metadata: run_metadata: 155 rows where experiment.library_layout = "PAIRED", experiment.platform = "BGISEQ" and tissue_curation

155 rows where experiment.library_layout = "PAIRED", experiment.platform = "BGISEQ" and tissue_curation_coarse = "All anatomical structures"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.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
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
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
55655	55655	SRR10674410	SRX7351703	SRS5811186	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.					BPS 100 1	isolate:biologocal replicate 10\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050110	bps050110	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_100_1_1.fq.gz BPS_100_1_2.fq.gz	fastq fastq	6958801200.0	69588012.0	BPS 100 1 1.fq.gz	0:100 1:100	A:1852139865;C:1635606671;G:1596180575;T:1874072794;N:801295	100	100	1852139865	1635606671	1596180575	1874072794	801295	SRX7351703	SRS5811186	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94716		0.09824		0.68475		0.47195		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55656	55656	SRR10674411	SRX7351702	SRS5811185	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.					BPS 10 3	isolate:biologocal replicate 9\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050109	bps050109	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_10_3_1.fq.gz BPS_10_3_2.fq.gz	fastq fastq	6969574800.0	69695748.0	BPS 10 3 1.fq.gz	0:100 1:100	A:1860393053;C:1631995190;G:1597357772;T:1879188120;N:640665	100	100	1860393053	1631995190	1597357772	1879188120	640665	SRX7351702	SRS5811185	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94597		0.10542		0.68016		0.4666		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55657	55657	SRR10674412	SRX7351701	SRS5811182	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.					BPS 10 2	isolate:biologocal replicate 8\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050108	bps050108	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_10_2_1.fq.gz BPS_10_2_2.fq.gz	fastq fastq	6709340400.0	67093404.0	BPS 10 2 1.fq.gz	0:100 1:100	A:2036224090;C:1319652145;G:1297564214;T:2055258677;N:641274	100	100	2036224090	1319652145	1297564214	2055258677	641274	SRX7351701	SRS5811182	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.87778		0.38111		0.71543		0.56061		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55658	55658	SRR10674413	SRX7351700	SRS5811181	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.					BPS 10 1	isolate:biologocal replicate 7\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050107	bps050107	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_10_1_1.fq.gz BPS_10_1_2.fq.gz	fastq fastq	6717746800.0	67177468.0	BPS 10 1 1.fq.gz	0:100 1:100	A:1787637885;C:1578942212;G:1548400030;T:1802147201;N:619472	100	100	1787637885	1578942212	1548400030	1802147201	619472	SRX7351700	SRS5811181	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94726		0.10123		0.68919		0.45234		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55659	55659	SRR10674414	SRX7351699	SRS5811184	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.					BPS 1 3	isolate:biologocal replicate 6\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050106	bps050106	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_1_3_2.fq.gz BPS_1_3_1.fq.gz	fastq fastq	6726522800.0	67265228.0	BPS 1 3 1.fq.gz	0:100 1:100	A:1789486049;C:1582069064;G:1548432478;T:1805913744;N:621465	100	100	1789486049	1582069064	1548432478	1805913744	621465	SRX7351699	SRS5811184	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.9465		0.09858		0.68442		0.45032		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55660	55660	SRR10674415	SRX7351698	SRS5811180	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.					BPS 1 2	isolate:biologocal replicate 5\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050105	bps050105	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_1_2_2.fq.gz BPS_1_2_1.fq.gz	fastq fastq	6959685000.0	69596850.0	BPS 1 2 1.fq.gz	0:100 1:100	A:1914426129;C:1574998719;G:1542052351;T:1927550147;N:657654	100	100	1914426129	1574998719	1542052351	1927550147	657654	SRX7351698	SRS5811180	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94034		0.14574		0.69934		0.47033		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55661	55661	SRR10674416	SRX7351697	SRS5811183	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.					BPS 1 1	isolate:biologocal replicate 4\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050104	bps050104	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_1_1_1.fq.gz BPS_1_1_2.fq.gz	fastq fastq	7040826400.0	70408264.0	BPS 1 1 1.fq.gz	0:100 1:100	A:1915125100;C:1612334047;G:1578924466;T:1933922418;N:520369	100	100	1915125100	1612334047	1578924466	1933922418	520369	SRX7351697	SRS5811183	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94114		0.13158		0.68903		0.47739		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55662	55662	SRR10674417	SRX7351696	SRS5811179	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.					BPS 0 1 3	isolate:biologocal replicate 3\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050103	bps050103	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_0_1_3_1.fq.gz BPS_0_1_3_2.fq.gz	fastq fastq	6992676800.0	69926768.0	BPS 0 1 3 1.fq.gz	0:100 1:100	A:1860627581;C:1643489002;G:1610508221;T:1877536968;N:515028	100	100	1860627581	1643489002	1610508221	1877536968	515028	SRX7351696	SRS5811179	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94485		0.101		0.68314		0.45711		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55663	55663	SRR10674418	SRX7351695	SRS5811178	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.					Cntrol3	isolate:biologocal replicate 18\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050118	bps050118	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	Cntrol3_1.fq.gz Cntrol3_2.fq.gz	fastq fastq	6742983200.0	67429832.0	Cntrol3 1.fq.gz	0:100 1:100	A:1801392073;C:1577630219;G:1545614005;T:1817857809;N:489094	100	100	1801392073	1577630219	1545614005	1817857809	489094	SRX7351695	SRS5811178	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94386		0.10779		0.68832		0.45545		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55664	55664	SRR10674419	SRX7351694	SRS5811177	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.					Cntrol2	isolate:biologocal replicate 17\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050117	bps050117	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	Cntrol2_1.fq.gz Cntrol2_2.fq.gz	fastq fastq	6750661000.0	67506610.0	Cntrol2 1.fq.gz	0:100 1:100	A:1796606666;C:1585909518;G:1556014239;T:1811284557;N:846020	100	100	1796606666	1585909518	1556014239	1811284557	846020	SRX7351694	SRS5811177	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94397		0.10007		0.68708		0.47779		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55665	55665	SRR10674420	SRX7351693	SRS5811174	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.					Cntrol1	isolate:biologocal replicate 16\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050116	bps050116	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	Cntrol1_1.fq.gz Cntrol1_2.fq.gz	fastq fastq	6766663000.0	67666630.0	Cntrol1 1.fq.gz	0:100 1:100	A:1825736389;C:1564390057;G:1532835305;T:1842876742;N:824507	100	100	1825736389	1564390057	1532835305	1842876742	824507	SRX7351693	SRS5811174	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94047		0.12338		0.68893		0.46407		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55666	55666	SRR10674421	SRX7351692	SRS5811176	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.					BPS 1000 3	isolate:biologocal replicate 15\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050115	bps050115	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_1000_3_1.fq.gz BPS_1000_3_2.fq.gz	fastq fastq	6507622200.0	65076222.0	BPS 1000 3 1.fq.gz	0:100 1:100	A:1735402948;C:1525938362;G:1493787016;T:1751945676;N:548198	100	100	1735402948	1525938362	1493787016	1751945676	548198	SRX7351692	SRS5811176	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94304		0.10593		0.6842		0.46348		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55667	55667	SRR10674422	SRX7351691	SRS5811173	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.					BPS 1000 2	isolate:biologocal replicate 14\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050114	bps050114	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_1000_2_1.fq.gz BPS_1000_2_2.fq.gz	fastq fastq	6740712000.0	67407120.0	BPS 1000 2 1.fq.gz	0:100 1:100	A:1816870993;C:1562402111;G:1527381283;T:1833284067;N:773546	100	100	1816870993	1562402111	1527381283	1833284067	773546	SRX7351691	SRS5811173	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94327		0.11511		0.70033		0.4551		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55668	55668	SRR10674423	SRX7351690	SRS5811175	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.					BPS 1000 1	isolate:biologocal replicate 13\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050113	bps050113	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_1000_1_1.fq.gz BPS_1000_1_2.fq.gz	fastq fastq	6727750400.0	67277504.0	BPS 1000 1 1.fq.gz	0:100 1:100	A:1803578734;C:1568712705;G:1535618959;T:1819016739;N:823263	100	100	1803578734	1568712705	1535618959	1819016739	823263	SRX7351690	SRS5811175	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94457		0.1118		0.69087		0.46815		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55669	55669	SRR10674424	SRX7351689	SRS5811172	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.					BPS 100 3	isolate:biologocal replicate 12\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050112	bps050112	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_100_3_1.fq.gz BPS_100_3_2.fq.gz	fastq fastq	6962431800.0	69624318.0	BPS 100 3 1.fq.gz	0:100 1:100	A:1865300693;C:1624120289;G:1585691091;T:1886538935;N:780792	100	100	1865300693	1624120289	1585691091	1886538935	780792	SRX7351689	SRS5811172	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94581		0.10195		0.68288		0.47174		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55670	55670	SRR10674425	SRX7351688	SRS5811171	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.					BPS 100 2	isolate:biologocal replicate 11\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050111	bps050111	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_100_2_1.fq.gz BPS_100_2_2.fq.gz	fastq fastq	7201035800.0	72010358.0	BPS 100 2 1.fq.gz	0:100 1:100	A:2115590854;C:1489181336;G:1459936470;T:2135514629;N:812511	100	100	2115590854	1489181336	1459936470	2135514629	812511	SRX7351688	SRS5811171	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.90678		0.29289		0.70735		0.49554		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55671	55671	SRR10674426	SRX7351687	SRS5811170	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.					BPS 0 1 2	isolate:biologocal replicate 2\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050102	bps050102	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_0_1_2_1.fq.gz BPS_0_1_2_2.fq.gz	fastq fastq	7022382800.0	70223828.0	BPS 0 1 2 1.fq.gz	0:100 1:100	A:1853514579;C:1663935080;G:1635277415;T:1869136960;N:518766	100	100	1853514579	1663935080	1635277415	1869136960	518766	SRX7351687	SRS5811170	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94712		0.09313		0.6814		0.47256		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55672	55672	SRR10674427	SRX7351686	SRS5811167	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.					BPS 0 1 1	isolate:biologocal replicate 1\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050101	bps050101	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_0_1_1_1.fq.gz BPS_0_1_1_2.fq.gz	fastq fastq	7013900400.0	70139004.0	BPS 0 1 1 1.fq.gz	0:100 1:100	A:1885826391;C:1629114228;G:1597181244;T:1901261511;N:517026	100	100	1885826391	1629114228	1597181244	1901261511	517026	SRX7351686	SRS5811167	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94226		0.11616		0.69014		0.45679		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
59480	59480	SRR11922874	SRX8468588	SRS6769276	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661		zebrafish embryo Aldh3a1 KO rep6	GSM4590772	source name:zebrafish embryo\|genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	zebrafish embryo Aldh3a1 KO rep6	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	GSM4590772	GSM4590772: zebrafish embryo Aldh3a1 KO rep6; Danio rerio; RNA Seq	GSM4590772		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590772	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	12_aldh3a1----homo-48hpf-6_1.fq.gz 12_aldh3a1----homo-48hpf-6_2.fq.gz	fastq fastq	4660603600.0	46606036.0	GSM4590772 r1	0:100 1:100	A:1396899993;C:924291840;G:902974172;T:1436437595;N:0	100	100	1396899993	924291840	902974172	1436437595	0	SRX8468588	SRS6769276	SRA1083013	GEO	ZMF, University Heidelberg	1	0.90281		0.2525		0.75943		0.62165		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59481	59481	SRR11922873	SRX8468587	SRS6769275	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661		zebrafish embryo Aldh3a1 KO rep5	GSM4590771	source name:zebrafish embryo\|genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	zebrafish embryo Aldh3a1 KO rep5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	GSM4590771	GSM4590771: zebrafish embryo Aldh3a1 KO rep5; Danio rerio; RNA Seq	GSM4590771		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590771	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	11_aldh3a1----homo-48hpf-5_1.fq.gz 11_aldh3a1----homo-48hpf-5_2.fq.gz	fastq fastq	3919649800.0	39196498.0	GSM4590771 r1	0:100 1:100	A:1203194756;C:742776682;G:744133378;T:1229544984;N:0	100	100	1203194756	742776682	744133378	1229544984	0	SRX8468587	SRS6769275	SRA1083013	GEO	ZMF, University Heidelberg	1	0.86745		0.31349		0.76702		0.63864		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59482	59482	SRR11922872	SRX8468586	SRS6769274	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661		zebrafish embryo Aldh3a1 KO rep4	GSM4590770	source name:zebrafish embryo\|genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	zebrafish embryo Aldh3a1 KO rep4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	GSM4590770	GSM4590770: zebrafish embryo Aldh3a1 KO rep4; Danio rerio; RNA Seq	GSM4590770		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590770	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	10_aldh3a1----homo-48hpf-4_2.fq.gz 10_aldh3a1----homo-48hpf-4_1.fq.gz	fastq fastq	4549625000.0	45496250.0	GSM4590770 r1	0:100 1:100	A:1345145181;C:925949636;G:905779914;T:1372750269;N:0	100	100	1345145181	925949636	905779914	1372750269	0	SRX8468586	SRS6769274	SRA1083013	GEO	ZMF, University Heidelberg	1	0.9117		0.23055		0.72545		0.50968		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59483	59483	SRR11922871	SRX8468585	SRS6769273	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661		zebrafish embryo Aldh3a1 KO rep3	GSM4590769	source name:zebrafish embryo\|genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	zebrafish embryo Aldh3a1 KO rep3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	GSM4590769	GSM4590769: zebrafish embryo Aldh3a1 KO rep3; Danio rerio; RNA Seq	GSM4590769		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590769	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	9_aldh3a1----homo-48hpf-3_1.fq.gz 9_aldh3a1----homo-48hpf-3_2.fq.gz	fastq fastq	4194991600.0	41949916.0	GSM4590769 r1	0:100 1:100	A:1258296885;C:833884600;G:816600639;T:1286209476;N:0	100	100	1258296885	833884600	816600639	1286209476	0	SRX8468585	SRS6769273	SRA1083013	GEO	ZMF, University Heidelberg	1	0.89574		0.28139		0.73397		0.56688		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59484	59484	SRR11922870	SRX8468584	SRS6769272	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661		zebrafish embryo Aldh3a1 KO rep2	GSM4590768	source name:zebrafish embryo\|genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	zebrafish embryo Aldh3a1 KO rep2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	GSM4590768	GSM4590768: zebrafish embryo Aldh3a1 KO rep2; Danio rerio; RNA Seq	GSM4590768		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590768	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	8_aldh3a1----homo-48hpf-2_1.fq.gz 8_aldh3a1----homo-48hpf-2_2.fq.gz	fastq fastq	5097901600.0	50979016.0	GSM4590768 r1	0:100 1:100	A:1487281075;C:1055394796;G:1035616985;T:1519608744;N:0	100	100	1487281075	1055394796	1035616985	1519608744	0	SRX8468584	SRS6769272	SRA1083013	GEO	ZMF, University Heidelberg	1	0.92556		0.18622		0.73026		0.5187		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59485	59485	SRR11922869	SRX8468583	SRS6769271	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661		zebrafish embryo Aldh3a1 KO rep1	GSM4590767	source name:zebrafish embryo\|genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	zebrafish embryo Aldh3a1 KO rep1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	GSM4590767	GSM4590767: zebrafish embryo Aldh3a1 KO rep1; Danio rerio; RNA Seq	GSM4590767		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590767	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	7_aldh3a1----homo-48hpf-1_1.fq.gz 7_aldh3a1----homo-48hpf-1_2.fq.gz	fastq fastq	5075421000.0	50754210.0	GSM4590767 r1	0:100 1:100	A:1523744143;C:1008915874;G:985443760;T:1557317223;N:0	100	100	1523744143	1008915874	985443760	1557317223	0	SRX8468583	SRS6769271	SRA1083013	GEO	ZMF, University Heidelberg	1	0.90167		0.27915		0.75879		0.6673		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59486	59486	SRR11922868	SRX8468582	SRS6769270	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661		zebrafish embryo wildtype rep5	GSM4590766	source name:zebrafish embryo\|genotype:WT\|tissue:embryo\|age:48 hpf	zebrafish embryo wildtype rep5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:WT\|tissue:embryo\|age:48 hpf	GSM4590766	GSM4590766: zebrafish embryo wildtype rep5; Danio rerio; RNA Seq	GSM4590766		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590766	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	6_aldh3a1+-+-wt-48hpf-R_1.fq.gz 6_aldh3a1+-+-wt-48hpf-R_2.fq.gz	fastq fastq	5097636600.0	50976366.0	GSM4590766 r1	0:100 1:100	A:1402424015;C:1146863463;G:1121174200;T:1427174922;N:0	100	100	1402424015	1146863463	1121174200	1427174922	0	SRX8468582	SRS6769270	SRA1083013	GEO	ZMF, University Heidelberg	1	0.95115		0.09816		0.69781		0.46194		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59487	59487	SRR11922867	SRX8468581	SRS6769269	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661		zebrafish embryo wildtype rep4	GSM4590765	source name:zebrafish embryo\|genotype:WT\|tissue:embryo\|age:48 hpf	zebrafish embryo wildtype rep4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:WT\|tissue:embryo\|age:48 hpf	GSM4590765	GSM4590765: zebrafish embryo wildtype rep4; Danio rerio; RNA Seq	GSM4590765		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590765	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	4_aldh3a1+-+-wt-48hpf-4_1.fq.gz 4_aldh3a1+-+-wt-48hpf-4_2.fq.gz	fastq fastq	4847250800.0	48472508.0	GSM4590765 r1	0:100 1:100	A:1351516729;C:1070410976;G:1050113082;T:1375210013;N:0	100	100	1351516729	1070410976	1050113082	1375210013	0	SRX8468581	SRS6769269	SRA1083013	GEO	ZMF, University Heidelberg	1	0.94418		0.12404		0.69374		0.49948		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59488	59488	SRR11922866	SRX8468580	SRS6769268	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661		zebrafish embryo wildtype rep3	GSM4590764	source name:zebrafish embryo\|genotype:WT\|tissue:embryo\|age:48 hpf	zebrafish embryo wildtype rep3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:WT\|tissue:embryo\|age:48 hpf	GSM4590764	GSM4590764: zebrafish embryo wildtype rep3; Danio rerio; RNA Seq	GSM4590764		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590764	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	3_aldh3a1+-+-wt-48hpf-3_1.fq.gz 3_aldh3a1+-+-wt-48hpf-3_2.fq.gz	fastq fastq	5083417400.0	50834174.0	GSM4590764 r1	0:100 1:100	A:1375006484;C:1168556107;G:1139277849;T:1400576960;N:0	100	100	1375006484	1168556107	1139277849	1400576960	0	SRX8468580	SRS6769268	SRA1083013	GEO	ZMF, University Heidelberg	1	0.95419		0.09201		0.69209		0.48244		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59489	59489	SRR11922865	SRX8468579	SRS6769267	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661		zebrafish embryo wildtype rep2	GSM4590763	source name:zebrafish embryo\|genotype:WT\|tissue:embryo\|age:48 hpf	zebrafish embryo wildtype rep2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:WT\|tissue:embryo\|age:48 hpf	GSM4590763	GSM4590763: zebrafish embryo wildtype rep2; Danio rerio; RNA Seq	GSM4590763		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590763	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	2_aldh3a1+-+-wt-48hpf-2_1.fq.gz 2_aldh3a1+-+-wt-48hpf-2_2.fq.gz	fastq fastq	5089646400.0	50896464.0	GSM4590763 r1	0:100 1:100	A:1384714450;C:1161015785;G:1138313445;T:1405602720;N:0	100	100	1384714450	1161015785	1138313445	1405602720	0	SRX8468579	SRS6769267	SRA1083013	GEO	ZMF, University Heidelberg	1	0.95309		0.09301		0.69798		0.48524		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59490	59490	SRR11922864	SRX8468578	SRS6769266	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661		zebrafish embryo wildtype rep1	GSM4590762	source name:zebrafish embryo\|genotype:WT\|tissue:embryo\|age:48 hpf	zebrafish embryo wildtype rep1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:WT\|tissue:embryo\|age:48 hpf	GSM4590762	GSM4590762: zebrafish embryo wildtype rep1; Danio rerio; RNA Seq	GSM4590762		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590762	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	1_aldh3a1+-+-wt-48hpf-1_1.fq.gz 1_aldh3a1+-+-wt-48hpf-1_2.fq.gz	fastq fastq	5098267400.0	50982674.0	GSM4590762 r1	0:100 1:100	A:1406329756;C:1147290302;G:1118206731;T:1426440611;N:0	100	100	1406329756	1147290302	1118206731	1426440611	0	SRX8468578	SRS6769266	SRA1083013	GEO	ZMF, University Heidelberg	1	0.95039		0.10482		0.69641		0.47979		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
60496	60496	SRR12328853	SRX8829078	SRS7048444	SRP273655	PRJNA648800	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA	PRJNA648800	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C2	C2 C2 2 4	replicate:biological replicate 2\|strain:AB\|isolate:C2\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:100ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C2C220200712	C2C220200712	RNA seq of zebrafish in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP273655	C2_C2_2_4_1.fq.gz C2_C2_2_4_2.fq.gz	fastq fastq	6974294600.0	69742946.0	C2 C2 2 4 1.fq.gz	0:100 1:100	A:2057162032;C:1418016219;G:1425580374;T:2073535975;N:0	100	100	2057162032	1418016219	1425580374	2073535975	0	SRX8829078	SRS7048444	SRA1103962	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.93171		0.17455		0.71626		0.54961		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-07-27	Undetermined	Embryo	Whole Organism	All anatomical structures
60497	60497	SRR12328854	SRX8829077	SRS7048443	SRP273655	PRJNA648800	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA	PRJNA648800	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C2	C2 C2 1 4	replicate:biological replicate 1\|strain:AB\|isolate:C2\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:100ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C2C220200711	C2C220200711	RNA seq of zebrafish in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP273655	C2_C2_1_4_2.fq.gz C2_C2_1_4_1.fq.gz	fastq fastq	6942905200.0	69429052.0	C2 C2 1 4 1.fq.gz	0:100 1:100	A:2025129308;C:1433430820;G:1434784226;T:2049560846;N:0	100	100	2025129308	1433430820	1434784226	2049560846	0	SRX8829077	SRS7048443	SRA1103962	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.93211		0.16662		0.71001		0.53674		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-07-27	Undetermined	Embryo	Whole Organism	All anatomical structures
60498	60498	SRR12328855	SRX8829076	SRS7048442	SRP273655	PRJNA648800	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA	PRJNA648800	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C1	C1 C1 2 4	replicate:biological replicate 2\|strain:AB\|isolate:C1\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:1ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C1C120200712	C1C120200712	RNA seq of zebrafish in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP273655	C1_C1_2_4_1.fq.gz C1_C1_2_4_2.fq.gz	fastq fastq	6973657600.0	69736576.0	C1 C1 2 4 1.fq.gz	0:100 1:100	A:2050440259;C:1423350359;G:1423015668;T:2076851314;N:0	100	100	2050440259	1423350359	1423015668	2076851314	0	SRX8829076	SRS7048442	SRA1103962	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.92911		0.1877		0.72025		0.58085		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-07-27	Undetermined	Embryo	Whole Organism	All anatomical structures
60499	60499	SRR12328856	SRX8829075	SRS7048441	SRP273655	PRJNA648800	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA	PRJNA648800	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C1	C1 C1 1 4	replicate:biological replicate 1\|strain:AB\|isolate:C1\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:1ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C1C120200711	C1C120200711	RNA seq of zebrafish in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP273655	C1_C1_1_4_1.fq.gz C1_C1_1_4_2.fq.gz	fastq fastq	6746729200.0	67467292.0	C1 C1 1 4 1.fq.gz	0:100 1:100	A:2004203843;C:1356765594;G:1357760526;T:2027999237;N:0	100	100	2004203843	1356765594	1357760526	2027999237	0	SRX8829075	SRS7048441	SRA1103962	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.92733		0.19903		0.72228		0.59259		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-07-27	Undetermined	Embryo	Whole Organism	All anatomical structures
60500	60500	SRR12328857	SRX8829074	SRS7048440	SRP273655	PRJNA648800	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA	PRJNA648800	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C0	C0 C0 2 4	replicate:biological replicate 2\|strain:AB\|isolate:C0\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:0ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C0C020200712	C0C020200712	RNA seq of zebrafish in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP273655	C0_C0_2_4_1.fq.gz C0_C0_2_4_2.fq.gz	fastq fastq	6924724800.0	69247248.0	C0 C0 2 4 1.fq.gz	0:100 1:100	A:1974618038;C:1471821932;G:1482725702;T:1995559128;N:0	100	100	1974618038	1471821932	1482725702	1995559128	0	SRX8829074	SRS7048440	SRA1103962	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.93473		0.14676		0.69649		0.50413		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-07-27	Undetermined	Embryo	Whole Organism	All anatomical structures
60501	60501	SRR12328858	SRX8829073	SRS7048439	SRP273655	PRJNA648800	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA	PRJNA648800	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C0	C0 C0 1 4	replicate:biological replicate 1\|strain:AB\|isolate:C0\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:0ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C0C020200711	C0C020200711	RNA seq of zebrafish in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP273655	C0_C0_1_4_1.fq.gz C0_C0_1_4_2.fq.gz	fastq fastq	6899505600.0	68995056.0	C0 C0 1 4 1.fq.gz	0:100 1:100	A:1957459931;C:1477351919;G:1482435319;T:1982258431;N:0	100	100	1957459931	1477351919	1482435319	1982258431	0	SRX8829073	SRS7048439	SRA1103962	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.93567		0.14057		0.6883		0.48707		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-07-27	Undetermined	Embryo	Whole Organism	All anatomical structures
65852	65852	SRR15657174	SRX11954177	SRS9963999	SRP334492	PRJNA758398	Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]	GSE182945	Transcriptome Analysis	Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq.	parent bioproject:PRJNA758396			embryo Cu 0.156uM 96hpf	GSM5543529	tissue:embryo Cu 0.156uM 96hpf\|cell type:embryos at 96hpf whose parents were exposed to 0.156μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	embryo Cu 0.156uM 96hpf	Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample	embryo Cu 0.156uM 96hpf	50 60 embryos F1 from each group	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	embryos F1 cultured in normal water environment	cell type:embryos at 96hpf hours post fertilization\|treatment:embryos whose parents were exposed to 0.156μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	GSM5543529	GSM5543529: embryo Cu 0.156uM 96hpf; Danio rerio; RNA Seq	GSM5543529		1	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	GEO Accession:GSM5543529	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP334492	Cu_0.156uM_96hpf_R1.fastq.gz Cu_0.156uM_96hpf_R2.fastq.gz	fastq fastq	7167443000.0	71674430.0	GSM5543529 r1	0:100 1:100	A:1930084120;C:1646651059;G:1623549050;T:1966203424;N:955347	100	100	1930084120	1646651059	1623549050	1966203424	955347	SRX11954177	SRS9963999	SRA1284991	GEO	college of informatics, Huazhong Agricultural University	1	0.94339		0.113		0.6549		0.4857		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2021-08-27	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
65853	65853	SRR15657173	SRX11954176	SRS9963998	SRP334492	PRJNA758398	Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]	GSE182945	Transcriptome Analysis	Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq.	parent bioproject:PRJNA758396			embryo Cu 0.156uM 24hpf	GSM5543528	tissue:embryo Cu 0.156uM 24hpf\|cell type:embryos at 24hpf whose parents were exposed to 0.156μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	embryo Cu 0.156uM 24hpf	Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample	embryo Cu 0.156uM 24hpf	50 60 embryos F1 from each group	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	embryos F1 cultured in normal water environment	cell type:embryos at 24hpf hours post fertilization\|treatment:embryos whose parents were exposed to 0.156μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	GSM5543528	GSM5543528: embryo Cu 0.156uM 24hpf; Danio rerio; RNA Seq	GSM5543528		1	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	GEO Accession:GSM5543528	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP334492	Cu_0.156uM_24hpf_R1.fastq.gz Cu_0.156uM_24hpf_R2.fastq.gz	fastq fastq	7164832400.0	71648324.0	GSM5543528 r1	0:100 1:100	A:1929135591;C:1646939515;G:1617401036;T:1970900148;N:456110	100	100	1929135591	1646939515	1617401036	1970900148	456110	SRX11954176	SRS9963998	SRA1284991	GEO	college of informatics, Huazhong Agricultural University	1	0.94344		0.10713		0.68919		0.47118		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2021-08-27	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
65854	65854	SRR15657172	SRX11954175	SRS9963997	SRP334492	PRJNA758398	Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]	GSE182945	Transcriptome Analysis	Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq.	parent bioproject:PRJNA758396			embryo Cu 0.078uM 96hpf	GSM5543527	tissue:embryo Cu 0.078uM 96hpf\|cell type:embryos at 96hpf whose parents were exposed to 0.078μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	embryo Cu 0.078uM 96hpf	Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample	embryo Cu 0.078uM 96hpf	50 60 embryos F1 from each group	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	embryos F1 cultured in normal water environment	cell type:embryos at 96hpf hours post fertilization\|treatment:embryos whose parents were exposed to 0.078μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	GSM5543527	GSM5543527: embryo Cu 0.078uM 96hpf; Danio rerio; RNA Seq	GSM5543527		1	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	GEO Accession:GSM5543527	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP334492	Cu_0.078uM_96hpf_R1.fastq.gz Cu_0.078uM_96hpf_R2.fastq.gz	fastq fastq	7135774800.0	71357748.0	GSM5543527 r1	0:100 1:100	A:1928230196;C:1633490990;G:1605871113;T:1967776814;N:405687	100	100	1928230196	1633490990	1605871113	1967776814	405687	SRX11954175	SRS9963997	SRA1284991	GEO	college of informatics, Huazhong Agricultural University	1	0.94191		0.11803		0.65614		0.48225		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2021-08-27	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
65855	65855	SRR15657171	SRX11954174	SRS9963995	SRP334492	PRJNA758398	Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]	GSE182945	Transcriptome Analysis	Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq.	parent bioproject:PRJNA758396			embryo Cu 0.078uM 24hpf	GSM5543526	tissue:embryo Cu 0.078uM 24hpf\|cell type:embryos at 24hpf whose parents were exposed to 0.078μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	embryo Cu 0.078uM 24hpf	Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample	embryo Cu 0.078uM 24hpf	50 60 embryos F1 from each group	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	embryos F1 cultured in normal water environment	cell type:embryos at 24hpf hours post fertilization\|treatment:embryos whose parents were exposed to 0.078μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	GSM5543526	GSM5543526: embryo Cu 0.078uM 24hpf; Danio rerio; RNA Seq	GSM5543526		1	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	GEO Accession:GSM5543526	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP334492	Cu_0.078uM_24hpf_R1.fastq.gz Cu_0.078uM_24hpf_R2.fastq.gz	fastq fastq	6934019600.0	69340196.0	GSM5543526 r1	0:100 1:100	A:1865548284;C:1597354050;G:1569395022;T:1901304271;N:417973	100	100	1865548284	1597354050	1569395022	1901304271	417973	SRX11954174	SRS9963995	SRA1284991	GEO	college of informatics, Huazhong Agricultural University	1	0.94389		0.10356		0.68726		0.47794		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2021-08-27	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
65856	65856	SRR15657170	SRX11954173	SRS9963996	SRP334492	PRJNA758398	Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]	GSE182945	Transcriptome Analysis	Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq.	parent bioproject:PRJNA758396			embryo Control 96hpf	GSM5543525	tissue:embryo Control 96hpf\|cell type:embryos at 96hpf whose parents were exposed to normal water environment F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	embryo Control 96hpf	Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample	embryo Control 96hpf	50 60 embryos F1 from each group	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	embryos F1 cultured in normal water environment	cell type:embryos at 96hpf hours post fertilization\|treatment:embryos whose parents were exposed to normal water environment F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	GSM5543525	GSM5543525: embryo Control 96hpf; Danio rerio; RNA Seq	GSM5543525		1	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	GEO Accession:GSM5543525	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP334492	Control_96hpf_R1.fastq.gz Control_96hpf_R2.fastq.gz	fastq fastq	6698614400.0	66986144.0	GSM5543525 r1	0:100 1:100	A:1816763075;C:1526218454;G:1496202651;T:1858550518;N:879702	100	100	1816763075	1526218454	1496202651	1858550518	879702	SRX11954173	SRS9963996	SRA1284991	GEO	college of informatics, Huazhong Agricultural University	1	0.93836		0.12432		0.65504		0.47564		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2021-08-27	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
65857	65857	SRR15657169	SRX11954172	SRS9963994	SRP334492	PRJNA758398	Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]	GSE182945	Transcriptome Analysis	Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq.	parent bioproject:PRJNA758396			embryo Control 24hpf	GSM5543524	tissue:embryo Control 24hpf\|cell type:embryos at 24hpf whose parents were exposed to normal water environment F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	embryo Control 24hpf	Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample	embryo Control 24hpf	50 60 embryos F1 from each group	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	embryos F1 cultured in normal water environment	cell type:embryos at 24hpf hours post fertilization\|treatment:embryos whose parents were exposed to normal water environment F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	GSM5543524	GSM5543524: embryo Control 24hpf; Danio rerio; RNA Seq	GSM5543524		1	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	GEO Accession:GSM5543524	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP334492	Control_24hpf_R1.fastq.gz Control_24hpf_R2.fastq.gz	fastq fastq	6911559200.0	69115592.0	GSM5543524 r1	0:100 1:100	A:1858569189;C:1592355971;G:1564572369;T:1895593185;N:468486	100	100	1858569189	1592355971	1564572369	1895593185	468486	SRX11954172	SRS9963994	SRA1284991	GEO	college of informatics, Huazhong Agricultural University	1	0.93745		0.09795		0.69059		0.48209		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2021-08-27	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
65984	65984	SRR15859821	SRX12150937	SRS10130028	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			levonorgestrel treatment at high concentration treatment	LNG H 1	AN	strain:not collected2\|isolate:whole fish13\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 1'\|BioSampleModel:Model organism or animal									LNG H 1	BM	BM	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	50_1_R1.clean.fq.gz 50_1_R2.clean.fq.gz	fastq fastq	6850889266.0	22893917.0	50 1 R1.clean.fq.gz	0:149.83 1:149.42	A:1908972876;C:1556853849;G:1559240564;T:1825804841;N:17136	149	149	1908972876	1556853849	1559240564	1825804841	17136	SRX12150937	SRS10130028	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93957	0.92386	0.09467	0.08944	0.66582	0.67142	0.50349	0.499	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65985	65985	SRR15859822	SRX12150936	SRS10130027	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			levonorgestrel treatment at low concentration treatment	LNG L 4	M	strain:not collected2\|isolate:whole fish12\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 4'\|BioSampleModel:Model organism or animal									LNG L 4	BL	BL	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	5_4_R1.clean.fq.gz 5_4_R2.clean.fq.gz	fastq fastq	6757301758.0	22579367.0	5 4 R1.clean.fq.gz	0:149.83 1:149.44	A:1886236851;C:1526321374;G:1529138861;T:1815587663;N:17009	149	149	1886236851	1526321374	1529138861	1815587663	17009	SRX12150936	SRS10130027	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93955	0.92322	0.09955	0.0937	0.66612	0.67056	0.4936	0.50296	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65986	65986	SRR15859823	SRX12150935	SRS10130026	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			levonorgestrel treatment at low concentration treatment	LNG L 3	AL	strain:not collected2\|isolate:whole fish11\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 3 prime\|BioSampleModel:Model organism or animal									LNG L 3	BK	BK	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	5_3_R1.clean.fq.gz 5_3_R2.clean.fq.gz	fastq fastq	6942028867.0	23178890.0	5 3 R1.clean.fq.gz	0:149.82 1:149.68	A:1895507796;C:1573477638;G:1599422601;T:1873160988;N:459844	149	149	1895507796	1573477638	1599422601	1873160988	459844	SRX12150935	SRS10130026	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.92261	0.9213	0.10308	0.10394	0.67298	0.67677	0.50615	0.5026	150	145	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65987	65987	SRR15859824	SRX12150934	SRS10130025	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Solvent control	SC2	AC	strain:not collected2\|isolate:whole fish2\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 2'\|BioSampleModel:Model organism or animal									SC2	BB	BB	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	SC_2_R1.clean.fq.gz SC_2_R2.clean.fq.gz	fastq fastq	6847074418.0	22905359.0	SC 2 R1.clean.fq.gz	0:149.58 1:149.35	A:1835075664;C:1586631096;G:1607651961;T:1817247855;N:467842	149	149	1835075664	1586631096	1607651961	1817247855	467842	SRX12150934	SRS10130025	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93172	0.93195	0.07691	0.0771	0.67265	0.67665	0.48862	0.49579	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65988	65988	SRR15859825	SRX12150933	SRS10130024	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Solvent control	SC1	AB	strain:not collected2\|isolate:whole fish1\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 1'\|BioSampleModel:Model organism or animal									SC1	BA	BA	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	SC_1_R1.clean.fq.gz SC_1_R2.clean.fq.gz	fastq fastq	7101595814.0	23743270.0	SC 1 R1.clean.fq.gz	0:149.65 1:149.45	A:1888007422;C:1656304946;G:1683234514;T:1873563589;N:485343	149	149	1888007422	1656304946	1683234514	1873563589	485343	SRX12150933	SRS10130024	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93193	0.93408	0.08101	0.08156	0.6744	0.67785	0.49761	0.49038	150	149	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65989	65989	SRR15859826	SRX12150932	SRS10130023	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			levonorgestrel treatment at low concentration treatment	LNG L 2	AK	strain:not collected2\|isolate:whole fish10\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 2'\|BioSampleModel:Model organism or animal									LNG L 2	BJ	BJ	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	5_2_R1.clean.fq.gz 5_2_R2.clean.fq.gz	fastq fastq	6978116268.0	23316955.0	5 2 R1.clean.fq.gz	0:149.72 1:149.55	A:1877413088;C:1609547451;G:1632121199;T:1858563731;N:470799	149	149	1877413088	1609547451	1632121199	1858563731	470799	SRX12150932	SRS10130023	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93086	0.93049	0.08702	0.08712	0.68357	0.68844	0.49793	0.48668	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65990	65990	SRR15859827	SRX12150931	SRS10130022	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			levonorgestrel treatment at low concentration treatment	LNG L 1	AJ	strain:not collected2\|isolate:whole fish9\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 1'\|BioSampleModel:Model organism or animal									LNG L 1	BI	BI	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	5_1_R1.clean.fq.gz 5_1_R2.clean.fq.gz	fastq fastq	6306082896.0	21075245.0	5 1 R1.clean.fq.gz	0:149.70 1:149.52	A:1679788198;C:1469939151;G:1489873755;T:1666053801;N:427991	149	149	1679788198	1469939151	1489873755	1666053801	427991	SRX12150931	SRS10130022	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93145	0.93206	0.08123	0.08188	0.67951	0.68432	0.48499	0.48763	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65991	65991	SRR15859828	SRX12150930	SRS10130021	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			dydrogesterone treatment	DDG 4	AI	strain:not collected2\|isolate:whole fish8\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 4'\|BioSampleModel:Model organism or animal									DDG 4	BH	BH	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	100_4_R1.clean.fq.gz 100_4_R2.clean.fq.gz	fastq fastq	7014679884.0	23437449.0	100 4 R1.clean.fq.gz	0:149.72 1:149.57	A:1882114669;C:1625037935;G:1641102139;T:1865959279;N:465862	149	149	1882114669	1625037935	1641102139	1865959279	465862	SRX12150930	SRS10130021	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93236	0.93264	0.08797	0.08919	0.67574	0.67965	0.50279	0.495	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65992	65992	SRR15859829	SRX12150929	SRS10130019	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			dydrogesterone treatment	DDG 3	AH	strain:not collected2\|isolate:whole fish7\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 3 prime\|BioSampleModel:Model organism or animal									DDG 3	BG	BG	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	100_3_R1.clean.fq.gz 100_3_R2.clean.fq.gz	fastq fastq	7000790030.0	23371313.0	100 3 R1.clean.fq.gz	0:149.83 1:149.72	A:1906942833;C:1592634521;G:1609492258;T:1891245267;N:475151	149	149	1906942833	1592634521	1609492258	1891245267	475151	SRX12150929	SRS10130019	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.92801	0.92781	0.09747	0.09744	0.66517	0.66776	0.50246	0.49531	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65993	65993	SRR15859830	SRX12150928	SRS10130020	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			dydrogesterone treatment	DDG 2	AG	strain:not collected2\|isolate:whole fish6\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 2'\|BioSampleModel:Model organism or animal									DDG 2	BF	BF	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	100_2_R1.clean.fq.gz 100_2_R2.clean.fq.gz	fastq fastq	7075813310.0	23625836.0	100 2 R1.clean.fq.gz	0:149.82 1:149.68	A:1918796036;C:1619755625;G:1637664383;T:1899135516;N:461750	149	149	1918796036	1619755625	1637664383	1899135516	461750	SRX12150928	SRS10130020	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.92935	0.92868	0.08886	0.08912	0.65717	0.6621	0.4843	0.49415	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65994	65994	SRR15859831	SRX12150927	SRS10130018	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			dydrogesterone treatment	DDG 1	AF	strain:not collected2\|isolate:whole fish5\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 1'\|BioSampleModel:Model organism or animal									DDG 1	BE	BE	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	100_1_R1.clean.fq.gz 100_1_R2.clean.fq.gz	fastq fastq	6740898004.0	22511996.0	100 1 R1.clean.fq.gz	0:149.79 1:149.65	A:1828418830;C:1542362815;G:1564205385;T:1805464983;N:445991	149	149	1828418830	1542362815	1564205385	1805464983	445991	SRX12150927	SRS10130018	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.92893	0.92836	0.08577	0.08614	0.67639	0.68077	0.48573	0.49544	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65995	65995	SRR15859832	SRX12150926	SRS10130016	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Solvent control	SC4	AE	strain:not collected2\|isolate:whole fish4\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 4'\|BioSampleModel:Model organism or animal									SC4	BD	BD	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	SC_4_R1.clean.fq.gz SC_4_R2.clean.fq.gz	fastq fastq	6051468288.0	20209797.0	SC 4 R1.clean.fq.gz	0:149.80 1:149.63	A:1652651735;C:1373191643;G:1392749062;T:1632474997;N:400851	149	149	1652651735	1373191643	1392749062	1632474997	400851	SRX12150926	SRS10130016	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.92672	0.92501	0.09038	0.09121	0.66259	0.66565	0.49636	0.49698	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65996	65996	SRR15859833	SRX12150925	SRS10130017	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Levonorgestrel at high concentration and dydrogesterone mixturestreatment	DDG+LNG H 1	AY	strain:not collected2\|isolate:whole fish24\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 4'\|BioSampleModel:Model organism or animal									DDG+LNG H 1	BX	BX	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	100_50_4_R1.clean.fq.gz 100_50_4_R2.clean.fq.gz	fastq fastq	6861007764.0	22938186.0	100 50 4 R1.clean.fq.gz	0:149.76 1:149.35	A:1881600852;C:1578987219;G:1582313999;T:1818088269;N:17425	149	149	1881600852	1578987219	1582313999	1818088269	17425	SRX12150925	SRS10130017	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93777	0.92424	0.09796	0.0931	0.66182	0.66746	0.49608	0.49787	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65997	65997	SRR15859834	SRX12150924	SRS10130015	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Levonorgestrel at high concentration and dydrogesterone mixtures treatment	DDG+LNG H 1	AX	strain:not collected2\|isolate:whole fish23\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 3 prime\|BioSampleModel:Model organism or animal									DDG+LNG H 1	BW	BW	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	100_50_3_R1.clean.fq.gz 100_50_3_R2.clean.fq.gz	fastq fastq	6448167527.0	21546554.0	100 50 3 R1.clean.fq.gz	0:149.84 1:149.43	A:1776900923;C:1483436670;G:1478517308;T:1709296399;N:16227	149	149	1776900923	1483436670	1478517308	1709296399	16227	SRX12150924	SRS10130015	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.94114	0.92751	0.08812	0.0842	0.66557	0.67052	0.49525	0.49796	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65998	65998	SRR15859835	SRX12150923	SRS10130014	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Levonorgestrel at high concentration and dydrogesterone mixtures treatment	DDG+LNG H 1	AW	strain:not collected2\|isolate:whole fish22\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 2'\|BioSampleModel:Model organism or animal									DDG+LNG H 1	BV	BV	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	100_50_2_R1.clean.fq.gz 100_50_2_R2.clean.fq.gz	fastq fastq	6097050612.0	20374795.0	100 50 2 R1.clean.fq.gz	0:149.83 1:149.42	A:1697937652;C:1387399999;G:1387536896;T:1624160680;N:15385	149	149	1697937652	1387399999	1387536896	1624160680	15385	SRX12150923	SRS10130014	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93921	0.92457	0.09156	0.08703	0.677	0.68268	0.51381	0.51338	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65999	65999	SRR15859836	SRX12150922	SRS10130013	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Levonorgestrel at high concentration and dydrogesterone mixtures treatment	DDG+LNG H 1	AV	strain:not collected2\|isolate:whole fish21\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 1'\|BioSampleModel:Model organism or animal									DDG+LNG H 1	BU	BU	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	100_50_1_R1.clean.fq.gz 100_50_1_R2.clean.fq.gz	fastq fastq	6200464490.0	20718210.0	100 50 1 R1.clean.fq.gz	0:149.84 1:149.44	A:1722773998;C:1411958803;G:1410364088;T:1655351787;N:15814	149	149	1722773998	1411958803	1410364088	1655351787	15814	SRX12150922	SRS10130013	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.94019	0.92317	0.09428	0.08799	0.66192	0.66813	0.50339	0.50384	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66000	66000	SRR15859837	SRX12150921	SRS10130012	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Solvent control	SC3	AD	strain:not collected2\|isolate:whole fish3\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 3 prime\|BioSampleModel:Model organism or animal									SC3	BC	BC	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	SC_3_R1.clean.fq.gz SC_3_R2.clean.fq.gz	fastq fastq	6744019219.0	22522868.0	SC 3 R1.clean.fq.gz	0:149.81 1:149.62	A:1832736009;C:1540439892;G:1560536404;T:1809859936;N:446978	149	149	1832736009	1540439892	1560536404	1809859936	446978	SRX12150921	SRS10130012	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.92908	0.92831	0.08407	0.08413	0.66748	0.67332	0.49151	0.50363	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66001	66001	SRR15859838	SRX12150920	SRS10130011	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Levonorgestrel at low concentration and dydrogesterone mixtures treatment	DDG+LNG L 4	AU	strain:not collected2\|isolate:whole fish20\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 4'\|BioSampleModel:Model organism or animal									DDG+LNG L 4	BT	BT	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	100_5_4_R1.clean.fq.gz 100_5_4_R2.clean.fq.gz	fastq fastq	6698715338.0	22386760.0	100 5 4 R1.clean.fq.gz	0:149.82 1:149.41	A:1854944489;C:1532319316;G:1533554376;T:1777880466;N:16691	149	149	1854944489	1532319316	1533554376	1777880466	16691	SRX12150920	SRS10130011	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93948	0.92423	0.09198	0.08752	0.66967	0.67513	0.49914	0.49616	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66002	66002	SRR15859839	SRX12150919	SRS10130010	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Levonorgestrel at low concentration and dydrogesterone mixtures treatment	DDG+LNG L 3	AT	strain:not collected2\|isolate:whole fish19\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 3 prime\|BioSampleModel:Model organism or animal									DDG+LNG L 3	BS	BS	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	100_5_3_R1.clean.fq.gz 100_5_3_R2.clean.fq.gz	fastq fastq	6731263096.0	22494392.0	100 5 3 R1.clean.fq.gz	0:149.82 1:149.42	A:1853865687;C:1546635036;G:1549005691;T:1781740007;N:16675	149	149	1853865687	1546635036	1549005691	1781740007	16675	SRX12150919	SRS10130010	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.94161	0.92699	0.09368	0.08881	0.67146	0.67671	0.49075	0.4916	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66003	66003	SRR15859840	SRX12150918	SRS10130009	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Levonorgestrel at low concentration and dydrogesterone mixtures treatment	DDG+LNG L 2	AS	strain:not collected2\|isolate:whole fish18\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 2'\|BioSampleModel:Model organism or animal									DDG+LNG L 2	BR	BR	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	100_5_2_R1.clean.fq.gz 100_5_2_R2.clean.fq.gz	fastq fastq	6856677730.0	22942302.0	100 5 2 R1.clean.fq.gz	0:149.63 1:149.23	A:1861833177;C:1593702006;G:1601437245;T:1799688067;N:17235	149	149	1861833177	1593702006	1601437245	1799688067	17235	SRX12150918	SRS10130009	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.94226	0.93085	0.08471	0.08039	0.67677	0.68191	0.48927	0.47969	150	148	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66004	66004	SRR15859841	SRX12150917	SRS10130007	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Levonorgestrel at low concentration and dydrogesterone mixtures treatment	DDG+LNG L 1	AR	strain:not collected2\|isolate:whole fish17\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 1'\|BioSampleModel:Model organism or animal									DDG+LNG L 1	BQ	BQ	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	100_5_1_R1.clean.fq.gz 100_5_1_R2.clean.fq.gz	fastq fastq	6734596961.0	22519168.0	100 5 1 R1.clean.fq.gz	0:149.72 1:149.34	A:1835515639;C:1562058332;G:1561380426;T:1775625709;N:16855	149	149	1835515639	1562058332	1561380426	1775625709	16855	SRX12150917	SRS10130007	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.94108	0.92768	0.09123	0.08716	0.66967	0.6747	0.50584	0.50347	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66005	66005	SRR15859842	SRX12150916	SRS10130006	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			levonorgestrel treatment at high concentration treatment	LNG H 4	AQ	strain:not collected2\|isolate:whole fish16\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 4'\|BioSampleModel:Model organism or animal									LNG H 4	BP	BP	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	50_4_R1.clean.fq.gz 50_4_R2.clean.fq.gz	fastq fastq	7033955938.0	23502039.0	50 4 R1.clean.fq.gz	0:149.84 1:149.46	A:1939982949;C:1612770444;G:1610988374;T:1870196531;N:17640	149	149	1939982949	1612770444	1610988374	1870196531	17640	SRX12150916	SRS10130006	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.94099	0.92749	0.09644	0.09215	0.67261	0.67838	0.49766	0.49584	150	149	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66006	66006	SRR15859843	SRX12150915	SRS10130008	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			levonorgestrel treatment at high concentration treatment	LNG H 3	AP	strain:not collected2\|isolate:whole fish15\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 3 prime\|BioSampleModel:Model organism or animal									LNG H 3	BO	BO	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	50_3_R1.clean.fq.gz 50_3_R2.clean.fq.gz	fastq fastq	5819952570.0	19444342.0	50 3 R1.clean.fq.gz	0:149.86 1:149.46	A:1615559082;C:1328350353;G:1325535770;T:1550492661;N:14704	149	149	1615559082	1328350353	1325535770	1550492661	14704	SRX12150915	SRS10130008	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.9397	0.92495	0.09375	0.08838	0.669	0.67338	0.50535	0.5146	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66007	66007	SRR15859844	SRX12150914	SRS10130005	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			levonorgestrel treatment at high concentration treatment	LNG H 2	AO	strain:not collected2\|isolate:whole fish14\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 2'\|BioSampleModel:Model organism or animal									LNG H 2	BN	BN	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743	50_2_R1.clean.fq.gz 50_2_R2.clean.fq.gz	fastq fastq	5888497480.0	19673249.0	50 2 R1.clean.fq.gz	0:149.84 1:149.47	A:1638307115;C:1337036459;G:1335389572;T:1577749137;N:15197	149	149	1638307115	1337036459	1335389572	1577749137	15197	SRX12150914	SRS10130005	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.9395	0.92471	0.09382	0.08964	0.66785	0.67144	0.50388	0.5077	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
67043	67043	SRR17017805	SRX13207904	SRS11133999	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.		pubmed:35114580		Aldh 2.1 / KO la3	GSM5701222	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	Aldh 2.1 / KO la3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	GSM5701222	GSM5701222: Aldh 2.1 / KO la3; Danio rerio; RNA Seq	GSM5701222 r1	GSM5701222	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444	3-KOla3_1.fq.gz 3-KOla3_2.fq.gz	fastq fastq	4974883400.0	49748834.0	GSM5701222 r1	0:100 1:100	A:1325503000;C:1131322113;G:1183075417;T:1334982870;N:0	100	100	1325503000	1131322113	1183075417	1334982870	0	SRX13207904	SRS11133999	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95156		0.10103		0.68917		0.50967		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67044	67044	SRR17017806	SRX13207903	SRS11133998	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.		pubmed:35114580		Aldh 2.1 / KO la2	GSM5701221	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	Aldh 2.1 / KO la2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	GSM5701221	GSM5701221: Aldh 2.1 / KO la2; Danio rerio; RNA Seq	GSM5701221 r1	GSM5701221	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444	2-KOla2_1.fq.gz 2-KOla2_2.fq.gz	fastq fastq	4993502200.0	49935022.0	GSM5701221 r1	0:100 1:100	A:1337290403;C:1130744731;G:1181303599;T:1344163467;N:0	100	100	1337290403	1130744731	1181303599	1344163467	0	SRX13207903	SRS11133998	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95056		0.09273		0.69207		0.5213		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67045	67045	SRR17017807	SRX13207902	SRS11133997	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.		pubmed:35114580		Aldh 2.1 / KO la1	GSM5701220	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	Aldh 2.1 / KO la1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	GSM5701220	GSM5701220: Aldh 2.1 / KO la1; Danio rerio; RNA Seq	GSM5701220 r1	GSM5701220	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444	1-KOla1_1.fq.gz 1-KOla1_2.fq.gz	fastq fastq	4982824800.0	49828248.0	GSM5701220 r1	0:100 1:100	A:1318751230;C:1142967126;G:1194575929;T:1326530515;N:0	100	100	1318751230	1142967126	1194575929	1326530515	0	SRX13207902	SRS11133997	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95468		0.09398		0.67917		0.50026		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67046	67046	SRR17017808	SRX13207901	SRS11133996	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.		pubmed:35114580		Aldh 2.1 +/+ WT la6	GSM5701229	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	Aldh 2.1 +/+ WT la6	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	GSM5701229	GSM5701229: Aldh 2.1 +/+ WT la6; Danio rerio; RNA Seq	GSM5701229 r1	GSM5701229	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444	10-WTla6_1.fq.gz 10-WTla6_2.fq.gz	fastq fastq	4990544400.0	49905444.0	GSM5701229 r1	0:100 1:100	A:1342332744;C:1123081871;G:1174336584;T:1350793201;N:0	100	100	1342332744	1123081871	1174336584	1350793201	0	SRX13207901	SRS11133996	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.94932		0.10692		0.69246		0.5131		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67047	67047	SRR17017809	SRX13207900	SRS11133995	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.		pubmed:35114580		Aldh 2.1 +/+ WT la5	GSM5701228	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	Aldh 2.1 +/+ WT la5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	GSM5701228	GSM5701228: Aldh 2.1 +/+ WT la5; Danio rerio; RNA Seq	GSM5701228 r1	GSM5701228	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444	9-WTla5_1.fq.gz 9-WTla5_2.fq.gz	fastq fastq	4990444600.0	49904446.0	GSM5701228 r1	0:100 1:100	A:1347054785;C:1118741393;G:1169087601;T:1355560821;N:0	100	100	1347054785	1118741393	1169087601	1355560821	0	SRX13207900	SRS11133995	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.94929		0.10427		0.69925		0.51838		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67048	67048	SRR17017810	SRX13207899	SRS11133994	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.		pubmed:35114580		Aldh 2.1 +/+ WT la3	GSM5701227	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	Aldh 2.1 +/+ WT la3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	GSM5701227	GSM5701227: Aldh 2.1 +/+ WT la3; Danio rerio; RNA Seq	GSM5701227 r1	GSM5701227	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444	8-WTla3_1.fq.gz 8-WTla3_2.fq.gz	fastq fastq	4986064600.0	49860646.0	GSM5701227 r1	0:100 1:100	A:1358143440;C:1107981393;G:1154357851;T:1365581916;N:0	100	100	1358143440	1107981393	1154357851	1365581916	0	SRX13207899	SRS11133994	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95037		0.10323		0.69499		0.54725		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67049	67049	SRR17017811	SRX13207898	SRS11133993	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.		pubmed:35114580		Aldh 2.1 +/+ WT la2	GSM5701226	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	Aldh 2.1 +/+ WT la2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	GSM5701226	GSM5701226: Aldh 2.1 +/+ WT la2; Danio rerio; RNA Seq	GSM5701226 r1	GSM5701226	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444	7-WTla2_1.fq.gz 7-WTla2_2.fq.gz	fastq fastq	4977068600.0	49770686.0	GSM5701226 r1	0:100 1:100	A:1341174868;C:1117869236;G:1167898570;T:1350125926;N:0	100	100	1341174868	1117869236	1167898570	1350125926	0	SRX13207898	SRS11133993	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.94822		0.11063		0.69514		0.51197		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67050	67050	SRR17017812	SRX13207897	SRS11133992	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.		pubmed:35114580		Aldh 2.1 +/+ WT la1	GSM5701225	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	Aldh 2.1 +/+ WT la1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	GSM5701225	GSM5701225: Aldh 2.1 +/+ WT la1; Danio rerio; RNA Seq	GSM5701225 r1	GSM5701225	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444	6-WTla1_1.fq.gz 6-WTla1_2.fq.gz	fastq fastq	4937740400.0	49377404.0	GSM5701225 r1	0:100 1:100	A:1322363529;C:1116877989;G:1169055598;T:1329443284;N:0	100	100	1322363529	1116877989	1169055598	1329443284	0	SRX13207897	SRS11133992	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95215		0.10081		0.69534		0.51784		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67051	67051	SRR17017813	SRX13207896	SRS11133991	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.		pubmed:35114580		Aldh 2.1 / KO la6	GSM5701224	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	Aldh 2.1 / KO la6	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	GSM5701224	GSM5701224: Aldh 2.1 / KO la6; Danio rerio; RNA Seq	GSM5701224 r1	GSM5701224	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444	5-KOla6_1.fq.gz 5-KOla6_2.fq.gz	fastq fastq	4875673200.0	48756732.0	GSM5701224 r1	0:100 1:100	A:1325527276;C:1084173307;G:1132675639;T:1333296978;N:0	100	100	1325527276	1084173307	1132675639	1333296978	0	SRX13207896	SRS11133991	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.94517		0.10711		0.69548		0.47813		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67052	67052	SRR17017814	SRX13207895	SRS11133990	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.		pubmed:35114580		Aldh 2.1 / KO la5	GSM5701223	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	Aldh 2.1 / KO la5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	GSM5701223	GSM5701223: Aldh 2.1 / KO la5; Danio rerio; RNA Seq	GSM5701223 r1	GSM5701223	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444	4-KOla5_1.fq.gz 4-KOla5_2.fq.gz	fastq fastq	4965270200.0	49652702.0	GSM5701223 r1	0:100 1:100	A:1348940910;C:1104562620;G:1155269060;T:1356497610;N:0	100	100	1348940910	1104562620	1155269060	1356497610	0	SRX13207895	SRS11133990	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.94849		0.11019		0.69988		0.53589		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67884	67884	SRR17868935	SRX14028691	SRS11864778	SRP358022	PRJNA793391	Effects of acute exposure to nano silver on zebrafish larvae	PRJNA793391	Other	Sliver nanoparticles AgNPs are widely used for industry agriculture and medicals which potentially result in adverse effects for human health and aquatic environment. In this present study we investigated the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.					C4 1	strain:danio rerio AgNPs4\|breed:zebrafish10\|age:3 day\|sex:pooled male and female\|tissue:fish\|BioSampleModel:Model organism or animal									DANIO RERIO 4 1	AG 4 1	AG 4 1	treatment7			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP358022	C4-1_1.fq.gz C4-1_2.fq.gz	fastq fastq	6830916900.0	45539446.0	C4 1 1.fq.gz	0:150 1:150	A:2011586443;C:1405775454;G:1388504965;T:2024992696;N:57342	150	150	2011586443	1405775454	1388504965	2024992696	57342	SRX14028691	SRS11864778	SRA1350965	Center for Neuroscience\|Shantou university	Center for Neuroscience	1	0.92344		0.21929		0.71043		0.46315		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-03	Larval	Larval	Whole Organism	All anatomical structures
67885	67885	SRR17868936	SRX14028690	SRS11864777	SRP358022	PRJNA793391	Effects of acute exposure to nano silver on zebrafish larvae	PRJNA793391	Other	Sliver nanoparticles AgNPs are widely used for industry agriculture and medicals which potentially result in adverse effects for human health and aquatic environment. In this present study we investigated the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.					C2 3	strain:danio rerio AgNPs2\|breed:zebrafish9\|age:3 day\|sex:pooled male and female\|tissue:fish\|BioSampleModel:Model organism or animal									DANIO RERIO 2 3	AG 2 3	AG 2 3	treatment6			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP358022	C2-3_1.fq.gz C2-3_2.fq.gz	fastq fastq	6782959200.0	45219728.0	C2 3 1.fq.gz	0:150 1:150	A:1949560199;C:1443524899;G:1428814233;T:1960921903;N:137966	150	150	1949560199	1443524899	1428814233	1960921903	137966	SRX14028690	SRS11864777	SRA1350965	Center for Neuroscience\|Shantou university	Center for Neuroscience	1	0.93181		0.17739		0.6927		0.50528		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-03	Larval	Larval	Whole Organism	All anatomical structures
67886	67886	SRR17868937	SRX14028689	SRS11864776	SRP358022	PRJNA793391	Effects of acute exposure to nano silver on zebrafish larvae	PRJNA793391	Other	Sliver nanoparticles AgNPs are widely used for industry agriculture and medicals which potentially result in adverse effects for human health and aquatic environment. In this present study we investigated the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.					C2 2	strain:danio rerio AgNPs2\|breed:zebrafish8\|age:3 day\|sex:pooled male and female\|tissue:fish\|BioSampleModel:Model organism or animal									DANIO RERIO 2 2	AG 2 2	AG 2 2	treatment5			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP358022	C2-2_1.fq.gz C2-2_2.fq.gz	fastq fastq	6817863300.0	45452422.0	C2 2 1.fq.gz	0:150 1:150	A:1964890519;C:1446826412;G:1428708103;T:1977297439;N:140827	150	150	1964890519	1446826412	1428708103	1977297439	140827	SRX14028689	SRS11864776	SRA1350965	Center for Neuroscience\|Shantou university	Center for Neuroscience	1	0.93045		0.17846		0.69116		0.48565		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-03	Larval	Larval	Whole Organism	All anatomical structures

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