metadata: run_metadata: 296 rows where devstage_curation_coarse = "Larval" and experiment.platform = "BGISEQ"

296 rows where devstage_curation_coarse = "Larval" and experiment.platform = "BGISEQ"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.description	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
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
31825	31825	SRR28700412	SRX24268115	SRS21034395	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				PN 2	isolate:PN2\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 2\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish	PN 2	PN 2	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894		PN_2_1.fq.gz PN_2_2.fq.gz	fastq fastq	6385048200.0	21283494.0	PN 2 1.fq.gz	0:150 1:150	A:1722127999;C:1463645587;G:1483173818;T:1716100796;N:0	150	150	1722127999	1463645587	1483173818	1716100796	0	SRX24268115	SRS21034395			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31826	31826	SRR28700413	SRX24268114	SRS21034397	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				PN 1	isolate:PN1\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 1\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish	PN 1	PN 1	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894		PN_1_1.fq.gz PN_1_2.fq.gz	fastq fastq	6692894100.0	22309647.0	PN 1 1.fq.gz	0:150 1:150	A:1827107021;C:1513034624;G:1533077624;T:1819674831;N:0	150	150	1827107021	1513034624	1533077624	1819674831	0	SRX24268114	SRS21034397			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31827	31827	SRR28700414	SRX24268113	SRS21034396	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				EC 4	isolate:EC4\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 4\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish	EC 4	EC 4	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894		EC_4_1.fq.gz EC_4_2.fq.gz	fastq fastq	6688857000.0	22296190.0	EC 4 1.fq.gz	0:150 1:150	A:1820989545;C:1516814697;G:1537970654;T:1813082104;N:0	150	150	1820989545	1516814697	1537970654	1813082104	0	SRX24268113	SRS21034396			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31828	31828	SRR28700415	SRX24268112	SRS21034392	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				EC 3	isolate:EC3\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 3\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish	EC 3	EC 3	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894		EC_3_1.fq.gz EC_3_2.fq.gz	fastq fastq	6696553800.0	22321846.0	EC 3 1.fq.gz	0:150 1:150	A:1821249100;C:1520587242;G:1541238550;T:1813478908;N:0	150	150	1821249100	1520587242	1541238550	1813478908	0	SRX24268112	SRS21034392			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31829	31829	SRR28700416	SRX24268111	SRS21034391	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				EC 2	isolate:EC2\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 2\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish	EC 2	EC 2	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894		EC_2_1.fq.gz EC_2_2.fq.gz	fastq fastq	6702179400.0	22340598.0	EC 2 1.fq.gz	0:150 1:150	A:1816692261;C:1527379142;G:1547365810;T:1810742187;N:0	150	150	1816692261	1527379142	1547365810	1810742187	0	SRX24268111	SRS21034391			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31830	31830	SRR28700417	SRX24268110	SRS21034390	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				EC 1	isolate:EC1\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 1\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish	EC 1	EC 1	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894		EC_1_1.fq.gz EC_1_2.fq.gz	fastq fastq	6686053500.0	22286845.0	EC 1 1.fq.gz	0:150 1:150	A:1812022780;C:1524359858;G:1544847441;T:1804823421;N:0	150	150	1812022780	1524359858	1544847441	1804823421	0	SRX24268110	SRS21034390			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31831	31831	SRR28700418	SRX24268109	SRS21034388	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				Control 4	isolate:con4\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 4\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish	Control 4	Control 4	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894		Control_4_1.fq.gz Control_4_2.fq.gz	fastq fastq	6669700500.0	22232335.0	Control 4 1.fq.gz	0:150 1:150	A:1804178265;C:1523547469;G:1543839484;T:1798135282;N:0	150	150	1804178265	1523547469	1543839484	1798135282	0	SRX24268109	SRS21034388			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31832	31832	SRR28700419	SRX24268108	SRS21034387	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				Control 3	isolate:con3\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 3\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish	Control 3	Control 3	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894		Control_3_1.fq.gz Control_3_2.fq.gz	fastq fastq	6683518800.0	22278396.0	Control 3 1.fq.gz	0:150 1:150	A:1808495506;C:1525725204;G:1545930043;T:1803368047;N:0	150	150	1808495506	1525725204	1545930043	1803368047	0	SRX24268108	SRS21034387			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31833	31833	SRR28700420	SRX24268107	SRS21034386	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				PN 4	isolate:PN4\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 4\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish	PN 4	PN 4	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894		PN_4_1.fq.gz PN_4_2.fq.gz	fastq fastq	6649316100.0	22164387.0	PN 4 1.fq.gz	0:150 1:150	A:1809816121;C:1508072480;G:1528272654;T:1803154845;N:0	150	150	1809816121	1508072480	1528272654	1803154845	0	SRX24268107	SRS21034386			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31834	31834	SRR28700421	SRX24268106	SRS21034389	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				PN 3	isolate:PN3\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 3\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish	PN 3	PN 3	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894		PN_3_1.fq.gz PN_3_2.fq.gz	fastq fastq	6616113900.0	22053713.0	PN 3 1.fq.gz	0:150 1:150	A:1802283686;C:1499008018;G:1519150002;T:1795672194;N:0	150	150	1802283686	1499008018	1519150002	1795672194	0	SRX24268106	SRS21034389			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31835	31835	SRR28700422	SRX24268105	SRS21034385	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				Control 2	isolate:con2\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 2\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish	Control 2	Control 2	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894		Control_2_1.fq.gz Control_2_2.fq.gz	fastq fastq	6701719200.0	22339064.0	Control 2 1.fq.gz	0:150 1:150	A:1812352260;C:1531672703;G:1551377072;T:1806317165;N:0	150	150	1812352260	1531672703	1551377072	1806317165	0	SRX24268105	SRS21034385			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
31836	31836	SRR28700423	SRX24268104	SRS21034384	SRP501894	PRJNA1100624	Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis	PRJNA1100624	Other	Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP.				Control 1	isolate:con1\|age:9dpf\|collection date:2023 07 13\|geo loc name:China:Hubei Xiangyang\|sex:not collected\|tissue:animal sample\|replicate:replicate = biological replicate 1\|BioSampleModel:Model organism or animal								RNA Seq of zebrafish	Control 1	Control 1	Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library.		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP501894		Control_1_1.fq.gz Control_1_2.fq.gz	fastq fastq	6720214500.0	22400715.0	Control 1 1.fq.gz	0:150 1:150	A:1814883015;C:1537948710;G:1559376116;T:1808006659;N:0	150	150	1814883015	1537948710	1559376116	1808006659	0	SRX24268104	SRS21034384			Xiangyang No.1 People's Hospital, Hubei University of Medicine												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-04-15	Larval	Larval	Undetermined	Undetermined
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
35980	35980	SRR33796117	SRX29017800	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal								RNA Seq of Danio rerio: embryo whole body	P2000 1	P2000 1	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371		P2000_1_1.fq.gz P2000_1_2.fq.gz	fastq fastq	6682157100.0	22273857.0	P2000 1 1.fq.gz	0:150 1:150	A:1750970707;C:1591819991;G:1593263349;T:1746103053;N:0	150	150	1750970707	1591819991	1593263349	1746103053	0	SRX29017800	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35981	35981	SRR33796118	SRX29017799	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal								RNA Seq of Danio rerio: embryo whole body	P1000 3	P1000 3	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371		P1000_3_1.fq.gz P1000_3_2.fq.gz	fastq fastq	6596943000.0	21989810.0	P1000 3 1.fq.gz	0:150 1:150	A:1725528987;C:1574140428;G:1576046656;T:1721226929;N:0	150	150	1725528987	1574140428	1576046656	1721226929	0	SRX29017799	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35982	35982	SRR33796119	SRX29017798	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal								RNA Seq of Danio rerio: embryo whole body	P1000 2	P1000 2	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371		P1000_2_1.fq.gz P1000_2_2.fq.gz	fastq fastq	6677331000.0	22257770.0	P1000 2 1.fq.gz	0:150 1:150	A:1758237128;C:1582217484;G:1584403835;T:1752472553;N:0	150	150	1758237128	1582217484	1584403835	1752472553	0	SRX29017798	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35983	35983	SRR33796120	SRX29017797	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal								RNA Seq of Danio rerio: embryo whole body	P1000 1	P1000 1	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371		P1000_1_1.fq.gz P1000_1_2.fq.gz	fastq fastq	6771926100.0	22573087.0	P1000 1 1.fq.gz	0:150 1:150	A:1788071352;C:1600799117;G:1602227700;T:1780827931;N:0	150	150	1788071352	1600799117	1602227700	1780827931	0	SRX29017797	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35984	35984	SRR33796121	SRX29017796	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal								RNA Seq of Danio rerio: embryo whole body	P500 3	P500 3	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371		P500_3_1.fq.gz P500_3_2.fq.gz	fastq fastq	6691956300.0	22306521.0	P500 3 1.fq.gz	0:150 1:150	A:1763763611;C:1584417511;G:1585842124;T:1757933054;N:0	150	150	1763763611	1584417511	1585842124	1757933054	0	SRX29017796	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35985	35985	SRR33796122	SRX29017795	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal								RNA Seq of Danio rerio: embryo whole body	P500 2	P500 2	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371		P500_2_1.fq.gz P500_2_2.fq.gz	fastq fastq	6720858300.0	22402861.0	P500 2 1.fq.gz	0:150 1:150	A:1752279513;C:1609781801;G:1611483135;T:1747313851;N:0	150	150	1752279513	1609781801	1611483135	1747313851	0	SRX29017795	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35986	35986	SRR33796123	SRX29017794	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal								RNA Seq of Danio rerio: embryo whole body	P500 1	P500 1	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371		P500_1_1.fq.gz P500_1_2.fq.gz	fastq fastq	6820862100.0	22736207.0	P500 1 1.fq.gz	0:150 1:150	A:1812260874;C:1601860387;G:1602603805;T:1804137034;N:0	150	150	1812260874	1601860387	1602603805	1804137034	0	SRX29017794	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35987	35987	SRR33796124	SRX29017793	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal								RNA Seq of Danio rerio: embryo whole body	MX 3	MX 3	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371		MX_3_1.fq.gz MX_3_2.fq.gz	fastq fastq	6795327600.0	22651092.0	MX 3 1.fq.gz	0:150 1:150	A:1768016462;C:1630727253;G:1632326554;T:1764257331;N:0	150	150	1768016462	1630727253	1632326554	1764257331	0	SRX29017793	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35988	35988	SRR33796125	SRX29017792	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal								RNA Seq of Danio rerio: embryo whole body	P2000 3	P2000 3	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371		P2000_3_1.fq.gz P2000_3_2.fq.gz	fastq fastq	6620786400.0	22069288.0	P2000 3 1.fq.gz	0:150 1:150	A:1736628496;C:1574653543;G:1577791512;T:1731712849;N:0	150	150	1736628496	1574653543	1577791512	1731712849	0	SRX29017792	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35989	35989	SRR33796126	SRX29017791	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal								RNA Seq of Danio rerio: embryo whole body	P2000 2	P2000 2	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371		P2000_2_1.fq.gz P2000_2_2.fq.gz	fastq fastq	6613914000.0	22046380.0	P2000 2 1.fq.gz	0:150 1:150	A:1733574880;C:1575483348;G:1576793005;T:1728062767;N:0	150	150	1733574880	1575483348	1576793005	1728062767	0	SRX29017791	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35990	35990	SRR33796127	SRX29017790	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal								RNA Seq of Danio rerio: embryo whole body	MX 2	MX 2	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371		MX_2_1.fq.gz MX_2_2.fq.gz	fastq fastq	6769929300.0	22566431.0	MX 2 1.fq.gz	0:150 1:150	A:1773923783;C:1611785261;G:1615111695;T:1769108561;N:0	150	150	1773923783	1611785261	1615111695	1769108561	0	SRX29017790	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
35991	35991	SRR33796128	SRX29017789	SRS25233880	SRP589371	PRJNA1256770	Danio rerio Raw sequence reads	PRJNA1256770	Whole Genome Sequencing	Transcriptome sequencing was used to identify genes regulated by the polysaccharides that affect the immune activity of zebrafish.			Model organism or animal sample from Danio rerio	Zebrafish treatment with polysaccharides	strain:transgenic neutrophil green fluorescent MPX\|age:3 dpf\|dev stage:embryo\|collection date:2024 05 01\|geo loc name:China: Zhejiang\|sex:pooled male and female\|tissue:whole body\|disease:Immunosuppression\|MX:control sample\|P500:immune suppression model treated with 500 ug/mL polysaccharide\|P1000:immune suppression model treated with 1000 ug/mL polysaccharide\|P2000:immune suppression model treated with 2000 ug/mL polysaccharide\|BioSampleModel:Model organism or animal								RNA Seq of Danio rerio: embryo whole body	MX 1	MX 1	Total RNA was extracted from zebrafish tissue using TRIzol reagent according to the manufacturer's protocol. RNA integrity was verified using an Agilent 2100 Bioanalyzer. mRNA was enriched using polyA selection and fragmented. First and second strand cDNA synthesis was performed followed by end repair A tailing and adapter ligation. The library was amplified by PCR and sequenced using the BGISEQ MGISEQ 2000RS platform with paired end 150 bp reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA_randomPriming	PAIRED	BGISEQ	MGISEQ-2000RS	SRP589371		MX_1_1.fq.gz MX_1_2.fq.gz	fastq fastq	6715295400.0	22384318.0	MX 1 1.fq.gz	0:150 1:150	A:1774590051;C:1584963102;G:1587348964;T:1768393283;N:0	150	150	1774590051	1584963102	1587348964	1768393283	0	SRX29017789	SRS25233880	SRA2141272	West Anhui Universiaty\|College of Biotechnology and Pharmaceutical Engine	West Anhui Universiaty												B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2025-06-02	Larval	Larval	Trunk	Surface Structure
52210	52210	SRR9021058	SRX5799154	SRS4730324	SRP195685	PRJNA541367	Global transcriptomic analysis of zebrafish glucagon receptor mutant	PRJNA541367	Other	We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.				WT 1	replicate:biological replicate 1\|strain:AB\|age:7 days\|sex:not applicable\|tissue:total\|BioSampleModel:Model organism or animal								Diano rerio transcriptome	WT 1 20190506 1	WT 1 20190506 1	RNA seq of WT Diano rerio		RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	BGISEQ	BGISEQ-500	SRP195685	loader:fastq load.py	WT1.1.fq	fastq	1094498950.0	21889979.0	WT1.1.fq	0:50	A:291195764;C:255539280;G:262638316;T:284737693;N:387897	50		291195764	255539280	262638316	284737693	387897	SRX5799154	SRS4730324	SRA883435	Xiamen University\|School of Pharmaceutical Sciences	Xiamen University	1	0.94195		0.09713		0.66689		0.47749		50		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-01-18	Larval	Larval	Undetermined	Undetermined
52211	52211	SRR9021059	SRX5799153	SRS4730323	SRP195685	PRJNA541367	Global transcriptomic analysis of zebrafish glucagon receptor mutant	PRJNA541367	Other	We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.				WT 2	replicate:biological replicate 2\|strain:AB\|age:7 days\|sex:not applicable\|tissue:total\|BioSampleModel:Model organism or animal								Diano rerio transcriptome	WT 2 20190506 2	WT 2 20190506 2	RNA seq of WT Diano rerio		RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	BGISEQ	BGISEQ-500	SRP195685	loader:fastq load.py	WT2.1.fq	fastq	1095133200.0	21902664.0	WT2.1.fq	0:50	A:290594757;C:255644044;G:259681140;T:288014102;N:1199157	50		290594757	255644044	259681140	288014102	1199157	SRX5799153	SRS4730323	SRA883435	Xiamen University\|School of Pharmaceutical Sciences	Xiamen University	1	0.93368		0.09166		0.67085		0.46523		50		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-01-18	Larval	Larval	Undetermined	Undetermined
52212	52212	SRR9021060	SRX5799152	SRS4730322	SRP195685	PRJNA541367	Global transcriptomic analysis of zebrafish glucagon receptor mutant	PRJNA541367	Other	We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.				WT 3	replicate:biological replicate 3\|strain:AB\|age:7 days\|sex:not applicable\|tissue:total\|BioSampleModel:Model organism or animal								Diano rerio transcriptome	WT 3 20190506 3	WT 3 20190506 3	RNA seq of WT Diano rerio		RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	BGISEQ	BGISEQ-500	SRP195685	loader:fastq load.py	WT3.1.fq	fastq	1096083900.0	21921678.0	WT3.1.fq	0:50	A:290332094;C:256993500;G:263043956;T:285349722;N:364628	50		290332094	256993500	263043956	285349722	364628	SRX5799152	SRS4730322	SRA883435	Xiamen University\|School of Pharmaceutical Sciences	Xiamen University	1	0.94147		0.10157		0.66135		0.47301		50		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-01-18	Larval	Larval	Undetermined	Undetermined
52213	52213	SRR9021061	SRX5799151	SRS4730320	SRP195685	PRJNA541367	Global transcriptomic analysis of zebrafish glucagon receptor mutant	PRJNA541367	Other	We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.				gcgr 1	replicate:biological replicate 1\|strain:AB\|age:7 days\|sex:not applicable\|tissue:total\|BioSampleModel:Model organism or animal								Diano rerio transcriptome	gcgr 1 20190506 1	gcgr 1 20190506 1	RNA seq of Diano rerio with gcgr mutant		RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	BGISEQ	BGISEQ-500	SRP195685	loader:fastq load.py	gcgr1.1.fq	fastq	1096307200.0	21926144.0	gcgr1.1.fq	0:50	A:288839446;C:258297625;G:264630675;T:284199738;N:339716	50		288839446	258297625	264630675	284199738	339716	SRX5799151	SRS4730320	SRA883435	Xiamen University\|School of Pharmaceutical Sciences	Xiamen University	1	0.94131		0.09307		0.67574		0.46993		50		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-01-18	Larval	Larval	Undetermined	Undetermined
52214	52214	SRR9021062	SRX5799150	SRS4730321	SRP195685	PRJNA541367	Global transcriptomic analysis of zebrafish glucagon receptor mutant	PRJNA541367	Other	We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.				gcgr 2	replicate:biological replicate 2\|strain:AB\|age:7 days\|sex:not applicable\|tissue:total\|BioSampleModel:Model organism or animal								Diano rerio transcriptome	gcgr 2 20190506 2	gcgr 2 20190506 2	RNA seq of Diano rerio with gcgr mutant		RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	BGISEQ	BGISEQ-500	SRP195685	loader:fastq load.py	gcgr2.1.fq	fastq	1094410100.0	21888202.0	gcgr2.1.fq	0:50	A:290062779;C:256358687;G:264488431;T:282812212;N:687991	50		290062779	256358687	264488431	282812212	687991	SRX5799150	SRS4730321	SRA883435	Xiamen University\|School of Pharmaceutical Sciences	Xiamen University	1	0.94074		0.09337		0.67633		0.46861		50		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-01-18	Larval	Larval	Undetermined	Undetermined
52215	52215	SRR9021063	SRX5799149	SRS4730319	SRP195685	PRJNA541367	Global transcriptomic analysis of zebrafish glucagon receptor mutant	PRJNA541367	Other	We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.				gcgr 3	replicate:biological replicate 3\|strain:AB\|age:7 days\|sex:not applicable\|tissue:total\|BioSampleModel:Model organism or animal								Diano rerio transcriptome	gcgr 3 20190506 3	gcgr 3 20190506 3	RNA seq of Diano rerio with gcgr mutant		RNA-Seq	TRANSCRIPTOMIC	other	SINGLE	BGISEQ	BGISEQ-500	SRP195685	loader:fastq load.py	gcgr3.1.fq	fastq	1094284800.0	21885696.0	gcgr3.1.fq	0:50	A:289313514;C:257096636;G:264011408;T:283143600;N:719642	50		289313514	257096636	264011408	283143600	719642	SRX5799149	SRS4730319	SRA883435	Xiamen University\|School of Pharmaceutical Sciences	Xiamen University	1	0.94222		0.09557		0.67521		0.46664		50		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-01-18	Larval	Larval	Undetermined	Undetermined
55643	55643	SRR10604044	SRX7283593	SRS5777402	SRP235014	PRJNA594101	Danio rerio Transcriptome	PRJNA594101	Other	Danio rerio Transcriptome post cGAS and STING knockout				stko2	strain:not collected\|isolate:sting knockout 2\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:7 days\|dev stage:larvae\|sex:not applicable\|tissue:larvae\|biomaterial provider:Yang xiaojun\|BioSampleModel:Model organism or animal								RNA Seq of zebraish larvae	sting knockout 2	sting knockout 2	RNA seq		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP235014		stko2_1.fastq.gz stko2_2.fastq.gz	fastq fastq	10635609300.0	70904062.0	stko2 1.fastq.gz	0:150 1:150	A:2864931942;C:2450585568;G:2436540783;T:2882828480;N:722527	150	150	2864931942	2450585568	2436540783	2882828480	722527	SRX7283593	SRS5777402	SRA1007465	Shantou university medical college\|Neuroscience Center	Shantou university medical college	1	0.93079		0.07849		0.70301		0.47872		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2019-12-08	Larval	Larval	Undetermined	Undetermined
55644	55644	SRR10604045	SRX7283592	SRS5777401	SRP235014	PRJNA594101	Danio rerio Transcriptome	PRJNA594101	Other	Danio rerio Transcriptome post cGAS and STING knockout				stko1	strain:not collected\|isolate:sting knockout 1\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:7 days\|dev stage:larvae\|sex:not applicable\|tissue:larvae\|biomaterial provider:Yang xiaojun\|BioSampleModel:Model organism or animal								RNA Seq of zebraish larvae	sting knockout 1	sting knockout 1	RNA seq		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP235014		stko1_1.fastq.gz stko1_2.fastq.gz	fastq fastq	10453959000.0	69693060.0	stko1 1.fastq.gz	0:150 1:150	A:2823253748;C:2400078679;G:2379662427;T:2850274552;N:689594	150	150	2823253748	2400078679	2379662427	2850274552	689594	SRX7283592	SRS5777401	SRA1007465	Shantou university medical college\|Neuroscience Center	Shantou university medical college	1	0.92736		0.08475		0.69822		0.47233		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2019-12-08	Larval	Larval	Undetermined	Undetermined
55645	55645	SRR10604046	SRX7283591	SRS5777400	SRP235014	PRJNA594101	Danio rerio Transcriptome	PRJNA594101	Other	Danio rerio Transcriptome post cGAS and STING knockout				cgko2	strain:not collected\|isolate:cgas knockout 2\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:7 days\|dev stage:larvae\|sex:not applicable\|tissue:larvae\|biomaterial provider:Yang xiaojun\|BioSampleModel:Model organism or animal								RNA Seq of zebraish larvae	cgas knockout 2	cgas knockout 2	RNA seq		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP235014		cgko2_1.fastq.gz cgko2_2.fastq.gz	fastq fastq	10462236900.0	69748246.0	cgko2 1.fastq.gz	0:150 1:150	A:2836737922;C:2388112649;G:2370425883;T:2866326601;N:633845	150	150	2836737922	2388112649	2370425883	2866326601	633845	SRX7283591	SRS5777400	SRA1007465	Shantou university medical college\|Neuroscience Center	Shantou university medical college	1	0.93603		0.10606		0.67765		0.46153		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2019-12-08	Larval	Larval	Undetermined	Undetermined
55646	55646	SRR10604047	SRX7283590	SRS5777399	SRP235014	PRJNA594101	Danio rerio Transcriptome	PRJNA594101	Other	Danio rerio Transcriptome post cGAS and STING knockout				cgko1	strain:not collected\|isolate:cgas knockout 1\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:7 days\|dev stage:larvae\|sex:not applicable\|tissue:larvae\|biomaterial provider:Yang xiaojun\|BioSampleModel:Model organism or animal								RNA Seq of zebraish larvae	cgas knockout 1	cgas knockout 1	RNA seq		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP235014		cgko1_2.fastq.gz cgko1_1.fastq.gz	fastq fastq	10498495500.0	69989970.0	cgko1 1.fastq.gz	0:150 1:150	A:2845684832;C:2398817161;G:2379300746;T:2874108573;N:584188	150	150	2845684832	2398817161	2379300746	2874108573	584188	SRX7283590	SRS5777399	SRA1007465	Shantou university medical college\|Neuroscience Center	Shantou university medical college	1	0.93684		0.10589		0.67933		0.48363		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2019-12-08	Larval	Larval	Undetermined	Undetermined
55647	55647	SRR10604048	SRX7283589	SRS5777398	SRP235014	PRJNA594101	Danio rerio Transcriptome	PRJNA594101	Other	Danio rerio Transcriptome post cGAS and STING knockout				wt2	strain:not collected\|isolate:normal 2\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:7 days\|dev stage:larvae\|sex:not applicable\|tissue:larvae\|biomaterial provider:Yang xiaojun\|BioSampleModel:Model organism or animal								RNA Seq of zebraish larvae	wt normal 2	wt normal 2	RNA seq		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP235014		wt2_1.fastq.gz wt2_2.fastq.gz	fastq fastq	10660916400.0	71072776.0	wt2 1.fastq.gz	0:150 1:150	A:2906473511;C:2417423798;G:2405111864;T:2931146507;N:760720	150	150	2906473511	2417423798	2405111864	2931146507	760720	SRX7283589	SRS5777398	SRA1007465	Shantou university medical college\|Neuroscience Center	Shantou university medical college	1	0.94167		0.11781		0.66831		0.4757		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2019-12-08	Larval	Larval	Undetermined	Undetermined
55648	55648	SRR10604049	SRX7283588	SRS5777397	SRP235014	PRJNA594101	Danio rerio Transcriptome	PRJNA594101	Other	Danio rerio Transcriptome post cGAS and STING knockout				wt1	strain:not collected\|isolate:normal 1\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:7 days\|dev stage:larvae\|sex:not applicable\|tissue:larvae\|biomaterial provider:Yang xiaojun\|BioSampleModel:Model organism or animal								RNA Seq of zebraish larvae	wt nomal 1	wt nomal 1	RNA seq		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP235014		wt1_1.fastq.gz wt1_2.fastq.gz	fastq fastq	10599804000.0	70665360.0	wt1 1.fastq.gz	0:150 1:150	A:2896989124;C:2397285811;G:2382705623;T:2922067937;N:755505	150	150	2896989124	2397285811	2382705623	2922067937	755505	SRX7283588	SRS5777397	SRA1007465	Shantou university medical college\|Neuroscience Center	Shantou university medical college	1	0.93947		0.11723		0.67203		0.45826		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2019-12-08	Larval	Larval	Undetermined	Undetermined
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
61375	61375	SRR12687500	SRX9167472	SRS7406198	SRP284444	PRJNA664479	RNA sequencing of transcriptome in zebrafish larvae	PRJNA664479	Other	Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae.				AlCl3 1	host:missing\|isolation source:zebrafish larvae\|collection date:2019 03 20\|geo loc name:China: Nanjing\|lat lon:missing\|tmp:10\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal								transcriptome	AlCl3 1	AlCl3 1	RNA sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP284444		AlCl3_1_1.fq AlCl3_1_2.fq	fastq fastq	6318129000.0	63181290.0	AlCl3 1 1.fq	0:100 1:100	A:1703650974;C:1436858038;G:1474640143;T:1702979845;N:0	100	100	1703650974	1436858038	1474640143	1702979845	0	SRX9167472	SRS7406198	SRA1129451	China Pharmaceutical University\|department of pharmacognosy	China Pharmaceutical University	1	0.92336		0.1173		0.6981		0.47069		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2020-09-21	Larval	Larval	Undetermined	Undetermined
61376	61376	SRR12687501	SRX9167471	SRS7406199	SRP284444	PRJNA664479	RNA sequencing of transcriptome in zebrafish larvae	PRJNA664479	Other	Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae.				S3 3	host:missing\|isolation source:zebrafish larvae\|collection date:2019 03 20\|geo loc name:China: Nanjing\|lat lon:missing\|tmp:9\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal								transcriptome	S3 3	S3 3	RNA sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP284444		S3_3_1.fq S3_3_2.fq	fastq fastq	6896170000.0	68961700.0	S3 3 1.fq	0:100 1:100	A:1952511528;C:1476189599;G:1495880823;T:1971588050;N:0	100	100	1952511528	1476189599	1495880823	1971588050	0	SRX9167471	SRS7406199	SRA1129451	China Pharmaceutical University\|department of pharmacognosy	China Pharmaceutical University	1	0.93819		0.18403		0.69881		0.51999		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2020-09-21	Larval	Larval	Undetermined	Undetermined
61377	61377	SRR12687502	SRX9167470	SRS7406197	SRP284444	PRJNA664479	RNA sequencing of transcriptome in zebrafish larvae	PRJNA664479	Other	Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae.				S3 2	host:missing\|isolation source:zebrafish larvae\|collection date:2019 03 20\|geo loc name:China: Nanjing\|lat lon:missing\|tmp:8\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal								transcriptome	S3 2	S3 2	RNA sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP284444		S3_2_1.fq S3_2_2.fq	fastq fastq	7144137200.0	71441372.0	S3 2 1.fq	0:100 1:100	A:2053632992;C:1499315470;G:1512455113;T:2078733625;N:0	100	100	2053632992	1499315470	1512455113	2078733625	0	SRX9167470	SRS7406197	SRA1129451	China Pharmaceutical University\|department of pharmacognosy	China Pharmaceutical University	1	0.93285		0.2066		0.70997		0.52936		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2020-09-21	Larval	Larval	Undetermined	Undetermined
61378	61378	SRR12687503	SRX9167469	SRS7406196	SRP284444	PRJNA664479	RNA sequencing of transcriptome in zebrafish larvae	PRJNA664479	Other	Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae.				S3 1	host:missing\|isolation source:zebrafish larvae\|collection date:2019 03 20\|geo loc name:China: Nanjing\|lat lon:missing\|tmp:7\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal								transcriptome	S3 1	S3 1	RNA sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP284444		S3_1_1.fq S3_1_2.fq	fastq fastq	6903489600.0	69034896.0	S3 1 1.fq	0:100 1:100	A:1984004671;C:1447920035;G:1460546712;T:2011018182;N:0	100	100	1984004671	1447920035	1460546712	2011018182	0	SRX9167469	SRS7406196	SRA1129451	China Pharmaceutical University\|department of pharmacognosy	China Pharmaceutical University	1	0.93549		0.20561		0.70569		0.53065		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2020-09-21	Larval	Larval	Undetermined	Undetermined
61379	61379	SRR12687504	SRX9167468	SRS7406195	SRP284444	PRJNA664479	RNA sequencing of transcriptome in zebrafish larvae	PRJNA664479	Other	Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae.				Pre 3	host:missing\|isolation source:zebrafish larvae\|collection date:2019 03 20\|geo loc name:China: Nanjing\|lat lon:missing\|tmp:6\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal								transcriptome	Pre 3	Pre 3	RNA sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP284444		Pre_3_1.fq Pre_3_2.fq	fastq fastq	7052506400.0	70525064.0	Pre 3 1.fq	0:100 1:100	A:1970281685;C:1535313771;G:1548483633;T:1998427311;N:0	100	100	1970281685	1535313771	1548483633	1998427311	0	SRX9167468	SRS7406195	SRA1129451	China Pharmaceutical University\|department of pharmacognosy	China Pharmaceutical University	1	0.93825		0.16689		0.69071		0.5149		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2020-09-21	Larval	Larval	Undetermined	Undetermined
61380	61380	SRR12687505	SRX9167467	SRS7406194	SRP284444	PRJNA664479	RNA sequencing of transcriptome in zebrafish larvae	PRJNA664479	Other	Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae.				Pre 2	host:missing\|isolation source:zebrafish larvae\|collection date:2019 03 20\|geo loc name:China: Nanjing\|lat lon:missing\|tmp:5\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal								transcriptome	Pre 2	Pre 2	RNA sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP284444		Pre_2_1.fq Pre_2_2.fq	fastq fastq	6917153000.0	69171530.0	Pre 2 1.fq	0:100 1:100	A:1954028740;C:1484690033;G:1500546828;T:1977887399;N:0	100	100	1954028740	1484690033	1500546828	1977887399	0	SRX9167467	SRS7406194	SRA1129451	China Pharmaceutical University\|department of pharmacognosy	China Pharmaceutical University	1	0.93653		0.18216		0.6939		0.50553		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2020-09-21	Larval	Larval	Undetermined	Undetermined
61381	61381	SRR12687506	SRX9167466	SRS7406193	SRP284444	PRJNA664479	RNA sequencing of transcriptome in zebrafish larvae	PRJNA664479	Other	Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae.				Pre 1	host:missing\|isolation source:zebrafish larvae\|collection date:2019 03 20\|geo loc name:China: Nanjing\|lat lon:missing\|tmp:4\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal								transcriptome	Pre 1	Pre 1	RNA sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP284444		Pre_1_1.fq Pre_1_2.fq	fastq fastq	7121559800.0	71215598.0	Pre 1 1.fq	0:100 1:100	A:2016438936;C:1525107488;G:1542345073;T:2037668303;N:0	100	100	2016438936	1525107488	1542345073	2037668303	0	SRX9167466	SRS7406193	SRA1129451	China Pharmaceutical University\|department of pharmacognosy	China Pharmaceutical University	1	0.93748		0.18677		0.69234		0.51095		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2020-09-21	Larval	Larval	Undetermined	Undetermined
61382	61382	SRR12687507	SRX9167465	SRS7406192	SRP284444	PRJNA664479	RNA sequencing of transcriptome in zebrafish larvae	PRJNA664479	Other	Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae.				Ctrl 3	host:missing\|isolation source:zebrafish larvae\|collection date:2019 03 20\|geo loc name:China: Nanjing\|lat lon:missing\|tmp:3\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal								transcriptome	Ctrl 3	Ctrl 3	RNA sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP284444		Ctrl_3_1.fq Ctrl_3_2.fq	fastq fastq	6901468000.0	69014680.0	Ctrl 3 1.fq	0:100 1:100	A:1958667379;C:1474001137;G:1490669190;T:1978130294;N:0	100	100	1958667379	1474001137	1490669190	1978130294	0	SRX9167465	SRS7406192	SRA1129451	China Pharmaceutical University\|department of pharmacognosy	China Pharmaceutical University	1	0.93909		0.19338		0.71021		0.5203		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2020-09-21	Larval	Larval	Undetermined	Undetermined
61383	61383	SRR12687508	SRX9167464	SRS7406191	SRP284444	PRJNA664479	RNA sequencing of transcriptome in zebrafish larvae	PRJNA664479	Other	Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae.				ECH 3	host:missing\|isolation source:zebrafish larvae\|collection date:2019 03 20\|geo loc name:China: Nanjing\|lat lon:missing\|tmp:15\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal								transcriptome	ECH 3	ECH 3	RNA sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP284444		ECH_3_1.fq ECH_3_2.fq	fastq fastq	6337825200.0	63378252.0	ECH 3 1.fq	0:100 1:100	A:1737819108;C:1411890760;G:1450506396;T:1737608936;N:0	100	100	1737819108	1411890760	1450506396	1737608936	0	SRX9167464	SRS7406191	SRA1129451	China Pharmaceutical University\|department of pharmacognosy	China Pharmaceutical University	1	0.91909		0.14386		0.69526		0.46915		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2020-09-21	Larval	Larval	Undetermined	Undetermined
61384	61384	SRR12687509	SRX9167463	SRS7406190	SRP284444	PRJNA664479	RNA sequencing of transcriptome in zebrafish larvae	PRJNA664479	Other	Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae.				ECH 2	host:missing\|isolation source:zebrafish larvae\|collection date:2019 03 20\|geo loc name:China: Nanjing\|lat lon:missing\|tmp:14\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal								transcriptome	ECH 2	ECH 2	RNA sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP284444		ECH_2_1.fq ECH_2_2.fq	fastq fastq	6082199400.0	60821994.0	ECH 2 1.fq	0:100 1:100	A:1665545787;C:1356011539;G:1398853438;T:1661788636;N:0	100	100	1665545787	1356011539	1398853438	1661788636	0	SRX9167463	SRS7406190	SRA1129451	China Pharmaceutical University\|department of pharmacognosy	China Pharmaceutical University	1	0.91909		0.13924		0.70019		0.47327		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2020-09-21	Larval	Larval	Undetermined	Undetermined
61385	61385	SRR12687510	SRX9167462	SRS7406189	SRP284444	PRJNA664479	RNA sequencing of transcriptome in zebrafish larvae	PRJNA664479	Other	Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae.				ECH 1	host:missing\|isolation source:zebrafish larvae\|collection date:2019 03 20\|geo loc name:China: Nanjing\|lat lon:missing\|tmp:13\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal								transcriptome	ECH 1	ECH 1	RNA sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP284444		ECH_1_1.fq ECH_1_2.fq	fastq fastq	6528165600.0	65281656.0	ECH 1 1.fq	0:100 1:100	A:1756958748;C:1486036851;G:1521185932;T:1763984069;N:0	100	100	1756958748	1486036851	1521185932	1763984069	0	SRX9167462	SRS7406189	SRA1129451	China Pharmaceutical University\|department of pharmacognosy	China Pharmaceutical University	1	0.92456		0.1171		0.6858		0.48296		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2020-09-21	Larval	Larval	Undetermined	Undetermined
61386	61386	SRR12687511	SRX9167461	SRS7406188	SRP284444	PRJNA664479	RNA sequencing of transcriptome in zebrafish larvae	PRJNA664479	Other	Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae.				AlCl3 3	host:missing\|isolation source:zebrafish larvae\|collection date:2019 03 20\|geo loc name:China: Nanjing\|lat lon:missing\|tmp:12\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal								transcriptome	AlCl3 3	AlCl3 3	RNA sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP284444		AlCl3_3_1.fq AlCl3_3_2.fq	fastq fastq	6554672200.0	65546722.0	AlCl3 3 1.fq	0:100 1:100	A:1789583657;C:1466854253;G:1506361550;T:1791872740;N:0	100	100	1789583657	1466854253	1506361550	1791872740	0	SRX9167461	SRS7406188	SRA1129451	China Pharmaceutical University\|department of pharmacognosy	China Pharmaceutical University	1	0.91837		0.13792		0.69199		0.46699		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2020-09-21	Larval	Larval	Undetermined	Undetermined
61387	61387	SRR12687512	SRX9167460	SRS7406187	SRP284444	PRJNA664479	RNA sequencing of transcriptome in zebrafish larvae	PRJNA664479	Other	Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae.				AlCl3 2	host:missing\|isolation source:zebrafish larvae\|collection date:2019 03 20\|geo loc name:China: Nanjing\|lat lon:missing\|tmp:11\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal								transcriptome	AlCl3 2	AlCl3 2	RNA sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP284444		AlCl3_2_1.fq AlCl3_2_2.fq	fastq fastq	6313522800.0	63135228.0	AlCl3 2 1.fq	0:100 1:100	A:1703974139;C:1432828723;G:1472463459;T:1704256479;N:0	100	100	1703974139	1432828723	1472463459	1704256479	0	SRX9167460	SRS7406187	SRA1129451	China Pharmaceutical University\|department of pharmacognosy	China Pharmaceutical University	1	0.92027		0.12251		0.6913		0.46774		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2020-09-21	Larval	Larval	Undetermined	Undetermined
61388	61388	SRR12687513	SRX9167459	SRS7406186	SRP284444	PRJNA664479	RNA sequencing of transcriptome in zebrafish larvae	PRJNA664479	Other	Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae.				Ctrl 2	host:missing\|isolation source:zebrafish larvae\|collection date:2019 03 20\|geo loc name:China: Nanjing\|lat lon:missing\|tmp:2\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal								transcriptome	Ctrl 2	Ctrl 2	RNA sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP284444		Ctrl_2_1.fq Ctrl_2_2.fq	fastq fastq	7158573600.0	71585736.0	Ctrl 2 1.fq	0:100 1:100	A:2037477785;C:1523658736;G:1537763707;T:2059673372;N:0	100	100	2037477785	1523658736	1537763707	2059673372	0	SRX9167459	SRS7406186	SRA1129451	China Pharmaceutical University\|department of pharmacognosy	China Pharmaceutical University	1	0.93876		0.19782		0.71315		0.52076		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2020-09-21	Larval	Larval	Undetermined	Undetermined
61389	61389	SRR12687514	SRX9167458	SRS7406185	SRP284444	PRJNA664479	RNA sequencing of transcriptome in zebrafish larvae	PRJNA664479	Other	Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae.				Ctrl 1	host:missing\|isolation source:zebrafish larvae\|collection date:2019 03 20\|geo loc name:China: Nanjing\|lat lon:missing\|tmp:1\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal								transcriptome	Ctrl 1	Ctrl 1	RNA sequencing		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP284444		Ctrl_1_1.fq Ctrl_1_2.fq	fastq fastq	7128907800.0	71289078.0	Ctrl 1 1.fq	0:100 1:100	A:2024706079;C:1521330507;G:1536206815;T:2046664399;N:0	100	100	2024706079	1521330507	1536206815	2046664399	0	SRX9167458	SRS7406185	SRA1129451	China Pharmaceutical University\|department of pharmacognosy	China Pharmaceutical University	1	0.94262		0.19339		0.71522		0.43982		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2020-09-21	Larval	Larval	Undetermined	Undetermined
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

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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");;