastq	4544759600.0	22723798.0	GSM8031709 r1	0:100 1:100	A:1194011331;C:1066502346;G:1077923006;T:1206322917;N:0	100	100	1194011331	1066502346	1077923006	1206322917	0	SRX23366856	SRS20229174	SRA1790727	NTNU	NTNU	2	0.945	0.95433	0.09733	0.09796	0.66034	0.65951	0.477	0.47705	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30079	30079	SRR27700031	SRX23366855	SRS20229172	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.	pubmed:39798091		Smh control clutch 4	GSM8031708	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh control clutch 4	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM8031708	GSM8031708: Smh control clutch 4; Danio rerio; RNA Seq	GSM8031708 r1	GSM8031708	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459	SmhCTRL4_1.fq.gz SmhCTRL4_2.fq.gz	fastq fastq	4536141000.0	22680705.0	GSM8031708 r1	0:100 1:100	A:1196842043;C:1059535727;G:1071488375;T:1208274855;N:0	100	100	1196842043	1059535727	1071488375	1208274855	0	SRX23366855	SRS20229172	SRA1790727	NTNU	NTNU	2	0.94102	0.95093	0.09453	0.09431	0.66403	0.6631	0.49804	0.49818	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30080	30080	SRR27700032	SRX23366854	SRS20229170	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.	pubmed:39798091		Smh control clutch 3	GSM8031707	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh control clutch 3	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM8031707	GSM8031707: Smh control clutch 3; Danio rerio; RNA Seq	GSM8031707 r1	GSM8031707	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459	SmhCTRL3_1.fq.gz SmhCTRL3_2.fq.gz	fastq fastq	4543416000.0	22717080.0	GSM8031707 r1	0:100 1:100	A:1189755812;C:1071666785;G:1082665579;T:1199327824;N:0	100	100	1189755812	1071666785	1082665579	1199327824	0	SRX23366854	SRS20229170	SRA1790727	NTNU	NTNU	2	0.94571	0.95506	0.08989	0.09005	0.6632	0.66107	0.49631	0.49649	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30081	30081	SRR27700033	SRX23366853	SRS20229169	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.	pubmed:39798091		Smh control clutch 2	GSM8031706	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh control clutch 2	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM8031706	GSM8031706: Smh control clutch 2; Danio rerio; RNA Seq	GSM8031706 r1	GSM8031706	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459	SmhCTRL2_2.fq.gz SmhCTRL2_1.fq.gz	fastq fastq	4536576000.0	22682880.0	GSM8031706 r1	0:100 1:100	A:1180961957;C:1074391564;G:1088552770;T:1192669709;N:0	100	100	1180961957	1074391564	1088552770	1192669709	0	SRX23366853	SRS20229169	SRA1790727	NTNU	NTNU	2	0.94324	0.95313	0.08618	0.08685	0.66399	0.66216	0.49362	0.49644	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30082	30082	SRR27700034	SRX23366852	SRS20229168	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.	pubmed:39798091		Smh control clutch 1	GSM8031705	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh control clutch 1	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM8031705	GSM8031705: Smh control clutch 1; Danio rerio; RNA Seq	GSM8031705 r1	GSM8031705	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459	SmhCTRL1_1.fq.gz SmhCTRL1_2.fq.gz	fastq fastq	4546026800.0	22730134.0	GSM8031705 r1	0:100 1:100	A:1201447089;C:1060722844;G:1073012718;T:1210844149;N:0	100	100	1201447089	1060722844	1073012718	1210844149	0	SRX23366852	SRS20229168	SRA1790727	NTNU	NTNU	2	0.94554	0.95419	0.09192	0.09168	0.66436	0.66222	0.4762	0.48114	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
31825	31825	SRR28700412	SRX24268115	SRS21034395	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				PN 2	isolate:PN2\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 2\|BioSampleModel:Model organism or animal									RNA Seq of zebrafish	PN 2	PN 2	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894	PN_2_1.fq.gz PN_2_2.fq.gz	fastq fastq	6385048200.0	21283494.0	PN 2 1.fq.gz	0:150 1:150	A:1722127999;C:1463645587;G:1483173818;T:1716100796;N:0	150	150	1722127999	1463645587	1483173818	1716100796	0	SRX24268115	SRS21034395			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31826	31826	SRR28700413	SRX24268114	SRS21034397	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				PN 1	isolate:PN1\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 1\|BioSampleModel:Model organism or animal									RNA Seq of zebrafish	PN 1	PN 1	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894	PN_1_1.fq.gz PN_1_2.fq.gz	fastq fastq	6692894100.0	22309647.0	PN 1 1.fq.gz	0:150 1:150	A:1827107021;C:1513034624;G:1533077624;T:1819674831;N:0	150	150	1827107021	1513034624	1533077624	1819674831	0	SRX24268114	SRS21034397			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31827	31827	SRR28700414	SRX24268113	SRS21034396	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				EC 4	isolate:EC4\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 4\|BioSampleModel:Model organism or animal									RNA Seq of zebrafish	EC 4	EC 4	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894	EC_4_1.fq.gz EC_4_2.fq.gz	fastq fastq	6688857000.0	22296190.0	EC 4 1.fq.gz	0:150 1:150	A:1820989545;C:1516814697;G:1537970654;T:1813082104;N:0	150	150	1820989545	1516814697	1537970654	1813082104	0	SRX24268113	SRS21034396			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31828	31828	SRR28700415	SRX24268112	SRS21034392	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				EC 3	isolate:EC3\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 3\|BioSampleModel:Model organism or animal									RNA Seq of zebrafish	EC 3	EC 3	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894	EC_3_1.fq.gz EC_3_2.fq.gz	fastq fastq	6696553800.0	22321846.0	EC 3 1.fq.gz	0:150 1:150	A:1821249100;C:1520587242;G:1541238550;T:1813478908;N:0	150	150	1821249100	1520587242	1541238550	1813478908	0	SRX24268112	SRS21034392			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31829	31829	SRR28700416	SRX24268111	SRS21034391	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				EC 2	isolate:EC2\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 2\|BioSampleModel:Model organism or animal									RNA Seq of zebrafish	EC 2	EC 2	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894	EC_2_1.fq.gz EC_2_2.fq.gz	fastq fastq	6702179400.0	22340598.0	EC 2 1.fq.gz	0:150 1:150	A:1816692261;C:1527379142;G:1547365810;T:1810742187;N:0	150	150	1816692261	1527379142	1547365810	1810742187	0	SRX24268111	SRS21034391			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31830	31830	SRR28700417	SRX24268110	SRS21034390	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				EC 1	isolate:EC1\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 1\|BioSampleModel:Model organism or animal									RNA Seq of zebrafish	EC 1	EC 1	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894	EC_1_1.fq.gz EC_1_2.fq.gz	fastq fastq	6686053500.0	22286845.0	EC 1 1.fq.gz	0:150 1:150	A:1812022780;C:1524359858;G:1544847441;T:1804823421;N:0	150	150	1812022780	1524359858	1544847441	1804823421	0	SRX24268110	SRS21034390			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31831	31831	SRR28700418	SRX24268109	SRS21034388	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				Control 4	isolate:con4\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 4\|BioSampleModel:Model organism or animal									RNA Seq of zebrafish	Control 4	Control 4	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894	Control_4_1.fq.gz Control_4_2.fq.gz	fastq fastq	6669700500.0	22232335.0	Control 4 1.fq.gz	0:150 1:150	A:1804178265;C:1523547469;G:1543839484;T:1798135282;N:0	150	150	1804178265	1523547469	1543839484	1798135282	0	SRX24268109	SRS21034388			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31832	31832	SRR28700419	SRX24268108	SRS21034387	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				Control 3	isolate:con3\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 3\|BioSampleModel:Model organism or animal									RNA Seq of zebrafish	Control 3	Control 3	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894	Control_3_1.fq.gz Control_3_2.fq.gz	fastq fastq	6683518800.0	22278396.0	Control 3 1.fq.gz	0:150 1:150	A:1808495506;C:1525725204;G:1545930043;T:1803368047;N:0	150	150	1808495506	1525725204	1545930043	1803368047	0	SRX24268108	SRS21034387			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31833	31833	SRR28700420	SRX24268107	SRS21034386	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				PN 4	isolate:PN4\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 4\|BioSampleModel:Model organism or animal									RNA Seq of zebrafish	PN 4	PN 4	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894	PN_4_1.fq.gz PN_4_2.fq.gz	fastq fastq	6649316100.0	22164387.0	PN 4 1.fq.gz	0:150 1:150	A:1809816121;C:1508072480;G:1528272654;T:1803154845;N:0	150	150	1809816121	1508072480	1528272654	1803154845	0	SRX24268107	SRS21034386			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31834	31834	SRR28700421	SRX24268106	SRS21034389	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				PN 3	isolate:PN3\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 3\|BioSampleModel:Model organism or animal									RNA Seq of zebrafish	PN 3	PN 3	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894	PN_3_1.fq.gz PN_3_2.fq.gz	fastq fastq	6616113900.0	22053713.0	PN 3 1.fq.gz	0:150 1:150	A:1802283686;C:1499008018;G:1519150002;T:1795672194;N:0	150	150	1802283686	1499008018	1519150002	1795672194	0	SRX24268106	SRS21034389			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31835	31835	SRR28700422	SRX24268105	SRS21034385	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				Control 2	isolate:con2\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 2\|BioSampleModel:Model organism or animal									RNA Seq of zebrafish	Control 2	Control 2	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894	Control_2_1.fq.gz Control_2_2.fq.gz	fastq fastq	6701719200.0	22339064.0	Control 2 1.fq.gz	0:150 1:150	A:1812352260;C:1531672703;G:1551377072;T:1806317165;N:0	150	150	1812352260	1531672703	1551377072	1806317165	0	SRX24268105	SRS21034385			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31836	31836	SRR28700423	SRX24268104	SRS21034384	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				Control 1	isolate:con1\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 1\|BioSampleModel:Model organism or animal									RNA Seq of zebrafish	Control 1	Control 1	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894	Control_1_1.fq.gz Control_1_2.fq.gz	fastq fastq	6720214500.0	22400715.0	Control 1 1.fq.gz	0:150 1:150	A:1814883015;C:1537948710;G:1559376116;T:1808006659;N:0	150	150	1814883015	1537948710	1559376116	1808006659	0	SRX24268104	SRS21034384			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
33164	33164	SRR29809736	SRX25309007	SRS21984115	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 20mM STS 5	GSM8393514	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:20\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 20mM STS 5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:20\|agent:STS	GSM8393514	GSM8393514: pdx1 morpholino + 20mM STS 5; Danio rerio; RNA Seq	GSM8393514 r1	GSM8393514	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	6_2.fq.gz 6_1.fq.gz	fastq fastq	4827420200.0	24137101.0	GSM8393514 r1	0:100 1:100	A:1278807278;C:1130198430;G:1150325506;T:1268088986;N:0	100	100	1278807278	1130198430	1150325506	1268088986	0	SRX25309007	SRS21984115	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.9409	0.94542	0.08059	0.07981	0.69021	0.68887	0.47275	0.47095	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33165	33165	SRR29809737	SRX25309006	SRS21984114	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 20mM STS 4	GSM8393513	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:20\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 20mM STS 4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:20\|agent:STS	GSM8393513	GSM8393513: pdx1 morpholino + 20mM STS 4; Danio rerio; RNA Seq	GSM8393513 r1	GSM8393513	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	30_2.fq.gz 30_1.fq.gz	fastq fastq	4240862400.0	21204312.0	GSM8393513 r1	0:100 1:100	A:1146088921;C:972830110;G:990127288;T:1131816081;N:0	100	100	1146088921	972830110	990127288	1131816081	0	SRX25309006	SRS21984114	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.93888	0.9444	0.08826	0.08671	0.70431	0.70212	0.48083	0.48199	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33166	33166	SRR29809738	SRX25309005	SRS21984113	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 20mM STS 3	GSM8393512	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:20\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 20mM STS 3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:20\|agent:STS	GSM8393512	GSM8393512: pdx1 morpholino + 20mM STS 3; Danio rerio; RNA Seq	GSM8393512 r1	GSM8393512	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	24_2.fq.gz 24_1.fq.gz	fastq fastq	4822516400.0	24112582.0	GSM8393512 r1	0:100 1:100	A:1276866727;C:1130641795;G:1148897951;T:1266109927;N:0	100	100	1276866727	1130641795	1148897951	1266109927	0	SRX25309005	SRS21984113	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94126	0.94446	0.07837	0.07762	0.6911	0.69037	0.46251	0.4642	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33167	33167	SRR29809739	SRX25309004	SRS21984112	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 20mM STS 2	GSM8393511	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:20\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 20mM STS 2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:20\|agent:STS	GSM8393511	GSM8393511: pdx1 morpholino + 20mM STS 2; Danio rerio; RNA Seq	GSM8393511 r1	GSM8393511	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	18_2.fq.gz 18_1.fq.gz	fastq fastq	4820332000.0	24101660.0	GSM8393511 r1	0:100 1:100	A:1306037553;C:1103383630;G:1122255994;T:1288654823;N:0	100	100	1306037553	1103383630	1122255994	1288654823	0	SRX25309004	SRS21984112	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94035	0.9445	0.08468	0.08417	0.71106	0.70897	0.47897	0.47969	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33168	33168	SRR29809740	SRX25309003	SRS21984111	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 20mM STS 1	GSM8393510	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:20\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 20mM STS 1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:20\|agent:STS	GSM8393510	GSM8393510: pdx1 morpholino + 20mM STS 1; Danio rerio; RNA Seq	GSM8393510 r1	GSM8393510	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	12_1.fq.gz 12_2.fq.gz	fastq fastq	4825742600.0	24128713.0	GSM8393510 r1	0:100 1:100	A:1264457552;C:1145133600;G:1160084092;T:1256067356;N:0	100	100	1264457552	1145133600	1160084092	1256067356	0	SRX25309003	SRS21984111	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94613	0.9501	0.06915	0.06812	0.68941	0.68852	0.45659	0.45507	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33169	33169	SRR29809741	SRX25309002	SRS21984110	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 15mM STS 5	GSM8393509	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:15\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 15mM STS 5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:15\|agent:STS	GSM8393509	GSM8393509: pdx1 morpholino + 15mM STS 5; Danio rerio; RNA Seq	GSM8393509 r1	GSM8393509	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	5_2.fq.gz 5_1.fq.gz	fastq fastq	4816068800.0	24080344.0	GSM8393509 r1	0:100 1:100	A:1278638535;C:1126555210;G:1141985166;T:1268889889;N:0	100	100	1278638535	1126555210	1141985166	1268889889	0	SRX25309002	SRS21984110	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.9414	0.94516	0.08012	0.07915	0.69284	0.69185	0.46526	0.46882	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33170	33170	SRR29809742	SRX25309001	SRS21984109	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 15mM STS 4	GSM8393508	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:15\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 15mM STS 4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:15\|agent:STS	GSM8393508	GSM8393508: pdx1 morpholino + 15mM STS 4; Danio rerio; RNA Seq	GSM8393508 r1	GSM8393508	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	29_2.fq.gz 29_1.fq.gz	fastq fastq	4386218400.0	21931092.0	GSM8393508 r1	0:100 1:100	A:1181773341;C:1011246416;G:1025789654;T:1167408989;N:0	100	100	1181773341	1011246416	1025789654	1167408989	0	SRX25309001	SRS21984109	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94168	0.94587	0.08215	0.08003	0.69682	0.69544	0.47251	0.47607	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33171	33171	SRR29809743	SRX25309000	SRS21984108	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 15mM STS 3	GSM8393507	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:15\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 15mM STS 3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:15\|agent:STS	GSM8393507	GSM8393507: pdx1 morpholino + 15mM STS 3; Danio rerio; RNA Seq	GSM8393507 r1	GSM8393507	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	23_2.fq.gz 23_1.fq.gz	fastq fastq	4808808800.0	24044044.0	GSM8393507 r1	0:100 1:100	A:1269564907;C:1132101674;G:1149286214;T:1257856005;N:0	100	100	1269564907	1132101674	1149286214	1257856005	0	SRX25309000	SRS21984108	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.9434	0.94774	0.07109	0.0703	0.69264	0.69183	0.45908	0.46455	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33172	33172	SRR29809744	SRX25308999	SRS21984107	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 15mM STS 2	GSM8393506	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:15\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 15mM STS 2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:15\|agent:STS	GSM8393506	GSM8393506: pdx1 morpholino + 15mM STS 2; Danio rerio; RNA Seq	GSM8393506 r1	GSM8393506	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	17_1.fq.gz 17_2.fq.gz	fastq fastq	4805883400.0	24029417.0	GSM8393506 r1	0:100 1:100	A:1299291748;C:1102517917;G:1122450422;T:1281623313;N:0	100	100	1299291748	1102517917	1122450422	1281623313	0	SRX25308999	SRS21984107	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94253	0.9461	0.08371	0.08155	0.70589	0.70423	0.4853	0.47925	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33173	33173	SRR29809745	SRX25308998	SRS21984106	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 15mM STS 1	GSM8393505	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:15\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 15mM STS 1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:15\|agent:STS	GSM8393505	GSM8393505: pdx1 morpholino + 15mM STS 1; Danio rerio; RNA Seq	GSM8393505 r1	GSM8393505	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	11_1.fq.gz 11_2.fq.gz	fastq fastq	4812111600.0	24060558.0	GSM8393505 r1	0:100 1:100	A:1269803704;C:1133657948;G:1150461915;T:1258188033;N:0	100	100	1269803704	1133657948	1150461915	1258188033	0	SRX25308998	SRS21984106	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94311	0.94708	0.07444	0.07235	0.69266	0.69158	0.46689	0.46584	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33174	33174	SRR29809746	SRX25308997	SRS21984105	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 0mM STS 5	GSM8393504	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:0\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 0mM STS 5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:0\|agent:STS	GSM8393504	GSM8393504: pdx1 morpholino + 0mM STS 5; Danio rerio; RNA Seq	GSM8393504 r1	GSM8393504	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	4_2.fq.gz 4_1.fq.gz	fastq fastq	4804978800.0	24024894.0	GSM8393504 r1	0:100 1:100	A:1266882676;C:1131396187;G:1149418875;T:1257281062;N:0	100	100	1266882676	1131396187	1149418875	1257281062	0	SRX25308997	SRS21984105	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94345	0.94707	0.07428	0.0741	0.6898	0.68856	0.4653	0.46918	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33175	33175	SRR29809747	SRX25308996	SRS21984104	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 0mM STS 4	GSM8393503	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:0\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 0mM STS 4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:0\|agent:STS	GSM8393503	GSM8393503: pdx1 morpholino + 0mM STS 4; Danio rerio; RNA Seq	GSM8393503 r1	GSM8393503	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	28_1.fq.gz 28_2.fq.gz	fastq fastq	4464066400.0	22320332.0	GSM8393503 r1	0:100 1:100	A:1209155509;C:1023407835;G:1040239673;T:1191263383;N:0	100	100	1209155509	1023407835	1040239673	1191263383	0	SRX25308996	SRS21984104	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.934	0.93723	0.08814	0.08601	0.69834	0.69798	0.47533	0.47611	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33176	33176	SRR29809748	SRX25308995	SRS21984103	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 0mM STS 3	GSM8393502	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:0\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 0mM STS 3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:0\|agent:STS	GSM8393502	GSM8393502: pdx1 morpholino + 0mM STS 3; Danio rerio; RNA Seq	GSM8393502 r1	GSM8393502	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	22_1.fq.gz 22_2.fq.gz	fastq fastq	4613819800.0	23069099.0	GSM8393502 r1	0:100 1:100	A:1218890904;C:1084874278;G:1104087523;T:1205967095;N:0	100	100	1218890904	1084874278	1104087523	1205967095	0	SRX25308995	SRS21984103	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.9426	0.94852	0.07601	0.07487	0.69197	0.69075	0.45872	0.45856	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33177	33177	SRR29809749	SRX25308994	SRS21984102	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 0mM STS 2	GSM8393501	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:0\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 0mM STS 2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:0\|agent:STS	GSM8393501	GSM8393501: pdx1 morpholino + 0mM STS 2; Danio rerio; RNA Seq	GSM8393501 r1	GSM8393501	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	16_1.fq.gz 16_2.fq.gz	fastq fastq	4818005000.0	24090025.0	GSM8393501 r1	0:100 1:100	A:1291680744;C:1114433015;G:1134463270;T:1277427971;N:0	100	100	1291680744	1114433015	1134463270	1277427971	0	SRX25308994	SRS21984102	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.93988	0.94257	0.08614	0.08554	0.69376	0.69367	0.47178	0.47111	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33178	33178	SRR29809750	SRX25308993	SRS21984101	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 0mM STS 1	GSM8393500	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:0\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 0mM STS 1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:0\|agent:STS	GSM8393500	GSM8393500: pdx1 morpholino + 0mM STS 1; Danio rerio; RNA Seq	GSM8393500 r1	GSM8393500	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	10_2.fq.gz 10_1.fq.gz	fastq fastq	4827935800.0	24139679.0	GSM8393500 r1	0:100 1:100	A:1267823750;C:1143323623;G:1156194469;T:1260593958;N:0	100	100	1267823750	1143323623	1156194469	1260593958	0	SRX25308993	SRS21984101	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94483	0.94829	0.07178	0.07025	0.69077	0.69025	0.46181	0.45982	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33179	33179	SRR29809751	SRX25308992	SRS21984100	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 20mM STS 5	GSM8393499	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:20\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 20mM STS 5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:20\|agent:STS	GSM8393499	GSM8393499: Control morpholino + 20mM STS 5; Danio rerio; RNA Seq	GSM8393499 r1	GSM8393499	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	9_1.fq.gz 9_2.fq.gz	fastq fastq	4822379000.0	24111895.0	GSM8393499 r1	0:100 1:100	A:1262977318;C:1145277730;G:1159167028;T:1254956924;N:0	100	100	1262977318	1145277730	1159167028	1254956924	0	SRX25308992	SRS21984100	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94642	0.94964	0.06863	0.0674	0.69288	0.69252	0.4574	0.44372	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33180	33180	SRR29809752	SRX25308991	SRS21984099	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 20mM STS 4	GSM8393498	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:20\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 20mM STS 4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:20\|agent:STS	GSM8393498	GSM8393498: Control morpholino + 20mM STS 4; Danio rerio; RNA Seq	GSM8393498 r1	GSM8393498	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	3_1.fq.gz 3_2.fq.gz	fastq fastq	4803150200.0	24015751.0	GSM8393498 r1	0:100 1:100	A:1253239300;C:1144350399;G:1158671984;T:1246888517;N:0	100	100	1253239300	1144350399	1158671984	1246888517	0	SRX25308991	SRS21984099	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94606	0.95015	0.06543	0.06441	0.68676	0.68611	0.44857	0.44396	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33181	33181	SRR29809753	SRX25308990	SRS21984098	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 20mM STS 3	GSM8393497	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:20\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 20mM STS 3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:20\|agent:STS	GSM8393497	GSM8393497: Control morpholino + 20mM STS 3; Danio rerio; RNA Seq	GSM8393497 r1	GSM8393497	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	27_1.fq.gz 27_2.fq.gz	fastq fastq	4277827200.0	21389136.0	GSM8393497 r1	0:100 1:100	A:1142589086;C:997230367;G:1005771965;T:1132235782;N:0	100	100	1142589086	997230367	1005771965	1132235782	0	SRX25308990	SRS21984098	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94201	0.94596	0.07754	0.07484	0.69794	0.69617	0.46286	0.45985	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33182	33182	SRR29809754	SRX25308989	SRS21984097	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 20mM STS 2	GSM8393496	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:20\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 20mM STS 2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:20\|agent:STS	GSM8393496	GSM8393496: Control morpholino + 20mM STS 2; Danio rerio; RNA Seq	GSM8393496 r1	GSM8393496	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	21_2.fq.gz 21_1.fq.gz	fastq fastq	4019456600.0	20097283.0	GSM8393496 r1	0:100 1:100	A:1053249649;C:953992221;G:968100759;T:1044113971;N:0	100	100	1053249649	953992221	968100759	1044113971	0	SRX25308989	SRS21984097	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94377	0.95125	0.06861	0.06745	0.68676	0.68523	0.45049	0.45168	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33183	33183	SRR29809755	SRX25308988	SRS21984096	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 20mM STS 1	GSM8393495	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:20\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 20mM STS 1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:20\|agent:STS	GSM8393495	GSM8393495: Control morpholino + 20mM STS 1; Danio rerio; RNA Seq	GSM8393495 r1	GSM8393495	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	15_1.fq.gz 15_2.fq.gz	fastq fastq	4829679200.0	24148396.0	GSM8393495 r1	0:100 1:100	A:1292193191;C:1119414896;G:1140502241;T:1277568872;N:0	100	100	1292193191	1119414896	1140502241	1277568872	0	SRX25308988	SRS21984096	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.9423	0.9467	0.07958	0.07808	0.69763	0.69658	0.46406	0.46623	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33184	33184	SRR29809756	SRX25308987	SRS21984095	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 15mM STS 5	GSM8393494	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:15\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 15mM STS 5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:15\|agent:STS	GSM8393494	GSM8393494: Control morpholino + 15mM STS 5; Danio rerio; RNA Seq	GSM8393494 r1	GSM8393494	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	8_2.fq.gz 8_1.fq.gz	fastq fastq	4803709800.0	24018549.0	GSM8393494 r1	0:100 1:100	A:1253733589;C:1143748058;G:1158768340;T:1247459813;N:0	100	100	1253733589	1143748058	1158768340	1247459813	0	SRX25308987	SRS21984095	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94718	0.94926	0.06582	0.06461	0.68791	0.68738	0.44759	0.44517	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33185	33185	SRR29809757	SRX25308986	SRS21984094	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 15mM STS 4	GSM8393493	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:15\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 15mM STS 4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:15\|agent:STS	GSM8393493	GSM8393493: Control morpholino + 15mM STS 4; Danio rerio; RNA Seq	GSM8393493 r1	GSM8393493	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	26_1.fq.gz 26_2.fq.gz	fastq fastq	4816718000.0	24083590.0	GSM8393493 r1	0:100 1:100	A:1278966223;C:1129131703;G:1144234415;T:1264385659;N:0	100	100	1278966223	1129131703	1144234415	1264385659	0	SRX25308986	SRS21984094	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94278	0.94713	0.07235	0.0704	0.69895	0.698	0.4536	0.45416	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33186	33186	SRR29809758	SRX25308985	SRS21984093	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 15mM STS 3	GSM8393492	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:15\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 15mM STS 3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:15\|agent:STS	GSM8393492	GSM8393492: Control morpholino + 15mM STS 3; Danio rerio; RNA Seq	GSM8393492 r1	GSM8393492	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	20_2.fq.gz 20_1.fq.gz	fastq fastq	4825880400.0	24129402.0	GSM8393492 r1	0:100 1:100	A:1263053657;C:1147908238;G:1161094243;T:1253824262;N:0	100	100	1263053657	1147908238	1161094243	1253824262	0	SRX25308985	SRS21984093	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94642	0.95164	0.06472	0.06312	0.69035	0.68909	0.44854	0.44216	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33187	33187	SRR29809759	SRX25308984	SRS21984092	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 15mM STS 2	GSM8393491	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:15\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 15mM STS 2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:15\|agent:STS	GSM8393491	GSM8393491: Control morpholino + 15mM STS 2; Danio rerio; RNA Seq	GSM8393491 r1	GSM8393491	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	2_1.fq.gz 2_2.fq.gz	fastq fastq	4805985200.0	24029926.0	GSM8393491 r1	0:100 1:100	A:1255841114;C:1143278337;G:1157783615;T:1249082134;N:0	100	100	1255841114	1143278337	1157783615	1249082134	0	SRX25308984	SRS21984092	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94666	0.94794	0.06553	0.06456	0.69181	0.69175	0.4359	0.44559	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33188	33188	SRR29809760	SRX25308983	SRS21984091	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 15mM STS 1	GSM8393490	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:15\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 15mM STS 1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:15\|agent:STS	GSM8393490	GSM8393490: Control morpholino + 15mM STS 1; Danio rerio; RNA Seq	GSM8393490 r1	GSM8393490	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	14_1.fq.gz 14_2.fq.gz	fastq fastq	4553465000.0	22767325.0	GSM8393490 r1	0:100 1:100	A:1209891078;C:1063666819;G:1082075995;T:1197831108;N:0	100	100	1209891078	1063666819	1082075995	1197831108	0	SRX25308983	SRS21984091	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.9432	0.94661	0.07696	0.07599	0.69763	0.69721	0.46463	0.46425	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33189	33189	SRR29809761	SRX25308982	SRS21984090	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 0mM STS 5	GSM8393489	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:0\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 0mM STS 5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:0\|agent:STS	GSM8393489	GSM8393489: Control morpholino + 0mM STS 5; Danio rerio; RNA Seq	GSM8393489 r1	GSM8393489	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	7_1.fq.gz 7_2.fq.gz	fastq fastq	4813770200.0	24068851.0	GSM8393489 r1	0:100 1:100	A:1251918123;C:1151936172;G:1164458418;T:1245457487;N:0	100	100	1251918123	1151936172	1164458418	1245457487	0	SRX25308982	SRS21984090	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.95021	0.95271	0.06538	0.06376	0.69171	0.68996	0.44317	0.4435	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33190	33190	SRR29809762	SRX25308981	SRS21984089	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 0mM STS 4	GSM8393488	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:0\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 0mM STS 4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:0\|agent:STS	GSM8393488	GSM8393488: Control morpholino + 0mM STS 4; Danio rerio; RNA Seq	GSM8393488 r1	GSM8393488	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	25_1.fq.gz 25_2.fq.gz	fastq fastq	4810346800.0	24051734.0	GSM8393488 r1	0:100 1:100	A:1275301780;C:1127999390;G:1144547869;T:1262497761;N:0	100	100	1275301780	1127999390	1144547869	1262497761	0	SRX25308981	SRS21984089	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94519	0.94834	0.06949	0.06803	0.69552	0.69524	0.44741	0.45052	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33191	33191	SRR29809763	SRX25308980	SRS21984088	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 0mM STS 3	GSM8393487	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:0\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 0mM STS 3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:0\|agent:STS	GSM8393487	GSM8393487: Control morpholino + 0mM STS 3; Danio rerio; RNA Seq	GSM8393487 r1	GSM8393487	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	19_1.fq.gz 19_2.fq.gz	fastq fastq	4811704200.0	24058521.0	GSM8393487 r1	0:100 1:100	A:1257129134;C:1146835083;G:1160663520;T:1247076463;N:0	100	100	1257129134	1146835083	1160663520	1247076463	0	SRX25308980	SRS21984088	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94691	0.95082	0.06344	0.06212	0.69014	0.69059	0.45386	0.43864	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33192	33192	SRR29809764	SRX25308979	SRS21984087	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 0mM STS 2	GSM8393486	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:0\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 0mM STS 2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:0\|agent:STS	GSM8393486	GSM8393486: Control morpholino + 0mM STS 2; Danio rerio; RNA Seq	GSM8393486 r1	GSM8393486	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	13_1.fq.gz 13_2.fq.gz	fastq fastq	4616178800.0	23080894.0	GSM8393486 r1	0:100 1:100	A:1225429879;C:1079094541;G:1096304865;T:1215349515;N:0	100	100	1225429879	1079094541	1096304865	1215349515	0	SRX25308979	SRS21984087	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94498	0.9498	0.07635	0.075	0.69319	0.6927	0.46598	0.466	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33193	33193	SRR29809765	SRX25308978	SRS21984086	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 0mM STS 1	GSM8393485	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:0\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 0mM STS 1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:0\|agent:STS	GSM8393485	GSM8393485: Control morpholino + 0mM STS 1; Danio rerio; RNA Seq	GSM8393485 r1	GSM8393485	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612	1_1.fq.gz 1_2.fq.gz	fastq fastq	4823953400.0	24119767.0	GSM8393485 r1	0:100 1:100	A:1270954678;C:1137736456;G:1155516940;T:1259745326;N:0	100	100	1270954678	1137736456	1155516940	1259745326	0	SRX25308978	SRS21984086	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94325	0.94699	0.06928	0.06864	0.69372	0.69307	0.44844	0.45647	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33609	33609	SRR30247666	SRX25709110	SRS22350227	SRP526520	PRJNA1148340	RNA Seq analyses of hey2 mutant and wild type sibling zebrafish hearts	PRJNA1148340	Other	To assess the effects of Hey2 deficiency we performed transcriptome analyses of hey2 mutant and wild type sibling zebrafish hearts at 3 mpf.			RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf rep3	KO3	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:not applicable\|collection date:not applicable\|geo loc name:not applicable\|sex:male and female\|tissue:Heart\|ID:OE replicate 3\|BioSampleModel:Model organism or animal									RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf rep3	hey25nt / replicate 3	hey25nt / replicate 3	RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf replicate 3			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	BGISEQ	BGISEQ-500	SRP526520	KO_3_1.fq.gz KO_3_2.fq.gz	fastq fastq	6793426200.0	22644754.0	KO 3 1.fq.gz	0:150 1:150	A:1845779030;C:1550159613;G:1539592354;T:1857860950;N:34253	150	150	1845779030	1550159613	1539592354	1857860950	34253	SRX25709110	SRS22350227	SRA1948261	East China Normal University\|School of Life Sciences	East China Normal University	2	0.94555	0.92523	0.0631	0.06139	0.76672	0.76968	0.56501	0.57019	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-08-15	Adult	Adult	Heart	Cardiovascular System
33610	33610	SRR30247667	SRX25709109	SRS22350226	SRP526520	PRJNA1148340	RNA Seq analyses of hey2 mutant and wild type sibling zebrafish hearts	PRJNA1148340	Other	To assess the effects of Hey2 deficiency we performed transcriptome analyses of hey2 mutant and wild type sibling zebrafish hearts at 3 mpf.			RNA Seq for hey25nt / mutantzebrafish hearts at 3 mpf rep2	KO2	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:not applicable\|collection date:not applicable\|geo loc name:not applicable\|sex:male and female\|tissue:Heart\|ID:OE replicate 2\|BioSampleModel:Model organism or animal									RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf rep2	hey25nt / replicate 2	hey25nt / replicate 2	RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf replicate 2			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	BGISEQ	BGISEQ-500	SRP526520	KO_2_1.fq.gz KO_2_2.fq.gz	fastq fastq	6577703400.0	21925678.0	KO 2 1.fq.gz	0:150 1:150	A:1795319867;C:1492750718;G:1485718638;T:1803881133;N:33044	150	150	1795319867	1492750718	1485718638	1803881133	33044	SRX25709109	SRS22350226	SRA1948261	East China Normal University\|School of Life Sciences	East China Normal University	2	0.94565	0.92404	0.06212	0.06008	0.77281	0.77546	0.55478	0.56589	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-08-15	Adult	Adult	Heart	Cardiovascular System
33611	33611	SRR30247668	SRX25709108	SRS22350225	SRP526520	PRJNA1148340	RNA Seq analyses of hey2 mutant and wild type sibling zebrafish hearts	PRJNA1148340	Other	To assess the effects of Hey2 deficiency we performed transcriptome analyses of hey2 mutant and wild type sibling zebrafish hearts at 3 mpf.			RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf rep1	KO1	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:not applicable\|collection date:not applicable\|geo loc name:not applicable\|sex:male and female\|tissue:Heart\|ID:OE replicate 1\|BioSampleModel:Model organism or animal									RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf rep1	hey25nt / replicate 1	hey25nt / replicate 1	RNA Seq for hey25nt / mutant zebrafish hearts at 3 mpf replicate 1			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	BGISEQ	BGISEQ-500	SRP526520	KO_1_2.fq.gz KO_1_1.fq.gz	fastq fastq	6592159500.0	21973865.0	KO 1 1.fq.gz	0:150 1:150	A:1800707634;C:1491918482;G:1484850929;T:1814648405;N:34050	150	150	1800707634	1491918482	1484850929	1814648405	34050	SRX25709108	SRS22350225	SRA1948261	East China Normal University\|School of Life Sciences	East China Normal University	2	0.94443	0.92689	0.06601	0.06488	0.76883	0.77033	0.58332	0.52175	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-08-15	Adult	Adult	Heart	Cardiovascular System
33612	33612	SRR30247669	SRX25709107	SRS22350224	SRP526520	PRJNA1148340	RNA Seq analyses of hey2 mutant and wild type sibling zebrafish hearts	PRJNA1148340	Other	To assess the effects of Hey2 deficiency we performed transcriptome analyses of hey2 mutant and wild type sibling zebrafish hearts at 3 mpf.			RNA Seq for hey2+/+ zebrafish hearts at 3 mpf rep3	WT3	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:not applicable\|collection date:not applicable\|geo loc name:not applicable\|sex:male and female\|tissue:Heart\|ID:CTL replicate 3\|BioSampleModel:Model organism or animal									RNA Seq for hey2+/+ zebrafish hearts at 3 mpf rep3	hey2+/+ replicate 3	hey2+/+ replicate 3	RNA Seq for hey2+/+ zebrafish hearts at 3 mpf replicate 3			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	BGISEQ	BGISEQ-500	SRP526520	WT_3_1.fq.gz WT_3_2.fq.gz	fastq fastq	6582842700.0	21942809.0	WT 3 1.fq.gz	0:150 1:150	A:1796301568;C:1494922823;G:1487154319;T:1804427831;N:36159	150	150	1796301568	1494922823	1487154319	1804427831	36159	SRX25709107	SRS22350224	SRA1948261	East China Normal University\|School of Life Sciences	East China Normal University	2	0.94446	0.92023	0.06492	0.06289	0.76694	0.7699	0.55651	0.53407	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-08-15	Adult	Adult	Heart	Cardiovascular System
33613	33613	SRR30247670	SRX25709106	SRS22350223	SRP526520	PRJNA1148340	RNA Seq analyses of hey2 mutant and wild type sibling zebrafish hearts	PRJNA1148340	Other	To assess the effects of Hey2 deficiency we performed transcriptome analyses of hey2 mutant and wild type sibling zebrafish hearts at 3 mpf.			RNA Seq for hey2+/+ zebrafish hearts at 3 mpf rep2	WT2	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:not applicable\|collection date:not applicable\|geo loc name:not applicable\|sex:male and female\|tissue:Heart\|ID:CTL replicate 2\|BioSampleModel:Model organism or animal									RNA Seq for hey2+/+ zebrafish hearts at 3 mpf rep2	hey2+/+ replicate 2	hey2+/+ replicate 2	RNA Seq for hey2+/+ zebrafish hearts at 3 mpf replicate 2			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	BGISEQ	BGISEQ-500	SRP526520	WT_2_2.fq.gz WT_2_1.fq.gz	fastq fastq	6632526000.0	22108420.0	WT 2 1.fq.gz	0:150 1:150	A:1811392253;C:1505075703;G:1495091968;T:1820928778;N:37298	150	150	1811392253	1505075703	1495091968	1820928778	37298	SRX25709106	SRS22350223	SRA1948261	East China Normal University\|School of Life Sciences	East China Normal University	2	0.94532	0.92096	0.06496	0.06227	0.76564	0.76909	0.56754	0.57117	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-08-15	Adult	Adult	Heart	Cardiovascular System
33614	33614	SRR30247671	SRX25709105	SRS22350222	SRP526520	PRJNA1148340	RNA Seq analyses of hey2 mutant and wild type sibling zebrafish hearts	PRJNA1148340	Other	To assess the effects of Hey2 deficiency we performed transcriptome analyses of hey2 mutant and wild type sibling zebrafish hearts at 3 mpf.			RNA Seq for hey2+/+ zebrafish hearts at 3 mpf rep1	WT1	strain:not applicable\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:not applicable\|collection date:not applicable\|geo loc name:not applicable\|sex:male and female\|tissue:Heart\|ID:CTL replicate 1\|BioSampleModel:Model organism or animal									RNA Seq for hey2+/+ zebrafish hearts at 3 mpf rep1	hey2+/+ replicate 1	hey2+/+ replicate 1	RNA Seq for hey2+/+ zebrafish hearts at 3 mpf replicate 1			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	BGISEQ	BGISEQ-500	SRP526520	WT_1_1.fq.gz WT_1_2.fq.gz	fastq fastq	6601461900.0	22004873.0	WT 1 1.fq.gz	0:150 1:150	A:1816453592;C:1485325900;G:1476423985;T:1823223402;N:35021	150	150	1816453592	1485325900	1476423985	1823223402	35021	SRX25709105	SRS22350222	SRA1948261	East China Normal University\|School of Life Sciences	East China Normal University	2	0.9482	0.92609	0.05744	0.0553	0.77423	0.77699	0.53884	0.54075	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-08-15	Adult	Adult	Heart	Cardiovascular System
34182	34182	SRR31399561	SRX26768859	SRS23256160	SRP546207	PRJNA1188114	Reduced EIF6 dosage attenuates TP53 activation in models of Shwachman Diamond syndrome	GSE282310	Transcriptome Analysis	Shwachman Diamond syndrome SDS is characterized by neutropenia exocrine pancreatic insufficiency and bony abnormalities with an increased risk of myeloid neoplasia. Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects. We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models confirmed in patient derived tissues and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression 5 25% of the wildtype levels that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS EIF6 TP53 and cellular stress responses offer promising insights into SDS pathogenesis somatic genetic rescue and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 / or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 / and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39 we used EBSeq R package for differentially expressed gene detection between eif6 / and eif6+/+ fold change > 2 and P < 0.05.			eif6 3	GSM8641203	source name:whole larvae\|tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 KO\|geo loc name:missing\|collection date:missing	eif6 3	Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally reads were removed if they: 1 lacked a 3’ adapter sequence 2 were 5’ 3’ adapter ligation products 3 were 5’ 5’ adapter ligation products 4 were shorter than 18 nt or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters: f N 0 M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values	whole larvae	5 dpf	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 KO	GSM8641203	GSM8641203: eif6 3; Danio rerio; RNA Seq	GSM8641203 r1	GSM8641203	1	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP546207	eif6_3_1.fq.gz eif6_3_2.fq.gz	fastq fastq	6955801200.0	34779006.0	GSM8641203 r1	0:100 1:100	A:1784502248;C:1653592398;G:1716091635;T:1801614919;N:0	100	100	1784502248	1653592398	1716091635	1801614919	0	SRX26768859	SRS23256160	SRA2017777	Cleveland Clinic	Cleveland Clinic												B	B	biological fallback assumption	bgi	bgi	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2024-11-19	Larval	Larval	Whole Organism	All anatomical structures
34183	34183	SRR31399562	SRX26768858	SRS23256161	SRP546207	PRJNA1188114	Reduced EIF6 dosage attenuates TP53 activation in models of Shwachman Diamond syndrome	GSE282310	Transcriptome Analysis	Shwachman Diamond syndrome SDS is characterized by neutropenia exocrine pancreatic insufficiency and bony abnormalities with an increased risk of myeloid neoplasia. Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects. We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models confirmed in patient derived tissues and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression 5 25% of the wildtype levels that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS EIF6 TP53 and cellular stress responses offer promising insights into SDS pathogenesis somatic genetic rescue and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 / or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 / and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39 we used EBSeq R package for differentially expressed gene detection between eif6 / and eif6+/+ fold change > 2 and P < 0.05.			eif6 2	GSM8641202	source name:whole larvae\|tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 KO\|geo loc name:missing\|collection date:missing	eif6 2	Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally reads were removed if they: 1 lacked a 3’ adapter sequence 2 were 5’ 3’ adapter ligation products 3 were 5’ 5’ adapter ligation products 4 were shorter than 18 nt or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters: f N 0 M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values	whole larvae	5 dpf	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 KO	GSM8641202	GSM8641202: eif6 2; Danio rerio; RNA Seq	GSM8641202 r1	GSM8641202	1	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP546207	eif6_2_1.fq.gz eif6_2_2.fq.gz	fastq fastq	6968721400.0	34843607.0	GSM8641202 r1	0:100 1:100	A:1798630009;C:1650901437;G:1708195694;T:1810994260;N:0	100	100	1798630009	1650901437	1708195694	1810994260	0	SRX26768858	SRS23256161	SRA2017777	Cleveland Clinic	Cleveland Clinic												B	B	biological fallback assumption	bgi	bgi	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2024-11-19	Larval	Larval	Whole Organism	All anatomical structures
34184	34184	SRR31399563	SRX26768857	SRS23256159	SRP546207	PRJNA1188114	Reduced EIF6 dosage attenuates TP53 activation in models of Shwachman Diamond syndrome	GSE282310	Transcriptome Analysis	Shwachman Diamond syndrome SDS is characterized by neutropenia exocrine pancreatic insufficiency and bony abnormalities with an increased risk of myeloid neoplasia. Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects. We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models confirmed in patient derived tissues and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression 5 25% of the wildtype levels that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS EIF6 TP53 and cellular stress responses offer promising insights into SDS pathogenesis somatic genetic rescue and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 / or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 / and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39 we used EBSeq R package for differentially expressed gene detection between eif6 / and eif6+/+ fold change > 2 and P < 0.05.			eif6 1	GSM8641201	source name:whole larvae\|tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 KO\|geo loc name:missing\|collection date:missing	eif6 1	Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally reads were removed if they: 1 lacked a 3’ adapter sequence 2 were 5’ 3’ adapter ligation products 3 were 5’ 5’ adapter ligation products 4 were shorter than 18 nt or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters: f N 0 M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values	whole larvae	5 dpf	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 KO	GSM8641201	GSM8641201: eif6 1; Danio rerio; RNA Seq	GSM8641201 r1	GSM8641201	1	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP546207	eif6_1_1.fq.gz eif6_1_2.fq.gz	fastq fastq	6976474200.0	34882371.0	GSM8641201 r1	0:100 1:100	A:1819387431;C:1630709320;G:1698463303;T:1827914146;N:0	100	100	1819387431	1630709320	1698463303	1827914146	0	SRX26768857	SRS23256159	SRA2017777	Cleveland Clinic	Cleveland Clinic												B	B	biological fallback assumption	bgi	bgi	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2024-11-19	Larval	Larval	Whole Organism	All anatomical structures
34185	34185	SRR31399564	SRX26768856	SRS23256158	SRP546207	PRJNA1188114	Reduced EIF6 dosage attenuates TP53 activation in models of Shwachman Diamond syndrome	GSE282310	Transcriptome Analysis	Shwachman Diamond syndrome SDS is characterized by neutropenia exocrine pancreatic insufficiency and bony abnormalities with an increased risk of myeloid neoplasia. Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects. We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models confirmed in patient derived tissues and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression 5 25% of the wildtype levels that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS EIF6 TP53 and cellular stress responses offer promising insights into SDS pathogenesis somatic genetic rescue and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 / or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 / and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39 we used EBSeq R package for differentially expressed gene detection between eif6 / and eif6+/+ fold change > 2 and P < 0.05.			wt3	GSM8641200	source name:whole larvae\|tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 wildtype\|geo loc name:missing\|collection date:missing	wt3	Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally reads were removed if they: 1 lacked a 3’ adapter sequence 2 were 5’ 3’ adapter ligation products 3 were 5’ 5’ adapter ligation products 4 were shorter than 18 nt or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters: f N 0 M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values	whole larvae	5 dpf	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 wildtype	GSM8641200	GSM8641200: wt3; Danio rerio; RNA Seq	GSM8641200 r1	GSM8641200	1	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP546207	wt3_1.fq.gz wt3_2.fq.gz	fastq fastq	6990771600.0	34953858.0	GSM8641200 r1	0:100 1:100	A:1823561732;C:1639273273;G:1691098287;T:1836838308;N:0	100	100	1823561732	1639273273	1691098287	1836838308	0	SRX26768856	SRS23256158	SRA2017777	Cleveland Clinic	Cleveland Clinic												B	B	biological fallback assumption	bgi	bgi	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2024-11-19	Larval	Larval	Whole Organism	All anatomical structures
34186	34186	SRR31399565	SRX26768855	SRS23256157	SRP546207	PRJNA1188114	Reduced EIF6 dosage attenuates TP53 activation in models of Shwachman Diamond syndrome	GSE282310	Transcriptome Analysis	Shwachman Diamond syndrome SDS is characterized by neutropenia exocrine pancreatic insufficiency and bony abnormalities with an increased risk of myeloid neoplasia. Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects. We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models confirmed in patient derived tissues and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression 5 25% of the wildtype levels that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS EIF6 TP53 and cellular stress responses offer promising insights into SDS pathogenesis somatic genetic rescue and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 / or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 / and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39 we used EBSeq R package for differentially expressed gene detection between eif6 / and eif6+/+ fold change > 2 and P < 0.05.			wt2	GSM8641199	source name:whole larvae\|tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 wildtype\|geo loc name:missing\|collection date:missing	wt2	Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally reads were removed if they: 1 lacked a 3’ adapter sequence 2 were 5’ 3’ adapter ligation products 3 were 5’ 5’ adapter ligation products 4 were shorter than 18 nt or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters: f N 0 M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values	whole larvae	5 dpf	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 wildtype	GSM8641199	GSM8641199: wt2; Danio rerio; RNA Seq	GSM8641199 r1	GSM8641199	1	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP546207	wt2_1.fq.gz wt2_2.fq.gz	fastq fastq	6996780600.0	34983903.0	GSM8641199 r1	0:100 1:100	A:1819793027;C:1646550105;G:1701161650;T:1829275818;N:0	100	100	1819793027	1646550105	1701161650	1829275818	0	SRX26768855	SRS23256157	SRA2017777	Cleveland Clinic	Cleveland Clinic												B	B	biological fallback assumption	bgi	bgi	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2024-11-19	Larval	Larval	Whole Organism	All anatomical structures
34187	34187	SRR31399566	SRX26768854	SRS23256156	SRP546207	PRJNA1188114	Reduced EIF6 dosage attenuates TP53 activation in models of Shwachman Diamond syndrome	GSE282310	Transcriptome Analysis	Shwachman Diamond syndrome SDS is characterized by neutropenia exocrine pancreatic insufficiency and bony abnormalities with an increased risk of myeloid neoplasia. Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects. We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models confirmed in patient derived tissues and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression 5 25% of the wildtype levels that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS EIF6 TP53 and cellular stress responses offer promising insights into SDS pathogenesis somatic genetic rescue and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 / or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 / and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39 we used EBSeq R package for differentially expressed gene detection between eif6 / and eif6+/+ fold change > 2 and P < 0.05.			wt1	GSM8641198	source name:whole larvae\|tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 wildtype\|geo loc name:missing\|collection date:missing	wt1	Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally reads were removed if they: 1 lacked a 3’ adapter sequence 2 were 5’ 3’ adapter ligation products 3 were 5’ 5’ adapter ligation products 4 were shorter than 18 nt or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters: f N 0 M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values	whole larvae	5 dpf	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 wildtype	GSM8641198	GSM8641198: wt1; Danio rerio; RNA Seq	GSM8641198 r1	GSM8641198	1	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP546207	wt1_1.fq.gz wt1_2.fq.gz	fastq fastq	6976844600.0	34884223.0	GSM8641198 r1	0:100 1:100	A:1807619362;C:1649374675;G:1693243894;T:1826606669;N:0	100	100	1807619362	1649374675	1693243894	1826606669	0	SRX26768854	SRS23256156	SRA2017777	Cleveland Clinic	Cleveland Clinic												B	B	biological fallback assumption	bgi	bgi	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2024-11-19	Larval	Larval	Whole Organism	All anatomical structures
35865	35865	SRR33094447	SRX28358130	SRS24687221	SRP578075	PRJNA1249535	P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy	PRJNA1249535	Other	Single cell transcriptome sequencing provides high resolution transcriptome data on the molecular mechanisms by which Tau P301S mediates Alzheimer's disease like pathological changes in zebrafish providing unique insights into the pathogenesis of Tau pathology mediated cell to cell interactions in AD.		TauP301S 4		TauP301S 4	breed:zebrafish\|age:4 month\|collection date:2024 05 18\|geo loc name:China:Shantou\|sex:not determined\|tissue:brain\|BioSampleModel:Model organism or animal									P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy	TauP301S 4	TauP301S 4	tissue			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	BGISEQ	BGISEQ-500	SRP578075	AD4_S1_L001_R1_001.fastq.gz AD4_S1_L001_R2_001.fastq.gz	fastq fastq	129145897746.0	427635423.0	AD4 S1 L001 R1 001.fastq.gz	0:151 1:151	A:37870495722;C:24917123133;G:22536537853;T:43764941649;N:56799389	151	151	37870495722	24917123133	22536537853	43764941649	56799389	SRX28358130	SRS24687221	SRA2110625	Shantou university medical college\|Neuroscience Center	Shantou university medical college												T	B	mate1 technical by mapping diff	bgi	bgi	unknown	poly_a	unknown	sc	unknown	unknown	China	2025-04-13	Adult	Adult	Brain	Nervous System
35866	35866	SRR33094448	SRX28358129	SRS24687220	SRP578075	PRJNA1249535	P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy	PRJNA1249535	Other	Single cell transcriptome sequencing provides high resolution transcriptome data on the molecular mechanisms by which Tau P301S mediates Alzheimer's disease like pathological changes in zebrafish providing unique insights into the pathogenesis of Tau pathology mediated cell to cell interactions in AD.		TauP301S 3		TauP301S 3	breed:zebrafish\|age:4 month\|collection date:2024 05 17\|geo loc name:China:Shantou\|sex:not determined\|tissue:brain\|BioSampleModel:Model organism or animal									P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy	TauP301S 3	TauP301S 3	tissue			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	BGISEQ	BGISEQ-500	SRP578075	AD3_S1_L001_R1_001.fastq.gz AD3_S1_L001_R2_001.fastq.gz	fastq fastq	130723873718.0	432860509.0	AD3 S1 L001 R1 001.fastq.gz	0:151 1:151	A:38509426012;C:25238065771;G:22586405501;T:44332442791;N:57533643	151	151	38509426012	25238065771	22586405501	44332442791	57533643	SRX28358129	SRS24687220	SRA2110625	Shantou university medical college\|Neuroscience Center	Shantou university medical college												T	B	mate1 technical by mapping diff	bgi	bgi	unknown	poly_a	unknown	sc	unknown	unknown	China	2025-04-13	Adult	Adult	Brain	Nervous System
35867	35867	SRR33094449	SRX28358128	SRS24687219	SRP578075	PRJNA1249535	P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy	PRJNA1249535	Other	Single cell transcriptome sequencing provides high resolution transcriptome data on the molecular mechanisms by which Tau P301S mediates Alzheimer's disease like pathological changes in zebrafish providing unique insights into the pathogenesis of Tau pathology mediated cell to cell interactions in AD.		TauP301S 2		TauP301S 2	breed:zebrafish\|age:4 month\|collection date:2024 05 16\|geo loc name:China:Shantou\|sex:not determined\|tissue:brain\|BioSampleModel:Model organism or animal									P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy	TauP301S 2	TauP301S 2	tissue			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	BGISEQ	BGISEQ-500	SRP578075	AD2_S1_L001_R1_001.fastq.gz AD2_S1_L001_R2_001.fastq.gz	fastq fastq	130145208498.0	430944399.0	AD2 S1 L001 R1 001.fastq.gz	0:151 1:151	A:37802929660;C:22980541562;G:20982421471;T:48304142442;N:75173363	151	151	37802929660	22980541562	20982421471	48304142442	75173363	SRX28358128	SRS24687219	SRA2110625	Shantou university medical college\|Neuroscience Center	Shantou university medical college												T	B	mate1 technical by mapping diff	bgi	bgi	unknown	poly_a	unknown	sc	unknown	unknown	China	2025-04-13	Adult	Adult	Brain	Nervous System
35868	35868	SRR33094450	SRX28358127	SRS24687218	SRP578075	PRJNA1249535	P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy	PRJNA1249535	Other	Single cell transcriptome sequencing provides high resolution transcriptome data on the molecular mechanisms by which Tau P301S mediates Alzheimer's disease like pathological changes in zebrafish providing unique insights into the pathogenesis of Tau pathology mediated cell to cell interactions in AD.		TauP301S 1		TauP301S 1	breed:zebrafish\|age:4 month\|collection date:2024 05 15\|geo loc name:China:Shantou\|sex:not determined\|tissue:brain\|BioSampleModel:Model organism or animal									P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy	TauP301S 1	TauP301S 1	tissue			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	BGISEQ	BGISEQ-500	SRP578075	AD1_S1_L001_R1_001.fastq.gz AD1_S1_L001_R2_001.fastq.gz	fastq fastq	151897861402.0	502973051.0	AD1 S1 L001 R1 001.fastq.gz	0:151 1:151	A:44290580650;C:26864167508;G:24611898618;T:56043760812;N:87453814	151	151	44290580650	26864167508	24611898618	56043760812	87453814	SRX28358127	SRS24687218	SRA2110625	Shantou university medical college\|Neuroscience Center	Shantou university medical college												T	B	mate1 technical by mapping diff	bgi	bgi	unknown	poly_a	unknown	sc	unknown	unknown	China	2025-04-13	Adult	Adult	Brain	Nervous System
35980	35980	SRR33796117	SRX29017800	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: embryo whole body	P2000 1	P2000 1	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.			RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371	P2000_1_1.fq.gz P2000_1_2.fq.gz	fastq fastq	6682157100.0	22273857.0	P2000 1 1.fq.gz	0:150 1:150	A:1750970707;C:1591819991;G:1593263349;T:1746103053;N:0	150	150	1750970707	1591819991	1593263349	1746103053	0	SRX29017800	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35981	35981	SRR33796118	SRX29017799	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: embryo whole body	P1000 3	P1000 3	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.			RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371	P1000_3_1.fq.gz P1000_3_2.fq.gz	fastq fastq	6596943000.0	21989810.0	P1000 3 1.fq.gz	0:150 1:150	A:1725528987;C:1574140428;G:1576046656;T:1721226929;N:0	150	150	1725528987	1574140428	1576046656	1721226929	0	SRX29017799	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35982	35982	SRR33796119	SRX29017798	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: embryo whole body	P1000 2	P1000 2	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.			RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371	P1000_2_1.fq.gz P1000_2_2.fq.gz	fastq fastq	6677331000.0	22257770.0	P1000 2 1.fq.gz	0:150 1:150	A:1758237128;C:1582217484;G:1584403835;T:1752472553;N:0	150	150	1758237128	1582217484	1584403835	1752472553	0	SRX29017798	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35983	35983	SRR33796120	SRX29017797	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: embryo whole body	P1000 1	P1000 1	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.			RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371	P1000_1_1.fq.gz P1000_1_2.fq.gz	fastq fastq	6771926100.0	22573087.0	P1000 1 1.fq.gz	0:150 1:150	A:1788071352;C:1600799117;G:1602227700;T:1780827931;N:0	150	150	1788071352	1600799117	1602227700	1780827931	0	SRX29017797	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35984	35984	SRR33796121	SRX29017796	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: embryo whole body	P500 3	P500 3	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.			RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371	P500_3_1.fq.gz P500_3_2.fq.gz	fastq fastq	6691956300.0	22306521.0	P500 3 1.fq.gz	0:150 1:150	A:1763763611;C:1584417511;G:1585842124;T:1757933054;N:0	150	150	1763763611	1584417511	1585842124	1757933054	0	SRX29017796	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35985	35985	SRR33796122	SRX29017795	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: embryo whole body	P500 2	P500 2	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.			RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371	P500_2_1.fq.gz P500_2_2.fq.gz	fastq fastq	6720858300.0	22402861.0	P500 2 1.fq.gz	0:150 1:150	A:1752279513;C:1609781801;G:1611483135;T:1747313851;N:0	150	150	1752279513	1609781801	1611483135	1747313851	0	SRX29017795	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35986	35986	SRR33796123	SRX29017794	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: embryo whole body	P500 1	P500 1	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.			RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371	P500_1_1.fq.gz P500_1_2.fq.gz	fastq fastq	6820862100.0	22736207.0	P500 1 1.fq.gz	0:150 1:150	A:1812260874;C:1601860387;G:1602603805;T:1804137034;N:0	150	150	1812260874	1601860387	1602603805	1804137034	0	SRX29017794	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35987	35987	SRR33796124	SRX29017793	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: embryo whole body	MX 3	MX 3	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.			RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371	MX_3_1.fq.gz MX_3_2.fq.gz	fastq fastq	6795327600.0	22651092.0	MX 3 1.fq.gz	0:150 1:150	A:1768016462;C:1630727253;G:1632326554;T:1764257331;N:0	150	150	1768016462	1630727253	1632326554	1764257331	0	SRX29017793	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35988	35988	SRR33796125	SRX29017792	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: embryo whole body	P2000 3	P2000 3	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.			RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371	P2000_3_1.fq.gz P2000_3_2.fq.gz	fastq fastq	6620786400.0	22069288.0	P2000 3 1.fq.gz	0:150 1:150	A:1736628496;C:1574653543;G:1577791512;T:1731712849;N:0	150	150	1736628496	1574653543	1577791512	1731712849	0	SRX29017792	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35989	35989	SRR33796126	SRX29017791	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: embryo whole body	P2000 2	P2000 2	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.			RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371	P2000_2_1.fq.gz P2000_2_2.fq.gz	fastq fastq	6613914000.0	22046380.0	P2000 2 1.fq.gz	0:150 1:150	A:1733574880;C:1575483348;G:1576793005;T:1728062767;N:0	150	150	1733574880	1575483348	1576793005	1728062767	0	SRX29017791	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35990	35990	SRR33796127	SRX29017790	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: embryo whole body	MX 2	MX 2	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.			RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371	MX_2_1.fq.gz MX_2_2.fq.gz	fastq fastq	6769929300.0	22566431.0	MX 2 1.fq.gz	0:150 1:150	A:1773923783;C:1611785261;G:1615111695;T:1769108561;N:0	150	150	1773923783	1611785261	1615111695	1769108561	0	SRX29017790	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35991	35991	SRR33796128	SRX29017789	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: embryo whole body	MX 1	MX 1	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.			RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371	MX_1_1.fq.gz MX_1_2.fq.gz	fastq fastq	6715295400.0	22384318.0	MX 1 1.fq.gz	0:150 1:150	A:1774590051;C:1584963102;G:1587348964;T:1768393283;N:0	150	150	1774590051	1584963102	1587348964	1768393283	0	SRX29017789	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
55373	55373	SRR10322141	SRX7032952	SRS5553012	SRP226571	PRJNA578840	RNA seq analysis for zebrafish tumors driven by overexpression of human IRF4	GSE139226	Transcriptome Analysis	RNA seq analysis was performed using zebrafish primary tumors and control thymus to analyze gene expression changes post IRF4 overexpression. Overall design: Human IRF4 gene was overexpressed under the zebrafish lck promoter. Tumor cells were harvested from IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. Normal thymus cells were also harvested from control zebrafish lck mCherry.	pubmed:35504924		IRF4 overexpression with p53 mutation RNA seq #2	GSM4134351	tissue:lck IRF4;p53+/ \|genotype/variation:IRF4 overexpression and p53 mutation	IRF4 overexpression with p53 mutation RNA seq #2	RNA seq datasets of two control thymus samples and four tumor samples two from lck:IRF4 and two from lRF4;p53+/ were aligned to the zebrafish genome GRCz11 using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount v1.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation GRCz11 gtf file Bioconductor package DESeq2 v1.12.4 with the intersection strict mode was used to analyze differential gene expression. Genome build: GRCz11 Supplementary files format and content: txt files for raw counts differentially expressed genes	lck IRF4;p53+/	No treatment	Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.	The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Normal thymus were also harvested from control zebrafish which was transduced only with mCherry. Total RNAs were harvested from each sample and then applied for RNA seq analysis.	genotype/variation:IRF4 overexpression and p53 mutation	GSM4134351	GSM4134351: IRF4 overexpression with p53 mutation RNA seq #2; Danio rerio; RNA Seq	GSM4134351		1	Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.	GEO Accession:GSM4134351	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP226571	IRF4xp53_3_1.fastq.gz IRF4xp53_3_2.fastq.gz	fastq fastq	8647695276.0	86535602.0	GSM4134351 r1	0:99.93 1:99.93	A:2336303355;C:1960332457;G:1974896588;T:2376162876;N:0	99	99	2336303355	1960332457	1974896588	2376162876	0	SRX7032952	SRS5553012	SRA982884	GEO	Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore	1	0.94146		0.26739		0.77739		0.49821		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2019-10-22	Undetermined	Undetermined	Multi-tissue	Multi-system
55374	55374	SRR10322140	SRX7032951	SRS5553011	SRP226571	PRJNA578840	RNA seq analysis for zebrafish tumors driven by overexpression of human IRF4	GSE139226	Transcriptome Analysis	RNA seq analysis was performed using zebrafish primary tumors and control thymus to analyze gene expression changes post IRF4 overexpression. Overall design: Human IRF4 gene was overexpressed under the zebrafish lck promoter. Tumor cells were harvested from IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. Normal thymus cells were also harvested from control zebrafish lck mCherry.	pubmed:35504924		IRF4 overexpression with p53 mutation RNA seq #1	GSM4134350	tissue:lck IRF4;p53+/ \|genotype/variation:IRF4 overexpression and p53 mutation	IRF4 overexpression with p53 mutation RNA seq #1	RNA seq datasets of two control thymus samples and four tumor samples two from lck:IRF4 and two from lRF4;p53+/ were aligned to the zebrafish genome GRCz11 using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount v1.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation GRCz11 gtf file Bioconductor package DESeq2 v1.12.4 with the intersection strict mode was used to analyze differential gene expression. Genome build: GRCz11 Supplementary files format and content: txt files for raw counts differentially expressed genes	lck IRF4;p53+/	No treatment	Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.	The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Normal thymus were also harvested from control zebrafish which was transduced only with mCherry. Total RNAs were harvested from each sample and then applied for RNA seq analysis.	genotype/variation:IRF4 overexpression and p53 mutation	GSM4134350	GSM4134350: IRF4 overexpression with p53 mutation RNA seq #1; Danio rerio; RNA Seq	GSM4134350		1	Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.	GEO Accession:GSM4134350	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP226571	IRF4xp53_1_1.fastq.gz IRF4xp53_1_2.fastq.gz	fastq fastq	8579468052.0	85855086.0	GSM4134350 r1	0:99.93 1:99.93	A:2293476693;C:1963039176;G:1985578185;T:2337373998;N:0	99	99	2293476693	1963039176	1985578185	2337373998	0	SRX7032951	SRS5553011	SRA982884	GEO	Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore	1	0.94576		0.27683		0.77589		0.47851		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2019-10-22	Undetermined	Undetermined	Multi-tissue	Multi-system
55375	55375	SRR10322139	SRX7032950	SRS5553010	SRP226571	PRJNA578840	RNA seq analysis for zebrafish tumors driven by overexpression of human IRF4	GSE139226	Transcriptome Analysis	RNA seq analysis was performed using zebrafish primary tumors and control thymus to analyze gene expression changes post IRF4 overexpression. Overall design: Human IRF4 gene was overexpressed under the zebrafish lck promoter. Tumor cells were harvested from IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. Normal thymus cells were also harvested from control zebrafish lck mCherry.	pubmed:35504924		IRF4 overexpression RNA seq #2	GSM4134349	tissue:lck IRF4\|genotype/variation:IRF4 overexpression	IRF4 overexpression RNA seq #2	RNA seq datasets of two control thymus samples and four tumor samples two from lck:IRF4 and two from lRF4;p53+/ were aligned to the zebrafish genome GRCz11 using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount v1.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation GRCz11 gtf file Bioconductor package DESeq2 v1.12.4 with the intersection strict mode was used to analyze differential gene expression. Genome build: GRCz11 Supplementary files format and content: txt files for raw counts differentially expressed genes	lck IRF4	No treatment	Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.	The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Normal thymus were also harvested from control zebrafish which was transduced only with mCherry. Total RNAs were harvested from each sample and then applied for RNA seq analysis.	genotype/variation:IRF4 overexpression	GSM4134349	GSM4134349: IRF4 overexpression RNA seq #2; Danio rerio; RNA Seq	GSM4134349		1	Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.	GEO Accession:GSM4134349	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP226571	IRF4_2_1.fastq.gz IRF4_2_2.fastq.gz	fastq fastq	8625409426.0	86311782.0	GSM4134349 r1	0:99.93 1:99.93	A:2345513123;C:1941948054;G:1962855201;T:2375093048;N:0	99	99	2345513123	1941948054	1962855201	2375093048	0	SRX7032950	SRS5553010	SRA982884	GEO	Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore	1	0.94815		0.35561		0.79117		0.50866		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2019-10-22	Undetermined	Undetermined	Multi-tissue	Multi-system
55376	55376	SRR10322138	SRX7032949	SRS5553009	SRP226571	PRJNA578840	RNA seq analysis for zebrafish tumors driven by overexpression of human IRF4	GSE139226	Transcriptome Analysis	RNA seq analysis was performed using zebrafish primary tumors and control thymus to analyze gene expression changes post IRF4 overexpression. Overall design: Human IRF4 gene was overexpressed under the zebrafish lck promoter. Tumor cells were harvested from IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. Normal thymus cells were also harvested from control zebrafish lck mCherry.	pubmed:35504924		IRF4 overexpression RNA seq #1	GSM4134348	tissue:lck IRF4\|genotype/variation:IRF4 overexpression	IRF4 overexpression RNA seq #1	RNA seq datasets of two control thymus samples and four tumor samples two from lck:IRF4 and two from lRF4;p53+/ were aligned to the zebrafish genome GRCz11 using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount v1.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation GRCz11 gtf file Bioconductor package DESeq2 v1.12.4 with the intersection strict mode was used to analyze differential gene expression. Genome build: GRCz11 Supplementary files format and content: txt files for raw counts differentially expressed genes	lck IRF4	No treatment	Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.	The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Normal thymus were also harvested from control zebrafish which was transduced only with mCherry. Total RNAs were harvested from each sample and then applied for RNA seq analysis.	genotype/variation:IRF4 overexpression	GSM4134348	GSM4134348: IRF4 overexpression RNA seq #1; Danio rerio; RNA Seq	GSM4134348		1	Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.	GEO Accession:GSM4134348	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP226571	IRF4_1_1.fastq.gz IRF4_1_2.fastq.gz	fastq fastq	8560288616.0	85661544.0	GSM4134348 r1	0:99.93 1:99.93	A:2300488079;C:1940898245;G:1978951452;T:2339950840;N:0	99	99	2300488079	1940898245	1978951452	2339950840	0	SRX7032949	SRS5553009	SRA982884	GEO	Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore	1	0.94019		0.24387		0.75789		0.49007		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2019-10-22	Undetermined	Undetermined	Multi-tissue	Multi-system
55377	55377	SRR10322137	SRX7032948	SRS5553008	SRP226571	PRJNA578840	RNA seq analysis for zebrafish tumors driven by overexpression of human IRF4	GSE139226	Transcriptome Analysis	RNA seq analysis was performed using zebrafish primary tumors and control thymus to analyze gene expression changes post IRF4 overexpression. Overall design: Human IRF4 gene was overexpressed under the zebrafish lck promoter. Tumor cells were harvested from IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. Normal thymus cells were also harvested from control zebrafish lck mCherry.	pubmed:35504924		mCherry control RNA seq #2	GSM4134347	tissue:lck mCherry\|genotype/variation:control	mCherry control RNA seq #2	RNA seq datasets of two control thymus samples and four tumor samples two from lck:IRF4 and two from lRF4;p53+/ were aligned to the zebrafish genome GRCz11 using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount v1.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation GRCz11 gtf file Bioconductor package DESeq2 v1.12.4 with the intersection strict mode was used to analyze differential gene expression. Genome build: GRCz11 Supplementary files format and content: txt files for raw counts differentially expressed genes	lck mCherry	No treatment	Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.	The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Normal thymus were also harvested from control zebrafish which was transduced only with mCherry. Total RNAs were harvested from each sample and then applied for RNA seq analysis.	genotype/variation:control	GSM4134347	GSM4134347: mCherry control RNA seq #2; Danio rerio; RNA Seq	GSM4134347		1	Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.	GEO Accession:GSM4134347	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP226571	Lck_mch_2_1.fastq.gz Lck_mch_2_2.fastq.gz	fastq fastq	8556568306.0	85629202.0	GSM4134347 r1	0:99.93 1:99.93	A:2299427498;C:1945648999;G:1981590842;T:2329900967;N:0	99	99	2299427498	1945648999	1981590842	2329900967	0	SRX7032948	SRS5553008	SRA982884	GEO	Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore	1	0.94792		0.25274		0.80085		0.51772		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2019-10-22	Undetermined	Undetermined	Multi-tissue	Multi-system
55378	55378	SRR10322136	SRX7032947	SRS5553007	SRP226571	PRJNA578840	RNA seq analysis for zebrafish tumors driven by overexpression of human IRF4	GSE139226	Transcriptome Analysis	RNA seq analysis was performed using zebrafish primary tumors and control thymus to analyze gene expression changes post IRF4 overexpression. Overall design: Human IRF4 gene was overexpressed under the zebrafish lck promoter. Tumor cells were harvested from IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. Normal thymus cells were also harvested from control zebrafish lck mCherry.	pubmed:35504924		mCherry control RNA seq #1	GSM4134346	tissue:lck mCherry\|genotype/variation:control	mCherry control RNA seq #1	RNA seq datasets of two control thymus samples and four tumor samples two from lck:IRF4 and two from lRF4;p53+/ were aligned to the zebrafish genome GRCz11 using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount v1.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation GRCz11 gtf file Bioconductor package DESeq2 v1.12.4 with the intersection strict mode was used to analyze differential gene expression. Genome build: GRCz11 Supplementary files format and content: txt files for raw counts differentially expressed genes	lck mCherry	No treatment	Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.	The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Normal thymus were also harvested from control zebrafish which was transduced only with mCherry. Total RNAs were harvested from each sample and then applied for RNA seq analysis.	genotype/variation:control	GSM4134346	GSM4134346: mCherry control RNA seq #1; Danio rerio; RNA Seq	GSM4134346		1	Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.	GEO Accession:GSM4134346	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP226571	Lck_mch_1_1.fastq.gz Lck_mch_1_2.fastq.gz	fastq fastq	8544218824.0	85502654.0	GSM4134346 r1	0:99.93 1:99.93	A:2294044731;C:1942271608;G:1967598065;T:2340304420;N:0	99	99	2294044731	1942271608	1967598065	2340304420	0	SRX7032947	SRS5553007	SRA982884	GEO	Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore	1	0.94337		0.28212		0.79239		0.47106		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Singapore	2019-10-22	Undetermined	Undetermined	Multi-tissue	Multi-system
55643	55643	SRR10604044	SRX7283593	SRS5777402	SRP235014	PRJNA594101	Danio rerio Transcriptome	PRJNA594101	Other	Danio rerio Transcriptome post cGAS and STING knockout				stko2	strain:not collected\|isolate:sting knockout 2\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:7 days\|dev stage:larvae\|sex:not applicable\|tissue:larvae\|biomaterial provider:Yang xiaojun\|BioSampleModel:Model organism or animal									RNA Seq of zebraish larvae	sting knockout 2	sting knockout 2	RNA seq			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP235014	stko2_1.fastq.gz stko2_2.fastq.gz	fastq fastq	10635609300.0	70904062.0	stko2 1.fastq.gz	0:150 1:150	A:2864931942;C:2450585568;G:2436540783;T:2882828480;N:722527	150	150	2864931942	2450585568	2436540783	2882828480	722527	SRX7283593	SRS5777402	SRA1007465	Shantou university medical college\|Neuroscience Center	Shantou university medical college	1	0.93079		0.07849		0.70301		0.47872		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2019-12-08	Larval	Larval	Undetermined	Undetermined
55644	55644	SRR10604045	SRX7283592	SRS5777401	SRP235014	PRJNA594101	Danio rerio Transcriptome	PRJNA594101	Other	Danio rerio Transcriptome post cGAS and STING knockout				stko1	strain:not collected\|isolate:sting knockout 1\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:7 days\|dev stage:larvae\|sex:not applicable\|tissue:larvae\|biomaterial provider:Yang xiaojun\|BioSampleModel:Model organism or animal									RNA Seq of zebraish larvae	sting knockout 1	sting knockout 1	RNA seq			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP235014	stko1_1.fastq.gz stko1_2.fastq.gz	fastq fastq	10453959000.0	69693060.0	stko1 1.fastq.gz	0:150 1:150	A:2823253748;C:2400078679;G:2379662427;T:2850274552;N:689594	150	150	2823253748	2400078679	2379662427	2850274552	689594	SRX7283592	SRS5777401	SRA1007465	Shantou university medical college\|Neuroscience Center	Shantou university medical college	1	0.92736		0.08475		0.69822		0.47233		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2019-12-08	Larval	Larval	Undetermined	Undetermined

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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");;