metadata: run_metadata: 120 rows where experiment.library_layout = "PAIRED", experiment.platform = "BGISEQ" and tissue

120 rows where experiment.library_layout = "PAIRED", experiment.platform = "BGISEQ" and tissue_curation = "Whole Organism"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.description	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.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
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
60496	60496	SRR12328853	SRX8829078	SRS7048444	SRP273655	PRJNA648800	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA	PRJNA648800	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.			C2	C2 C2 2 4	replicate:biological replicate 2\|strain:AB\|isolate:C2\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:100ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C2C220200712	C2C220200712	RNA seq of zebrafish in different conditions		RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP273655		C2_C2_2_4_1.fq.gz C2_C2_2_4_2.fq.gz	fastq fastq	6974294600.0	69742946.0	C2 C2 2 4 1.fq.gz	0:100 1:100	A:2057162032;C:1418016219;G:1425580374;T:2073535975;N:0	100	100	2057162032	1418016219	1425580374	2073535975	0	SRX8829078	SRS7048444	SRA1103962	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.93171		0.17455		0.71626		0.54961		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-07-27	Undetermined	Embryo	Whole Organism	All anatomical structures
60497	60497	SRR12328854	SRX8829077	SRS7048443	SRP273655	PRJNA648800	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA	PRJNA648800	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.			C2	C2 C2 1 4	replicate:biological replicate 1\|strain:AB\|isolate:C2\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:100ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C2C220200711	C2C220200711	RNA seq of zebrafish in different conditions		RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP273655		C2_C2_1_4_2.fq.gz C2_C2_1_4_1.fq.gz	fastq fastq	6942905200.0	69429052.0	C2 C2 1 4 1.fq.gz	0:100 1:100	A:2025129308;C:1433430820;G:1434784226;T:2049560846;N:0	100	100	2025129308	1433430820	1434784226	2049560846	0	SRX8829077	SRS7048443	SRA1103962	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.93211		0.16662		0.71001		0.53674		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-07-27	Undetermined	Embryo	Whole Organism	All anatomical structures
60498	60498	SRR12328855	SRX8829076	SRS7048442	SRP273655	PRJNA648800	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA	PRJNA648800	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.			C1	C1 C1 2 4	replicate:biological replicate 2\|strain:AB\|isolate:C1\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:1ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C1C120200712	C1C120200712	RNA seq of zebrafish in different conditions		RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP273655		C1_C1_2_4_1.fq.gz C1_C1_2_4_2.fq.gz	fastq fastq	6973657600.0	69736576.0	C1 C1 2 4 1.fq.gz	0:100 1:100	A:2050440259;C:1423350359;G:1423015668;T:2076851314;N:0	100	100	2050440259	1423350359	1423015668	2076851314	0	SRX8829076	SRS7048442	SRA1103962	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.92911		0.1877		0.72025		0.58085		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-07-27	Undetermined	Embryo	Whole Organism	All anatomical structures
60499	60499	SRR12328856	SRX8829075	SRS7048441	SRP273655	PRJNA648800	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA	PRJNA648800	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.			C1	C1 C1 1 4	replicate:biological replicate 1\|strain:AB\|isolate:C1\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:1ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C1C120200711	C1C120200711	RNA seq of zebrafish in different conditions		RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP273655		C1_C1_1_4_1.fq.gz C1_C1_1_4_2.fq.gz	fastq fastq	6746729200.0	67467292.0	C1 C1 1 4 1.fq.gz	0:100 1:100	A:2004203843;C:1356765594;G:1357760526;T:2027999237;N:0	100	100	2004203843	1356765594	1357760526	2027999237	0	SRX8829075	SRS7048441	SRA1103962	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.92733		0.19903		0.72228		0.59259		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-07-27	Undetermined	Embryo	Whole Organism	All anatomical structures
60500	60500	SRR12328857	SRX8829074	SRS7048440	SRP273655	PRJNA648800	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA	PRJNA648800	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.			C0	C0 C0 2 4	replicate:biological replicate 2\|strain:AB\|isolate:C0\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:0ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C0C020200712	C0C020200712	RNA seq of zebrafish in different conditions		RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP273655		C0_C0_2_4_1.fq.gz C0_C0_2_4_2.fq.gz	fastq fastq	6924724800.0	69247248.0	C0 C0 2 4 1.fq.gz	0:100 1:100	A:1974618038;C:1471821932;G:1482725702;T:1995559128;N:0	100	100	1974618038	1471821932	1482725702	1995559128	0	SRX8829074	SRS7048440	SRA1103962	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.93473		0.14676		0.69649		0.50413		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-07-27	Undetermined	Embryo	Whole Organism	All anatomical structures
60501	60501	SRR12328858	SRX8829073	SRS7048439	SRP273655	PRJNA648800	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA	PRJNA648800	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.			C0	C0 C0 1 4	replicate:biological replicate 1\|strain:AB\|isolate:C0\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:0ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C0C020200711	C0C020200711	RNA seq of zebrafish in different conditions		RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP273655		C0_C0_1_4_1.fq.gz C0_C0_1_4_2.fq.gz	fastq fastq	6899505600.0	68995056.0	C0 C0 1 4 1.fq.gz	0:100 1:100	A:1957459931;C:1477351919;G:1482435319;T:1982258431;N:0	100	100	1957459931	1477351919	1482435319	1982258431	0	SRX8829073	SRS7048439	SRA1103962	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.93567		0.14057		0.6883		0.48707		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-07-27	Undetermined	Embryo	Whole Organism	All anatomical structures
65984	65984	SRR15859821	SRX12150937	SRS10130028	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		levonorgestrel treatment at high concentration treatment	LNG H 1	AN	strain:not collected2\|isolate:whole fish13\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 1'\|BioSampleModel:Model organism or animal									LNG H 1	BM	BM	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		50_1_R1.clean.fq.gz 50_1_R2.clean.fq.gz	fastq fastq	6850889266.0	22893917.0	50 1 R1.clean.fq.gz	0:149.83 1:149.42	A:1908972876;C:1556853849;G:1559240564;T:1825804841;N:17136	149	149	1908972876	1556853849	1559240564	1825804841	17136	SRX12150937	SRS10130028	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93957	0.92386	0.09467	0.08944	0.66582	0.67142	0.50349	0.499	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65985	65985	SRR15859822	SRX12150936	SRS10130027	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		levonorgestrel treatment at low concentration treatment	LNG L 4	M	strain:not collected2\|isolate:whole fish12\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 4'\|BioSampleModel:Model organism or animal									LNG L 4	BL	BL	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		5_4_R1.clean.fq.gz 5_4_R2.clean.fq.gz	fastq fastq	6757301758.0	22579367.0	5 4 R1.clean.fq.gz	0:149.83 1:149.44	A:1886236851;C:1526321374;G:1529138861;T:1815587663;N:17009	149	149	1886236851	1526321374	1529138861	1815587663	17009	SRX12150936	SRS10130027	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93955	0.92322	0.09955	0.0937	0.66612	0.67056	0.4936	0.50296	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65986	65986	SRR15859823	SRX12150935	SRS10130026	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		levonorgestrel treatment at low concentration treatment	LNG L 3	AL	strain:not collected2\|isolate:whole fish11\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 3 prime\|BioSampleModel:Model organism or animal									LNG L 3	BK	BK	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		5_3_R1.clean.fq.gz 5_3_R2.clean.fq.gz	fastq fastq	6942028867.0	23178890.0	5 3 R1.clean.fq.gz	0:149.82 1:149.68	A:1895507796;C:1573477638;G:1599422601;T:1873160988;N:459844	149	149	1895507796	1573477638	1599422601	1873160988	459844	SRX12150935	SRS10130026	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.92261	0.9213	0.10308	0.10394	0.67298	0.67677	0.50615	0.5026	150	145	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65987	65987	SRR15859824	SRX12150934	SRS10130025	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		Solvent control	SC2	AC	strain:not collected2\|isolate:whole fish2\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 2'\|BioSampleModel:Model organism or animal									SC2	BB	BB	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		SC_2_R1.clean.fq.gz SC_2_R2.clean.fq.gz	fastq fastq	6847074418.0	22905359.0	SC 2 R1.clean.fq.gz	0:149.58 1:149.35	A:1835075664;C:1586631096;G:1607651961;T:1817247855;N:467842	149	149	1835075664	1586631096	1607651961	1817247855	467842	SRX12150934	SRS10130025	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93172	0.93195	0.07691	0.0771	0.67265	0.67665	0.48862	0.49579	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65988	65988	SRR15859825	SRX12150933	SRS10130024	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		Solvent control	SC1	AB	strain:not collected2\|isolate:whole fish1\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 1'\|BioSampleModel:Model organism or animal									SC1	BA	BA	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		SC_1_R1.clean.fq.gz SC_1_R2.clean.fq.gz	fastq fastq	7101595814.0	23743270.0	SC 1 R1.clean.fq.gz	0:149.65 1:149.45	A:1888007422;C:1656304946;G:1683234514;T:1873563589;N:485343	149	149	1888007422	1656304946	1683234514	1873563589	485343	SRX12150933	SRS10130024	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93193	0.93408	0.08101	0.08156	0.6744	0.67785	0.49761	0.49038	150	149	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65989	65989	SRR15859826	SRX12150932	SRS10130023	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		levonorgestrel treatment at low concentration treatment	LNG L 2	AK	strain:not collected2\|isolate:whole fish10\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 2'\|BioSampleModel:Model organism or animal									LNG L 2	BJ	BJ	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		5_2_R1.clean.fq.gz 5_2_R2.clean.fq.gz	fastq fastq	6978116268.0	23316955.0	5 2 R1.clean.fq.gz	0:149.72 1:149.55	A:1877413088;C:1609547451;G:1632121199;T:1858563731;N:470799	149	149	1877413088	1609547451	1632121199	1858563731	470799	SRX12150932	SRS10130023	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93086	0.93049	0.08702	0.08712	0.68357	0.68844	0.49793	0.48668	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65990	65990	SRR15859827	SRX12150931	SRS10130022	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		levonorgestrel treatment at low concentration treatment	LNG L 1	AJ	strain:not collected2\|isolate:whole fish9\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 1'\|BioSampleModel:Model organism or animal									LNG L 1	BI	BI	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		5_1_R1.clean.fq.gz 5_1_R2.clean.fq.gz	fastq fastq	6306082896.0	21075245.0	5 1 R1.clean.fq.gz	0:149.70 1:149.52	A:1679788198;C:1469939151;G:1489873755;T:1666053801;N:427991	149	149	1679788198	1469939151	1489873755	1666053801	427991	SRX12150931	SRS10130022	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93145	0.93206	0.08123	0.08188	0.67951	0.68432	0.48499	0.48763	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65991	65991	SRR15859828	SRX12150930	SRS10130021	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		dydrogesterone treatment	DDG 4	AI	strain:not collected2\|isolate:whole fish8\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 4'\|BioSampleModel:Model organism or animal									DDG 4	BH	BH	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_4_R1.clean.fq.gz 100_4_R2.clean.fq.gz	fastq fastq	7014679884.0	23437449.0	100 4 R1.clean.fq.gz	0:149.72 1:149.57	A:1882114669;C:1625037935;G:1641102139;T:1865959279;N:465862	149	149	1882114669	1625037935	1641102139	1865959279	465862	SRX12150930	SRS10130021	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93236	0.93264	0.08797	0.08919	0.67574	0.67965	0.50279	0.495	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65992	65992	SRR15859829	SRX12150929	SRS10130019	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		dydrogesterone treatment	DDG 3	AH	strain:not collected2\|isolate:whole fish7\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 3 prime\|BioSampleModel:Model organism or animal									DDG 3	BG	BG	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_3_R1.clean.fq.gz 100_3_R2.clean.fq.gz	fastq fastq	7000790030.0	23371313.0	100 3 R1.clean.fq.gz	0:149.83 1:149.72	A:1906942833;C:1592634521;G:1609492258;T:1891245267;N:475151	149	149	1906942833	1592634521	1609492258	1891245267	475151	SRX12150929	SRS10130019	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.92801	0.92781	0.09747	0.09744	0.66517	0.66776	0.50246	0.49531	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65993	65993	SRR15859830	SRX12150928	SRS10130020	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		dydrogesterone treatment	DDG 2	AG	strain:not collected2\|isolate:whole fish6\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 2'\|BioSampleModel:Model organism or animal									DDG 2	BF	BF	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_2_R1.clean.fq.gz 100_2_R2.clean.fq.gz	fastq fastq	7075813310.0	23625836.0	100 2 R1.clean.fq.gz	0:149.82 1:149.68	A:1918796036;C:1619755625;G:1637664383;T:1899135516;N:461750	149	149	1918796036	1619755625	1637664383	1899135516	461750	SRX12150928	SRS10130020	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.92935	0.92868	0.08886	0.08912	0.65717	0.6621	0.4843	0.49415	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65994	65994	SRR15859831	SRX12150927	SRS10130018	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		dydrogesterone treatment	DDG 1	AF	strain:not collected2\|isolate:whole fish5\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 1'\|BioSampleModel:Model organism or animal									DDG 1	BE	BE	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_1_R1.clean.fq.gz 100_1_R2.clean.fq.gz	fastq fastq	6740898004.0	22511996.0	100 1 R1.clean.fq.gz	0:149.79 1:149.65	A:1828418830;C:1542362815;G:1564205385;T:1805464983;N:445991	149	149	1828418830	1542362815	1564205385	1805464983	445991	SRX12150927	SRS10130018	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.92893	0.92836	0.08577	0.08614	0.67639	0.68077	0.48573	0.49544	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65995	65995	SRR15859832	SRX12150926	SRS10130016	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		Solvent control	SC4	AE	strain:not collected2\|isolate:whole fish4\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 4'\|BioSampleModel:Model organism or animal									SC4	BD	BD	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		SC_4_R1.clean.fq.gz SC_4_R2.clean.fq.gz	fastq fastq	6051468288.0	20209797.0	SC 4 R1.clean.fq.gz	0:149.80 1:149.63	A:1652651735;C:1373191643;G:1392749062;T:1632474997;N:400851	149	149	1652651735	1373191643	1392749062	1632474997	400851	SRX12150926	SRS10130016	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.92672	0.92501	0.09038	0.09121	0.66259	0.66565	0.49636	0.49698	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65996	65996	SRR15859833	SRX12150925	SRS10130017	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		Levonorgestrel at high concentration and dydrogesterone mixturestreatment	DDG+LNG H 1	AY	strain:not collected2\|isolate:whole fish24\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 4'\|BioSampleModel:Model organism or animal									DDG+LNG H 1	BX	BX	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_50_4_R1.clean.fq.gz 100_50_4_R2.clean.fq.gz	fastq fastq	6861007764.0	22938186.0	100 50 4 R1.clean.fq.gz	0:149.76 1:149.35	A:1881600852;C:1578987219;G:1582313999;T:1818088269;N:17425	149	149	1881600852	1578987219	1582313999	1818088269	17425	SRX12150925	SRS10130017	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93777	0.92424	0.09796	0.0931	0.66182	0.66746	0.49608	0.49787	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65997	65997	SRR15859834	SRX12150924	SRS10130015	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		Levonorgestrel at high concentration and dydrogesterone mixtures treatment	DDG+LNG H 1	AX	strain:not collected2\|isolate:whole fish23\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 3 prime\|BioSampleModel:Model organism or animal									DDG+LNG H 1	BW	BW	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_50_3_R1.clean.fq.gz 100_50_3_R2.clean.fq.gz	fastq fastq	6448167527.0	21546554.0	100 50 3 R1.clean.fq.gz	0:149.84 1:149.43	A:1776900923;C:1483436670;G:1478517308;T:1709296399;N:16227	149	149	1776900923	1483436670	1478517308	1709296399	16227	SRX12150924	SRS10130015	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.94114	0.92751	0.08812	0.0842	0.66557	0.67052	0.49525	0.49796	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65998	65998	SRR15859835	SRX12150923	SRS10130014	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		Levonorgestrel at high concentration and dydrogesterone mixtures treatment	DDG+LNG H 1	AW	strain:not collected2\|isolate:whole fish22\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 2'\|BioSampleModel:Model organism or animal									DDG+LNG H 1	BV	BV	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_50_2_R1.clean.fq.gz 100_50_2_R2.clean.fq.gz	fastq fastq	6097050612.0	20374795.0	100 50 2 R1.clean.fq.gz	0:149.83 1:149.42	A:1697937652;C:1387399999;G:1387536896;T:1624160680;N:15385	149	149	1697937652	1387399999	1387536896	1624160680	15385	SRX12150923	SRS10130014	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93921	0.92457	0.09156	0.08703	0.677	0.68268	0.51381	0.51338	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65999	65999	SRR15859836	SRX12150922	SRS10130013	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		Levonorgestrel at high concentration and dydrogesterone mixtures treatment	DDG+LNG H 1	AV	strain:not collected2\|isolate:whole fish21\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 1'\|BioSampleModel:Model organism or animal									DDG+LNG H 1	BU	BU	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_50_1_R1.clean.fq.gz 100_50_1_R2.clean.fq.gz	fastq fastq	6200464490.0	20718210.0	100 50 1 R1.clean.fq.gz	0:149.84 1:149.44	A:1722773998;C:1411958803;G:1410364088;T:1655351787;N:15814	149	149	1722773998	1411958803	1410364088	1655351787	15814	SRX12150922	SRS10130013	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.94019	0.92317	0.09428	0.08799	0.66192	0.66813	0.50339	0.50384	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66000	66000	SRR15859837	SRX12150921	SRS10130012	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		Solvent control	SC3	AD	strain:not collected2\|isolate:whole fish3\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 3 prime\|BioSampleModel:Model organism or animal									SC3	BC	BC	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		SC_3_R1.clean.fq.gz SC_3_R2.clean.fq.gz	fastq fastq	6744019219.0	22522868.0	SC 3 R1.clean.fq.gz	0:149.81 1:149.62	A:1832736009;C:1540439892;G:1560536404;T:1809859936;N:446978	149	149	1832736009	1540439892	1560536404	1809859936	446978	SRX12150921	SRS10130012	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.92908	0.92831	0.08407	0.08413	0.66748	0.67332	0.49151	0.50363	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66001	66001	SRR15859838	SRX12150920	SRS10130011	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		Levonorgestrel at low concentration and dydrogesterone mixtures treatment	DDG+LNG L 4	AU	strain:not collected2\|isolate:whole fish20\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 4'\|BioSampleModel:Model organism or animal									DDG+LNG L 4	BT	BT	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_5_4_R1.clean.fq.gz 100_5_4_R2.clean.fq.gz	fastq fastq	6698715338.0	22386760.0	100 5 4 R1.clean.fq.gz	0:149.82 1:149.41	A:1854944489;C:1532319316;G:1533554376;T:1777880466;N:16691	149	149	1854944489	1532319316	1533554376	1777880466	16691	SRX12150920	SRS10130011	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93948	0.92423	0.09198	0.08752	0.66967	0.67513	0.49914	0.49616	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66002	66002	SRR15859839	SRX12150919	SRS10130010	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		Levonorgestrel at low concentration and dydrogesterone mixtures treatment	DDG+LNG L 3	AT	strain:not collected2\|isolate:whole fish19\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 3 prime\|BioSampleModel:Model organism or animal									DDG+LNG L 3	BS	BS	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_5_3_R1.clean.fq.gz 100_5_3_R2.clean.fq.gz	fastq fastq	6731263096.0	22494392.0	100 5 3 R1.clean.fq.gz	0:149.82 1:149.42	A:1853865687;C:1546635036;G:1549005691;T:1781740007;N:16675	149	149	1853865687	1546635036	1549005691	1781740007	16675	SRX12150919	SRS10130010	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.94161	0.92699	0.09368	0.08881	0.67146	0.67671	0.49075	0.4916	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66003	66003	SRR15859840	SRX12150918	SRS10130009	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		Levonorgestrel at low concentration and dydrogesterone mixtures treatment	DDG+LNG L 2	AS	strain:not collected2\|isolate:whole fish18\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 2'\|BioSampleModel:Model organism or animal									DDG+LNG L 2	BR	BR	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_5_2_R1.clean.fq.gz 100_5_2_R2.clean.fq.gz	fastq fastq	6856677730.0	22942302.0	100 5 2 R1.clean.fq.gz	0:149.63 1:149.23	A:1861833177;C:1593702006;G:1601437245;T:1799688067;N:17235	149	149	1861833177	1593702006	1601437245	1799688067	17235	SRX12150918	SRS10130009	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.94226	0.93085	0.08471	0.08039	0.67677	0.68191	0.48927	0.47969	150	148	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66004	66004	SRR15859841	SRX12150917	SRS10130007	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		Levonorgestrel at low concentration and dydrogesterone mixtures treatment	DDG+LNG L 1	AR	strain:not collected2\|isolate:whole fish17\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 1'\|BioSampleModel:Model organism or animal									DDG+LNG L 1	BQ	BQ	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_5_1_R1.clean.fq.gz 100_5_1_R2.clean.fq.gz	fastq fastq	6734596961.0	22519168.0	100 5 1 R1.clean.fq.gz	0:149.72 1:149.34	A:1835515639;C:1562058332;G:1561380426;T:1775625709;N:16855	149	149	1835515639	1562058332	1561380426	1775625709	16855	SRX12150917	SRS10130007	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.94108	0.92768	0.09123	0.08716	0.66967	0.6747	0.50584	0.50347	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66005	66005	SRR15859842	SRX12150916	SRS10130006	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		levonorgestrel treatment at high concentration treatment	LNG H 4	AQ	strain:not collected2\|isolate:whole fish16\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 4'\|BioSampleModel:Model organism or animal									LNG H 4	BP	BP	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		50_4_R1.clean.fq.gz 50_4_R2.clean.fq.gz	fastq fastq	7033955938.0	23502039.0	50 4 R1.clean.fq.gz	0:149.84 1:149.46	A:1939982949;C:1612770444;G:1610988374;T:1870196531;N:17640	149	149	1939982949	1612770444	1610988374	1870196531	17640	SRX12150916	SRS10130006	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.94099	0.92749	0.09644	0.09215	0.67261	0.67838	0.49766	0.49584	150	149	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66006	66006	SRR15859843	SRX12150915	SRS10130008	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		levonorgestrel treatment at high concentration treatment	LNG H 3	AP	strain:not collected2\|isolate:whole fish15\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 3 prime\|BioSampleModel:Model organism or animal									LNG H 3	BO	BO	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		50_3_R1.clean.fq.gz 50_3_R2.clean.fq.gz	fastq fastq	5819952570.0	19444342.0	50 3 R1.clean.fq.gz	0:149.86 1:149.46	A:1615559082;C:1328350353;G:1325535770;T:1550492661;N:14704	149	149	1615559082	1328350353	1325535770	1550492661	14704	SRX12150915	SRS10130008	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.9397	0.92495	0.09375	0.08838	0.669	0.67338	0.50535	0.5146	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66007	66007	SRR15859844	SRX12150914	SRS10130005	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish		levonorgestrel treatment at high concentration treatment	LNG H 2	AO	strain:not collected2\|isolate:whole fish14\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 2'\|BioSampleModel:Model organism or animal									LNG H 2	BN	BN	zebraifsh exposure		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		50_2_R1.clean.fq.gz 50_2_R2.clean.fq.gz	fastq fastq	5888497480.0	19673249.0	50 2 R1.clean.fq.gz	0:149.84 1:149.47	A:1638307115;C:1337036459;G:1335389572;T:1577749137;N:15197	149	149	1638307115	1337036459	1335389572	1577749137	15197	SRX12150914	SRS10130005	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.9395	0.92471	0.09382	0.08964	0.66785	0.67144	0.50388	0.5077	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
67043	67043	SRR17017805	SRX13207904	SRS11133999	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.	pubmed:35114580		Aldh 2.1 / KO la3	GSM5701222	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	Aldh 2.1 / KO la3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	GSM5701222	GSM5701222: Aldh 2.1 / KO la3; Danio rerio; RNA Seq	GSM5701222 r1	GSM5701222	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444		3-KOla3_1.fq.gz 3-KOla3_2.fq.gz	fastq fastq	4974883400.0	49748834.0	GSM5701222 r1	0:100 1:100	A:1325503000;C:1131322113;G:1183075417;T:1334982870;N:0	100	100	1325503000	1131322113	1183075417	1334982870	0	SRX13207904	SRS11133999	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95156		0.10103		0.68917		0.50967		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67044	67044	SRR17017806	SRX13207903	SRS11133998	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.	pubmed:35114580		Aldh 2.1 / KO la2	GSM5701221	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	Aldh 2.1 / KO la2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	GSM5701221	GSM5701221: Aldh 2.1 / KO la2; Danio rerio; RNA Seq	GSM5701221 r1	GSM5701221	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444		2-KOla2_1.fq.gz 2-KOla2_2.fq.gz	fastq fastq	4993502200.0	49935022.0	GSM5701221 r1	0:100 1:100	A:1337290403;C:1130744731;G:1181303599;T:1344163467;N:0	100	100	1337290403	1130744731	1181303599	1344163467	0	SRX13207903	SRS11133998	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95056		0.09273		0.69207		0.5213		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67045	67045	SRR17017807	SRX13207902	SRS11133997	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.	pubmed:35114580		Aldh 2.1 / KO la1	GSM5701220	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	Aldh 2.1 / KO la1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	GSM5701220	GSM5701220: Aldh 2.1 / KO la1; Danio rerio; RNA Seq	GSM5701220 r1	GSM5701220	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444		1-KOla1_1.fq.gz 1-KOla1_2.fq.gz	fastq fastq	4982824800.0	49828248.0	GSM5701220 r1	0:100 1:100	A:1318751230;C:1142967126;G:1194575929;T:1326530515;N:0	100	100	1318751230	1142967126	1194575929	1326530515	0	SRX13207902	SRS11133997	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95468		0.09398		0.67917		0.50026		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67046	67046	SRR17017808	SRX13207901	SRS11133996	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.	pubmed:35114580		Aldh 2.1 +/+ WT la6	GSM5701229	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	Aldh 2.1 +/+ WT la6	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	GSM5701229	GSM5701229: Aldh 2.1 +/+ WT la6; Danio rerio; RNA Seq	GSM5701229 r1	GSM5701229	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444		10-WTla6_1.fq.gz 10-WTla6_2.fq.gz	fastq fastq	4990544400.0	49905444.0	GSM5701229 r1	0:100 1:100	A:1342332744;C:1123081871;G:1174336584;T:1350793201;N:0	100	100	1342332744	1123081871	1174336584	1350793201	0	SRX13207901	SRS11133996	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.94932		0.10692		0.69246		0.5131		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67047	67047	SRR17017809	SRX13207900	SRS11133995	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.	pubmed:35114580		Aldh 2.1 +/+ WT la5	GSM5701228	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	Aldh 2.1 +/+ WT la5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	GSM5701228	GSM5701228: Aldh 2.1 +/+ WT la5; Danio rerio; RNA Seq	GSM5701228 r1	GSM5701228	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444		9-WTla5_1.fq.gz 9-WTla5_2.fq.gz	fastq fastq	4990444600.0	49904446.0	GSM5701228 r1	0:100 1:100	A:1347054785;C:1118741393;G:1169087601;T:1355560821;N:0	100	100	1347054785	1118741393	1169087601	1355560821	0	SRX13207900	SRS11133995	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.94929		0.10427		0.69925		0.51838		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67048	67048	SRR17017810	SRX13207899	SRS11133994	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.	pubmed:35114580		Aldh 2.1 +/+ WT la3	GSM5701227	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	Aldh 2.1 +/+ WT la3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	GSM5701227	GSM5701227: Aldh 2.1 +/+ WT la3; Danio rerio; RNA Seq	GSM5701227 r1	GSM5701227	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444		8-WTla3_1.fq.gz 8-WTla3_2.fq.gz	fastq fastq	4986064600.0	49860646.0	GSM5701227 r1	0:100 1:100	A:1358143440;C:1107981393;G:1154357851;T:1365581916;N:0	100	100	1358143440	1107981393	1154357851	1365581916	0	SRX13207899	SRS11133994	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95037		0.10323		0.69499		0.54725		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67049	67049	SRR17017811	SRX13207898	SRS11133993	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.	pubmed:35114580		Aldh 2.1 +/+ WT la2	GSM5701226	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	Aldh 2.1 +/+ WT la2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	GSM5701226	GSM5701226: Aldh 2.1 +/+ WT la2; Danio rerio; RNA Seq	GSM5701226 r1	GSM5701226	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444		7-WTla2_1.fq.gz 7-WTla2_2.fq.gz	fastq fastq	4977068600.0	49770686.0	GSM5701226 r1	0:100 1:100	A:1341174868;C:1117869236;G:1167898570;T:1350125926;N:0	100	100	1341174868	1117869236	1167898570	1350125926	0	SRX13207898	SRS11133993	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.94822		0.11063		0.69514		0.51197		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67050	67050	SRR17017812	SRX13207897	SRS11133992	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.	pubmed:35114580		Aldh 2.1 +/+ WT la1	GSM5701225	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	Aldh 2.1 +/+ WT la1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	GSM5701225	GSM5701225: Aldh 2.1 +/+ WT la1; Danio rerio; RNA Seq	GSM5701225 r1	GSM5701225	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444		6-WTla1_1.fq.gz 6-WTla1_2.fq.gz	fastq fastq	4937740400.0	49377404.0	GSM5701225 r1	0:100 1:100	A:1322363529;C:1116877989;G:1169055598;T:1329443284;N:0	100	100	1322363529	1116877989	1169055598	1329443284	0	SRX13207897	SRS11133992	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95215		0.10081		0.69534		0.51784		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67051	67051	SRR17017813	SRX13207896	SRS11133991	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.	pubmed:35114580		Aldh 2.1 / KO la6	GSM5701224	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	Aldh 2.1 / KO la6	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	GSM5701224	GSM5701224: Aldh 2.1 / KO la6; Danio rerio; RNA Seq	GSM5701224 r1	GSM5701224	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444		5-KOla6_1.fq.gz 5-KOla6_2.fq.gz	fastq fastq	4875673200.0	48756732.0	GSM5701224 r1	0:100 1:100	A:1325527276;C:1084173307;G:1132675639;T:1333296978;N:0	100	100	1325527276	1084173307	1132675639	1333296978	0	SRX13207896	SRS11133991	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.94517		0.10711		0.69548		0.47813		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67052	67052	SRR17017814	SRX13207895	SRS11133990	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.	pubmed:35114580		Aldh 2.1 / KO la5	GSM5701223	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	Aldh 2.1 / KO la5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	GSM5701223	GSM5701223: Aldh 2.1 / KO la5; Danio rerio; RNA Seq	GSM5701223 r1	GSM5701223	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444		4-KOla5_1.fq.gz 4-KOla5_2.fq.gz	fastq fastq	4965270200.0	49652702.0	GSM5701223 r1	0:100 1:100	A:1348940910;C:1104562620;G:1155269060;T:1356497610;N:0	100	100	1348940910	1104562620	1155269060	1356497610	0	SRX13207895	SRS11133990	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.94849		0.11019		0.69988		0.53589		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67884	67884	SRR17868935	SRX14028691	SRS11864778	SRP358022	PRJNA793391	Effects of acute exposure to nano silver on zebrafish larvae	PRJNA793391	Other	Sliver nanoparticles AgNPs are widely used for industry agriculture and medicals which potentially result in adverse effects for human health and aquatic environment. In this present study we investigated the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.				C4 1	strain:danio rerio AgNPs4\|breed:zebrafish10\|age:3 day\|sex:pooled male and female\|tissue:fish\|BioSampleModel:Model organism or animal									DANIO RERIO 4 1	AG 4 1	AG 4 1	treatment7		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP358022		C4-1_1.fq.gz C4-1_2.fq.gz	fastq fastq	6830916900.0	45539446.0	C4 1 1.fq.gz	0:150 1:150	A:2011586443;C:1405775454;G:1388504965;T:2024992696;N:57342	150	150	2011586443	1405775454	1388504965	2024992696	57342	SRX14028691	SRS11864778	SRA1350965	Center for Neuroscience\|Shantou university	Center for Neuroscience	1	0.92344		0.21929		0.71043		0.46315		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-03	Larval	Larval	Whole Organism	All anatomical structures
67885	67885	SRR17868936	SRX14028690	SRS11864777	SRP358022	PRJNA793391	Effects of acute exposure to nano silver on zebrafish larvae	PRJNA793391	Other	Sliver nanoparticles AgNPs are widely used for industry agriculture and medicals which potentially result in adverse effects for human health and aquatic environment. In this present study we investigated the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.				C2 3	strain:danio rerio AgNPs2\|breed:zebrafish9\|age:3 day\|sex:pooled male and female\|tissue:fish\|BioSampleModel:Model organism or animal									DANIO RERIO 2 3	AG 2 3	AG 2 3	treatment6		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP358022		C2-3_1.fq.gz C2-3_2.fq.gz	fastq fastq	6782959200.0	45219728.0	C2 3 1.fq.gz	0:150 1:150	A:1949560199;C:1443524899;G:1428814233;T:1960921903;N:137966	150	150	1949560199	1443524899	1428814233	1960921903	137966	SRX14028690	SRS11864777	SRA1350965	Center for Neuroscience\|Shantou university	Center for Neuroscience	1	0.93181		0.17739		0.6927		0.50528		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-03	Larval	Larval	Whole Organism	All anatomical structures
67886	67886	SRR17868937	SRX14028689	SRS11864776	SRP358022	PRJNA793391	Effects of acute exposure to nano silver on zebrafish larvae	PRJNA793391	Other	Sliver nanoparticles AgNPs are widely used for industry agriculture and medicals which potentially result in adverse effects for human health and aquatic environment. In this present study we investigated the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.				C2 2	strain:danio rerio AgNPs2\|breed:zebrafish8\|age:3 day\|sex:pooled male and female\|tissue:fish\|BioSampleModel:Model organism or animal									DANIO RERIO 2 2	AG 2 2	AG 2 2	treatment5		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP358022		C2-2_1.fq.gz C2-2_2.fq.gz	fastq fastq	6817863300.0	45452422.0	C2 2 1.fq.gz	0:150 1:150	A:1964890519;C:1446826412;G:1428708103;T:1977297439;N:140827	150	150	1964890519	1446826412	1428708103	1977297439	140827	SRX14028689	SRS11864776	SRA1350965	Center for Neuroscience\|Shantou university	Center for Neuroscience	1	0.93045		0.17846		0.69116		0.48565		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-03	Larval	Larval	Whole Organism	All anatomical structures
67887	67887	SRR17868938	SRX14028688	SRS11864774	SRP358022	PRJNA793391	Effects of acute exposure to nano silver on zebrafish larvae	PRJNA793391	Other	Sliver nanoparticles AgNPs are widely used for industry agriculture and medicals which potentially result in adverse effects for human health and aquatic environment. In this present study we investigated the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.				C2 1	strain:danio rerio AgNPs2\|breed:zebrafish7\|age:3 day\|sex:pooled male and female\|tissue:fish\|BioSampleModel:Model organism or animal									DANIO RERIO 2 1	AG 2 1	AG 2 1	treatment4		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP358022		C2-1_1.fq.gz C2-1_2.fq.gz	fastq fastq	6795911700.0	45306078.0	C2 1 1.fq.gz	0:150 1:150	A:1910936263;C:1486390531;G:1471463982;T:1927036309;N:84615	150	150	1910936263	1486390531	1471463982	1927036309	84615	SRX14028688	SRS11864774	SRA1350965	Center for Neuroscience\|Shantou university	Center for Neuroscience	1	0.93638		0.14847		0.6814		0.46864		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-03	Larval	Larval	Whole Organism	All anatomical structures
67888	67888	SRR17868939	SRX14028687	SRS11864775	SRP358022	PRJNA793391	Effects of acute exposure to nano silver on zebrafish larvae	PRJNA793391	Other	Sliver nanoparticles AgNPs are widely used for industry agriculture and medicals which potentially result in adverse effects for human health and aquatic environment. In this present study we investigated the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.				C1 3	strain:danio rerio AgNPs1\|breed:zebrafish6\|age:3 day\|sex:pooled male and female\|tissue:fish\|BioSampleModel:Model organism or animal									DANIO RERIO 1 3	AG 1 3	AG 1 3	treatment3		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP358022		C1-3_1.fq.gz C1-3_2.fq.gz	fastq fastq	6788960100.0	45259734.0	C1 3 1.fq.gz	0:150 1:150	A:1883226902;C:1511814926;G:1492397960;T:1901504019;N:16293	150	150	1883226902	1511814926	1492397960	1901504019	16293	SRX14028687	SRS11864775	SRA1350965	Center for Neuroscience\|Shantou university	Center for Neuroscience	1	0.94253		0.12673		0.67623		0.49289		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-03	Larval	Larval	Whole Organism	All anatomical structures
67889	67889	SRR17868940	SRX14028686	SRS11864773	SRP358022	PRJNA793391	Effects of acute exposure to nano silver on zebrafish larvae	PRJNA793391	Other	Sliver nanoparticles AgNPs are widely used for industry agriculture and medicals which potentially result in adverse effects for human health and aquatic environment. In this present study we investigated the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.				C1 2	strain:danio rerio AgNPs1\|breed:zebrafish5\|age:3 day\|sex:pooled male and female\|tissue:fish\|BioSampleModel:Model organism or animal									DANIO RERIO 1 2	AG 1 2	AG 1 2	treatment2		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP358022		C1-2_1.fq.gz C1-2_2.fq.gz	fastq fastq	6781043100.0	45206954.0	C1 2 1.fq.gz	0:150 1:150	A:1890710017;C:1500221789;G:1482973456;T:1907121929;N:15909	150	150	1890710017	1500221789	1482973456	1907121929	15909	SRX14028686	SRS11864773	SRA1350965	Center for Neuroscience\|Shantou university	Center for Neuroscience	1	0.93834		0.13288		0.67777		0.49269		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-03	Larval	Larval	Whole Organism	All anatomical structures
67890	67890	SRR17868941	SRX14028685	SRS11864772	SRP358022	PRJNA793391	Effects of acute exposure to nano silver on zebrafish larvae	PRJNA793391	Other	Sliver nanoparticles AgNPs are widely used for industry agriculture and medicals which potentially result in adverse effects for human health and aquatic environment. In this present study we investigated the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.				C1 1	strain:danio rerio AgNPs1\|breed:zebrafish4\|age:3 day\|sex:pooled male and female\|tissue:fish\|BioSampleModel:Model organism or animal									DANIO RERIO 1 1	AG 1 1	AG 1 1	treatment1		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP358022		C1-1_1.fq.gz C1-1_2.fq.gz	fastq fastq	6760511100.0	45070074.0	C1 1 1.fq.gz	0:150 1:150	A:1875451292;C:1504527737;G:1489983693;T:1890505493;N:42885	150	150	1875451292	1504527737	1489983693	1890505493	42885	SRX14028685	SRS11864772	SRA1350965	Center for Neuroscience\|Shantou university	Center for Neuroscience	1	0.94039		0.1298		0.68071		0.49309		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-03	Larval	Larval	Whole Organism	All anatomical structures
67891	67891	SRR17868942	SRX14028684	SRS11864771	SRP358022	PRJNA793391	Effects of acute exposure to nano silver on zebrafish larvae	PRJNA793391	Other	Sliver nanoparticles AgNPs are widely used for industry agriculture and medicals which potentially result in adverse effects for human health and aquatic environment. In this present study we investigated the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.				WT3	strain:danio rerio con3\|breed:zebrafish3\|age:3 day\|sex:pooled male and female\|tissue:fish\|BioSampleModel:Model organism or animal									DANIO RERIO 0 3	WT 0 3	WT 0 3	control3		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP358022		WT3_1.fq.gz WT3_2.fq.gz	fastq fastq	6735369300.0	44902462.0	WT3 1.fq.gz	0:150 1:150	A:1853105410;C:1513363689;G:1496503080;T:1872187115;N:210006	150	150	1853105410	1513363689	1496503080	1872187115	210006	SRX14028684	SRS11864771	SRA1350965	Center for Neuroscience\|Shantou university	Center for Neuroscience	1	0.94653		0.11174		0.69116		0.49069		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-03	Larval	Larval	Whole Organism	All anatomical structures
67892	67892	SRR17868943	SRX14028683	SRS11864768	SRP358022	PRJNA793391	Effects of acute exposure to nano silver on zebrafish larvae	PRJNA793391	Other	Sliver nanoparticles AgNPs are widely used for industry agriculture and medicals which potentially result in adverse effects for human health and aquatic environment. In this present study we investigated the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.				C4 3	strain:danio rerio AgNPs4\|breed:zebrafish12\|age:3 day\|sex:pooled male and female\|tissue:fish\|BioSampleModel:Model organism or animal									DANIO RERIO 4 3	AG 4 3	AG 4 3	treatment9		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP358022		C4-3_1.fq.gz C4-3_2.fq.gz	fastq fastq	7066801800.0	47112012.0	C4 3 1.fq.gz	0:150 1:150	A:2079705050;C:1456973666;G:1436564156;T:2093467396;N:91532	150	150	2079705050	1456973666	1436564156	2093467396	91532	SRX14028683	SRS11864768	SRA1350965	Center for Neuroscience\|Shantou university	Center for Neuroscience	1	0.92264		0.21457		0.70236		0.52765		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-03	Larval	Larval	Whole Organism	All anatomical structures
67893	67893	SRR17868944	SRX14028682	SRS11864769	SRP358022	PRJNA793391	Effects of acute exposure to nano silver on zebrafish larvae	PRJNA793391	Other	Sliver nanoparticles AgNPs are widely used for industry agriculture and medicals which potentially result in adverse effects for human health and aquatic environment. In this present study we investigated the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.				C4 2	strain:danio rerio AgNPs4\|breed:zebrafish11\|age:3 day\|sex:pooled male and female\|tissue:fish\|BioSampleModel:Model organism or animal									DANIO RERIO 4 2	AG 4 2	AG 4 2	treatment8		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP358022		C4-2_1.fq.gz C4-2_2.fq.gz	fastq fastq	6813742200.0	45424948.0	C4 2 1.fq.gz	0:150 1:150	A:1969847243;C:1438590202;G:1418612399;T:1986677730;N:14626	150	150	1969847243	1438590202	1418612399	1986677730	14626	SRX14028682	SRS11864769	SRA1350965	Center for Neuroscience\|Shantou university	Center for Neuroscience	1	0.92909		0.18109		0.69029		0.50538		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-03	Larval	Larval	Whole Organism	All anatomical structures
67894	67894	SRR17868945	SRX14028681	SRS11864770	SRP358022	PRJNA793391	Effects of acute exposure to nano silver on zebrafish larvae	PRJNA793391	Other	Sliver nanoparticles AgNPs are widely used for industry agriculture and medicals which potentially result in adverse effects for human health and aquatic environment. In this present study we investigated the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.				WT2	strain:danio rerio con2\|breed:zebrafish2\|age:3 day\|sex:pooled male and female\|tissue:fish\|BioSampleModel:Model organism or animal									DANIO RERIO 0 2	WT 0 2	WT 0 2	control2		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP358022		WT2_1.fq.gz WT2_2.fq.gz	fastq fastq	6760866900.0	45072446.0	WT2 1.fq.gz	0:150 1:150	A:1893259201;C:1485992528;G:1471666738;T:1909709705;N:238728	150	150	1893259201	1485992528	1471666738	1909709705	238728	SRX14028681	SRS11864770	SRA1350965	Center for Neuroscience\|Shantou university	Center for Neuroscience	1	0.94132		0.13956		0.68596		0.48309		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-03	Larval	Larval	Whole Organism	All anatomical structures
67895	67895	SRR17868946	SRX14028680	SRS11864767	SRP358022	PRJNA793391	Effects of acute exposure to nano silver on zebrafish larvae	PRJNA793391	Other	Sliver nanoparticles AgNPs are widely used for industry agriculture and medicals which potentially result in adverse effects for human health and aquatic environment. In this present study we investigated the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.				WT1	strain:danio rerio con1\|breed:zebrafish1\|age:3 day\|sex:pooled male and female\|tissue:fish\|BioSampleModel:Model organism or animal									DANIO RERIO 0 1	WT 0 1	WT 0 1	control1		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP358022		WT1_1.fq.gz WT1_2.fq.gz	fastq fastq	7003449300.0	46689662.0	WT1 1.fq.gz	0:150 1:150	A:1946491315;C:1554368011;G:1539879203;T:1962458586;N:252185	150	150	1946491315	1554368011	1539879203	1962458586	252185	SRX14028680	SRS11864767	SRA1350965	Center for Neuroscience\|Shantou university	Center for Neuroscience	1	0.94236		0.12627		0.68369		0.49408		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-03	Larval	Larval	Whole Organism	All anatomical structures
68195	68195	SRR17658724	SRX13826757	SRS11705915	SRP355720	PRJNA798511	Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation	PRJNA798511	Other	heat treated zebrafish				C25d ZHT	strain:AB\|isolate:28\|breed:zebrafish\|cultivar:WT\|ecotype:CHINA\|age:25dpf\|sex:not collected\|tissue:whole organism\|BioSampleModel:Model organism or animal									RNAq of zebrafish	C25D	C25D	WT zebrafish		RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	BGISEQ	BGISEQ-500	SRP355720	loader:fastq load.py			20541691800.0	68472306.0	C25D.7z	0:150 1:150	A:5668751376;C:4596699177;G:4545478495;T:5730382931;N:379821	150	150	5668751376	4596699177	4545478495	5730382931	379821	SRX13826757	SRS11705915	SRA1358616	Hunan University of Science and Technology\|School of Life and Health Sciences	Hunan University of Science and Technology	2	0.84223	0.84372	0.07155	0.07222	0.70189	0.70321	0.47909	0.495	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-12-07	Larval	Larval	Whole Organism	All anatomical structures
68196	68196	SRR17658725	SRX13826756	SRS11705914	SRP355720	PRJNA798511	Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation	PRJNA798511	Other	heat treated zebrafish				T60d ZHT	strain:AB\|isolate:35\|breed:zebrafish\|cultivar:TEST\|ecotype:CHINA\|age:60dpf\|sex:not collected\|tissue:whole organism\|BioSampleModel:Model organism or animal									RNAq of zebrafish	T60D	T60D	heat treated zebrafish		RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	BGISEQ	BGISEQ-500	SRP355720	loader:fastq load.py			20334742200.0	67782474.0	T60D.7z	0:150 1:150	A:5482201207;C:4682998764;G:4635775004;T:5533378494;N:388731	150	150	5482201207	4682998764	4635775004	5533378494	388731	SRX13826756	SRS11705914	SRA1358616	Hunan University of Science and Technology\|School of Life and Health Sciences	Hunan University of Science and Technology	2	0.94378	0.94515	0.04989	0.04997	0.69848	0.69978	0.50317	0.5041	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-12-09	Juvenile	Juvenile	Whole Organism	All anatomical structures
68197	68197	SRR17658726	SRX13826755	SRS11705913	SRP355720	PRJNA798511	Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation	PRJNA798511	Other	heat treated zebrafish				T45d ZHT	strain:AB\|isolate:35\|breed:zebrafish\|cultivar:TEST\|ecotype:CHINA\|age:45dpf\|sex:not collected\|tissue:whole organism\|BioSampleModel:Model organism or animal									RNAq of zebrafish	T45D	T45D	heat treated zebrafish		RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	BGISEQ	BGISEQ-500	SRP355720	loader:fastq load.py			20230560300.0	67435201.0	T45D.7z	0:150 1:150	A:5444816209;C:4663007584;G:4631943733;T:5490408754;N:384020	150	150	5444816209	4663007584	4631943733	5490408754	384020	SRX13826755	SRS11705913	SRA1358616	Hunan University of Science and Technology\|School of Life and Health Sciences	Hunan University of Science and Technology	2	0.88041	0.881	0.04485	0.04492	0.72163	0.72236	0.52232	0.52307	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-12-09	Juvenile	Juvenile	Whole Organism	All anatomical structures
68198	68198	SRR17658727	SRX13826754	SRS11705912	SRP355720	PRJNA798511	Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation	PRJNA798511	Other	heat treated zebrafish				T35d ZHT	strain:AB\|isolate:35\|breed:zebrafish\|cultivar:TEST\|ecotype:CHINA\|age:35dpf\|sex:not collected\|tissue:whole organism\|BioSampleModel:Model organism or animal									RNAq of zebrafish	T35D	T35D	heat treated zebrafish		RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	BGISEQ	BGISEQ-500	SRP355720	loader:fastq load.py			20630503200.0	68768344.0	T35D.7z	0:150 1:150	A:5660657832;C:4654929757;G:4598083304;T:5716350276;N:482031	150	150	5660657832	4654929757	4598083304	5716350276	482031	SRX13826754	SRS11705912	SRA1358616	Hunan University of Science and Technology\|School of Life and Health Sciences	Hunan University of Science and Technology	2	0.9134	0.91476	0.06961	0.06972	0.69035	0.69215	0.52155	0.5154	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-12-09	Juvenile	Juvenile	Whole Organism	All anatomical structures
68199	68199	SRR17658728	SRX13826753	SRS11705911	SRP355720	PRJNA798511	Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation	PRJNA798511	Other	heat treated zebrafish				C60d ZHT	strain:AB\|isolate:28\|breed:zebrafish\|cultivar:WT\|ecotype:CHINA\|age:60dpf\|sex:not collected\|tissue:whole organism\|BioSampleModel:Model organism or animal									RNAq of zebrafish	C60D	C60D	WT zebrafish		RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	BGISEQ	BGISEQ-500	SRP355720	loader:fastq load.py			10921407600.0	44923977.0	C60D.7z		A:2992232295;C:2470688717;G:2440861228;T:3017432565;N:192795			2992232295	2470688717	2440861228	3017432565	192795	SRX13826753	SRS11705911	SRA1358616	Hunan University of Science and Technology\|School of Life and Health Sciences	Hunan University of Science and Technology	2	0.93932	0.94095	0.06489	0.06559	0.77871	0.77759	0.56384	0.56447	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-12-09	Juvenile	Juvenile	Whole Organism	All anatomical structures
68200	68200	SRR17658729	SRX13826752	SRS11705910	SRP355720	PRJNA798511	Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation	PRJNA798511	Other	heat treated zebrafish				C45d ZHT	strain:AB\|isolate:28\|breed:zebrafish\|cultivar:WT\|ecotype:CHINA\|age:45dpf\|sex:not collected\|tissue:whole organism\|BioSampleModel:Model organism or animal									RNAq of zebrafish	C45D	C45D	WT zebrafish		RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	BGISEQ	BGISEQ-500	SRP355720	loader:fastq load.py			20413229700.0	68044099.0	C45D.7z	0:150 1:150	A:5619395833;C:4581611789;G:4543973618;T:5667873613;N:374847	150	150	5619395833	4581611789	4543973618	5667873613	374847	SRX13826752	SRS11705910	SRA1358616	Hunan University of Science and Technology\|School of Life and Health Sciences	Hunan University of Science and Technology	2	0.86848	0.87064	0.0719	0.07252	0.69879	0.69834	0.52279	0.51074	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-12-09	Juvenile	Juvenile	Whole Organism	All anatomical structures
68201	68201	SRR17658730	SRX13826751	SRS11705909	SRP355720	PRJNA798511	Comparative analysis of transcriptome for heat induced zebrafish during sex differentiation	PRJNA798511	Other	heat treated zebrafish				C35d ZHT	strain:AB\|isolate:28\|breed:zebrafish\|cultivar:WT\|ecotype:CHINA\|age:35dpf\|sex:not collected\|tissue:whole organism\|BioSampleModel:Model organism or animal									RNAq of zebrafish	C35D	C35D	WT zebrafish		RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	BGISEQ	BGISEQ-500	SRP355720	loader:fastq load.py			20469803700.0	68232679.0	C35D.7z	0:150 1:150	A:5556774511;C:4678377106;G:4627472920;T:5606765895;N:413268	150	150	5556774511	4678377106	4627472920	5606765895	413268	SRX13826751	SRS11705909	SRA1358616	Hunan University of Science and Technology\|School of Life and Health Sciences	Hunan University of Science and Technology	2	0.93663	0.93871	0.06853	0.06895	0.6982	0.69901	0.51209	0.51148	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2022-12-09	Juvenile	Juvenile	Whole Organism	All anatomical structures
69610	69610	SRR18959644	SRX15036823	SRS12783659	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation	pubmed:35641933		T60d 3	GSM6070558	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:heat shock	T60d 3	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:heat shock	GSM6070558	GSM6070558: T60d 3; Danio rerio; RNA Seq	GSM6070558 r1	GSM6070558	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		T60d_3_1.fq.gz T60d_3_2.fq.gz	fastq fastq	6668586300.0	44457242.0	GSM6070558 r1	0:150 1:150	A:1798105768;C:1533776293;G:1519933345;T:1816635529;N:135365	150	150	1798105768	1533776293	1519933345	1816635529	135365	SRX15036823	SRS12783659	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.94696		0.03818		0.72754		0.44424		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69611	69611	SRR18959645	SRX15036822	SRS12783660	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation	pubmed:35641933		T60d 2	GSM6070557	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:heat shock	T60d 2	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:heat shock	GSM6070557	GSM6070557: T60d 2; Danio rerio; RNA Seq	GSM6070557 r1	GSM6070557	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		T60d_2_1.fq.gz T60d_2_2.fq.gz	fastq fastq	6790474800.0	45269832.0	GSM6070557 r1	0:150 1:150	A:1792022273;C:1601949824;G:1583360851;T:1813022005;N:119847	150	150	1792022273	1601949824	1583360851	1813022005	119847	SRX15036822	SRS12783660	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.9518		0.03662		0.72892		0.50564		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69612	69612	SRR18959646	SRX15036821	SRS12783661	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation	pubmed:35641933		T60d 1	GSM6070556	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:heat shock	T60d 1	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:heat shock	GSM6070556	GSM6070556: T60d 1; Danio rerio; RNA Seq	GSM6070556 r1	GSM6070556	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		T60d_1_1.fq.gz T60d_1_2.fq.gz	fastq fastq	6875681100.0	45837874.0	GSM6070556 r1	0:150 1:150	A:1892073166;C:1547272647;G:1532480808;T:1903720960;N:133519	150	150	1892073166	1547272647	1532480808	1903720960	133519	SRX15036821	SRS12783661	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.93516		0.0737		0.70394		0.55661		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69613	69613	SRR18959647	SRX15036820	SRS12783658	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation	pubmed:35641933		T45d 3	GSM6070555	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:heat shock	T45d 3	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:heat shock	GSM6070555	GSM6070555: T45d 3; Danio rerio; RNA Seq	GSM6070555 r1	GSM6070555	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		T45d_3_1.fq.gz T45d_3_2.fq.gz	fastq fastq	6677602800.0	44517352.0	GSM6070555 r1	0:150 1:150	A:1776927020;C:1564627916;G:1551750199;T:1784113081;N:184584	150	150	1776927020	1564627916	1551750199	1784113081	184584	SRX15036820	SRS12783658	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.95333		0.04626		0.79788		0.53869		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69614	69614	SRR18959648	SRX15036819	SRS12783657	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation	pubmed:35641933		T45d 2	GSM6070554	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:heat shock	T45d 2	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:heat shock	GSM6070554	GSM6070554: T45d 2; Danio rerio; RNA Seq	GSM6070554 r1	GSM6070554	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		T45d_2_1.fq.gz T45d_2_2.fq.gz	fastq fastq	6866885100.0	45779234.0	GSM6070554 r1	0:150 1:150	A:1855996561;C:1572989256;G:1559095064;T:1878636946;N:167273	150	150	1855996561	1572989256	1559095064	1878636946	167273	SRX15036819	SRS12783657	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.85691		0.0428		0.70059		0.48517		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69615	69615	SRR18959649	SRX15036818	SRS12783655	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation	pubmed:35641933		T45d 1	GSM6070553	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:heat shock	T45d 1	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:heat shock	GSM6070553	GSM6070553: T45d 1; Danio rerio; RNA Seq	GSM6070553 r1	GSM6070553	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		T45d_1_1.fq.gz T45d_1_2.fq.gz	fastq fastq	6686072400.0	44573816.0	GSM6070553 r1	0:150 1:150	A:1811892628;C:1525390412;G:1521098470;T:1827658727;N:32163	150	150	1811892628	1525390412	1521098470	1827658727	32163	SRX15036818	SRS12783655	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.83063		0.04482		0.75227		0.53268		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69616	69616	SRR18959650	SRX15036817	SRS12783656	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation	pubmed:35641933		T35d 3	GSM6070552	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:heat shock	T35d 3	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:heat shock	GSM6070552	GSM6070552: T35d 3; Danio rerio; RNA Seq	GSM6070552 r1	GSM6070552	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		T35d_3_1.fq.gz T35d_3_2.fq.gz	fastq fastq	6886247700.0	45908318.0	GSM6070552 r1	0:150 1:150	A:1822190170;C:1616493163;G:1597658988;T:1849741504;N:163875	150	150	1822190170	1616493163	1597658988	1849741504	163875	SRX15036817	SRS12783656	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.94299		0.03719		0.71165		0.49413		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69617	69617	SRR18959651	SRX15036816	SRS12783654	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation	pubmed:35641933		T35d 2	GSM6070551	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:heat shock	T35d 2	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:heat shock	GSM6070551	GSM6070551: T35d 2; Danio rerio; RNA Seq	GSM6070551 r1	GSM6070551	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		T35d_2_1.fq.gz T35d_2_2.fq.gz	fastq fastq	6851241900.0	45674946.0	GSM6070551 r1	0:150 1:150	A:1925245234;C:1503184374;G:1483632128;T:1939009289;N:170875	150	150	1925245234	1503184374	1483632128	1939009289	170875	SRX15036816	SRS12783654	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.86703		0.08277		0.70619		0.47871		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69618	69618	SRR18959652	SRX15036815	SRS12783653	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation	pubmed:35641933		T35d 1	GSM6070550	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:heat shock	T35d 1	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:heat shock	GSM6070550	GSM6070550: T35d 1; Danio rerio; RNA Seq	GSM6070550 r1	GSM6070550	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		T35d_1_1.fq.gz T35d_1_2.fq.gz	fastq fastq	6893013600.0	45953424.0	GSM6070550 r1	0:150 1:150	A:1913222428;C:1535252220;G:1516792188;T:1927599483;N:147281	150	150	1913222428	1535252220	1516792188	1927599483	147281	SRX15036815	SRS12783653	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.93126		0.08861		0.70711		0.53182		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69619	69619	SRR18959653	SRX15036814	SRS12783652	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation	pubmed:35641933		C60d 3	GSM6070549	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:control	C60d 3	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:control	GSM6070549	GSM6070549: C60d 3; Danio rerio; RNA Seq	GSM6070549 r1	GSM6070549	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		C60d_3_1.fq.gz C60d_3_2.fq.gz	fastq fastq	6732458700.0	44883058.0	GSM6070549 r1	0:150 1:150	A:1840891044;C:1527037740;G:1515664962;T:1848770869;N:94085	150	150	1840891044	1527037740	1515664962	1848770869	94085	SRX15036814	SRS12783652	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.94478		0.05996		0.73661		0.56885		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69620	69620	SRR18959654	SRX15036813	SRS12783651	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation	pubmed:35641933		C60d 2	GSM6070548	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:control	C60d 2	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:control	GSM6070548	GSM6070548: C60d 2; Danio rerio; RNA Seq	GSM6070548 r1	GSM6070548	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		C60d_2_1.fq.gz C60d_2_2.fq.gz	fastq fastq	6920478600.0	46136524.0	GSM6070548 r1	0:150 1:150	A:1860288879;C:1602876302;G:1589399217;T:1867783032;N:131170	150	150	1860288879	1602876302	1589399217	1867783032	131170	SRX15036813	SRS12783651	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.95235		0.05236		0.74836		0.55427		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69621	69621	SRR18959655	SRX15036812	SRS12783650	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation	pubmed:35641933		C60d 1	GSM6070547	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:control	C60d 1	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:60dpf\|treatment:control	GSM6070547	GSM6070547: C60d 1; Danio rerio; RNA Seq	GSM6070547 r1	GSM6070547	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		C60d_1_1.fq.gz C60d_1_2.fq.gz	fastq fastq	6744639300.0	44964262.0	GSM6070547 r1	0:150 1:150	A:1855599360;C:1516548729;G:1501772747;T:1870587619;N:130845	150	150	1855599360	1516548729	1501772747	1870587619	130845	SRX15036812	SRS12783650	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.93949		0.06857		0.73805		0.54443		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69622	69622	SRR18959656	SRX15036811	SRS12783649	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation	pubmed:35641933		C45d 3	GSM6070546	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:control	C45d 3	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:control	GSM6070546	GSM6070546: C45d 3; Danio rerio; RNA Seq	GSM6070546 r1	GSM6070546	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		C45d_3_1.fq.gz C45d_3_2.fq.gz	fastq fastq	6743568300.0	44957122.0	GSM6070546 r1	0:150 1:150	A:1852733188;C:1516814321;G:1505754587;T:1868137549;N:128655	150	150	1852733188	1516814321	1505754587	1868137549	128655	SRX15036811	SRS12783649	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.87046		0.07264		0.69996		0.51275		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69623	69623	SRR18959657	SRX15036810	SRS12783648	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation	pubmed:35641933		C45d 2	GSM6070545	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:control	C45d 2	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:control	GSM6070545	GSM6070545: C45d 2; Danio rerio; RNA Seq	GSM6070545 r1	GSM6070545	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		C45d_2_1.fq.gz C45d_2_2.fq.gz	fastq fastq	6742016100.0	44946774.0	GSM6070545 r1	0:150 1:150	A:1859613225;C:1508260261;G:1496299109;T:1877718155;N:125350	150	150	1859613225	1508260261	1496299109	1877718155	125350	SRX15036810	SRS12783648	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.84381		0.07253		0.68769		0.51224		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69624	69624	SRR18959658	SRX15036809	SRS12783647	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation	pubmed:35641933		C45d 1	GSM6070544	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:control	C45d 1	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:45dpf\|treatment:control	GSM6070544	GSM6070544: C45d 1; Danio rerio; RNA Seq	GSM6070544 r1	GSM6070544	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		C45d_1_1.fq.gz C45d_1_2.fq.gz	fastq fastq	6927645300.0	46184302.0	GSM6070544 r1	0:150 1:150	A:1907049420;C:1556537207;G:1541919922;T:1922017909;N:120842	150	150	1907049420	1556537207	1541919922	1922017909	120842	SRX15036809	SRS12783647	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.89529		0.07244		0.71703		0.53737		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69625	69625	SRR18959659	SRX15036808	SRS12783646	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation	pubmed:35641933		C35d 3	GSM6070543	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:control	C35d 3	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:control	GSM6070543	GSM6070543: C35d 3; Danio rerio; RNA Seq	GSM6070543 r1	GSM6070543	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		C35d_3_1.fq.gz C35d_3_2.fq.gz	fastq fastq	6874832400.0	45832216.0	GSM6070543 r1	0:150 1:150	A:1849406781;C:1586828671;G:1570455371;T:1867999362;N:142215	150	150	1849406781	1586828671	1570455371	1867999362	142215	SRX15036808	SRS12783646	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.94372		0.06412		0.71043		0.5035		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69626	69626	SRR18959660	SRX15036807	SRS12783645	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation	pubmed:35641933		C35d 2	GSM6070542	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:control	C35d 2	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:control	GSM6070542	GSM6070542: C35d 2; Danio rerio; RNA Seq	GSM6070542 r1	GSM6070542	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		C35d_2_1.fq.gz C35d_2_2.fq.gz	fastq fastq	6709504200.0	44730028.0	GSM6070542 r1	0:150 1:150	A:1832012065;C:1521825928;G:1505192413;T:1850347840;N:125954	150	150	1832012065	1521825928	1505192413	1850347840	125954	SRX15036807	SRS12783645	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.9254		0.07577		0.67537		0.51805		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69627	69627	SRR18959661	SRX15036806	SRS12783644	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation	pubmed:35641933		C35d 1	GSM6070541	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:control	C35d 1	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:35dpf\|treatment:control	GSM6070541	GSM6070541: C35d 1; Danio rerio; RNA Seq	GSM6070541 r1	GSM6070541	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		C35d_1_1.fq.gz C35d_1_2.fq.gz	fastq fastq	6885467100.0	45903114.0	GSM6070541 r1	0:150 1:150	A:1875355665;C:1569722507;G:1551825136;T:1888418693;N:145099	150	150	1875355665	1569722507	1551825136	1888418693	145099	SRX15036806	SRS12783644	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.9444		0.06579		0.73312		0.53564		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	Juvenile	Juvenile	Whole Organism	All anatomical structures
69628	69628	SRR18959662	SRX15036805	SRS12783643	SRP372606	PRJNA832865	Transcriptome comparative analysis of heat induced domesticated zebrafish during gonadal differentiation	GSE201748	Transcriptome Analysis	The influence of environmental factors especially temperature on sex ratio is of great significance to elucidate the mechanism of sex determination. However the molecular mechanisms by which temperature affects sex determination remains unclear although a few candidate genes have been found to play a role in the process. In this study we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171 1022 and 2921 differentially expressed genes DEGs between high temperature and normal temperature were identified at 35 45 dpf and 60 dpf dpf respectively revealing that DNA methyltransferases DNMTs and heat shock proteins HSPs were involved in the heat exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes KEGG pathway that were enriched in individuals post heat treatment included Fanconi anemia pathway cell cycle oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat induced masculinization and improve our understanding the molecular mechanisms of vertebrate sex determination. Overall design: Comparative gene expression profiling analysis of RNA seq data for heat induced domesticated zebrafish during gonadal differentiation	pubmed:35641933		C25d 3	GSM6070540	source name:Whole fish\|tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:25dpf\|treatment:control	C25d 3	The sequencing data was filtered with SOAPnuke v1.5.2 by removing reads containing sequencing adapter; removing reads whose low quality base ratio base quality less than or equal to 5 is more than 20%; removing reads whose unknown base‘N’ base ratio is more than 5%. The clean reads were mapped to GRCz11/dnaRer11 using HISAT2v2.0.4 pipeline. Bowtie2 v2.2.5 was applied to align the clean reads to the reference coding gene set GCF 000002035.6 GRCz11 then expression level of gene was calculated by RSEMv1.2.12. Differential expression analysis was performed using the DESeq2v1.4.5 with Q value ≤ 0.05. GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/ Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value≤ 0.05 by Bonferroni. Assembly: dnaRer11 Supplementary files format and content: tab delimited text files include genes expression and read count for each Sample	Whole fish	The control group was kept at 28℃ whereas the thermal treatment group was exposed to 35℃for 10 days during 25 dpf 35 dpf. And each group had three biological replicates. post the treatment fish were returned at 28℃ until the fish reached to sexual maturity 90 dpf.	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	The AB strain were maintained in a glass aquarium with a circulating water system at 28±0.5℃ with photoperiods of 14L 10D and the number of fish in each 5 liter tank was 50 55.	tissue:Whole fish\|strain:AB\|genotype:Wide type\|development stage:25dpf\|treatment:control	GSM6070540	GSM6070540: C25d 3; Danio rerio; RNA Seq	GSM6070540 r1	GSM6070540	1	Total RNA was extracted from the tissues using Trizol Invitrogen Carlsbad CA USA according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12 000xg at 4℃ then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol 24:1. The mix was shacked vigorously for 15s and then centrifuged at 12 000xg for 10 minutes at 4C. post centrifugation the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol then centrifuged at 13 600 rpm for 20 minutes at 4℃. post deserting the supernatant the RNA pellet was washed twice with 1 mL 75% ethanol then the mix was centrifuged at 13 600 rpm for 3 minutes at 4℃ to collect residual ethanol followed by the pellet air dry for 5 10 minutes in the biosafety cabinet. Finally 25μL100μL of DEPC treated water was added to dissolve the RNA. Subsequently total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer Thermo Fisher Scientific MA USA. RNA libraries for RNA seq were prepared using standard BGISEQ 500 protocols. OligodT attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First strand cDNA was generated using random hexamer primed reverse transcription followed by a second strand cDNA synthesis. postwards A Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR and products were purified by Ampure XP Beads then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP372606		C25d_3_1.fq.gz C25d_3_2.fq.gz	fastq fastq	6919024500.0	46126830.0	GSM6070540 r1	0:150 1:150	A:1895872624;C:1561159730;G:1542389546;T:1919479874;N:122726	150	150	1895872624	1561159730	1542389546	1919479874	122726	SRX15036805	SRS12783643	SRA1411536	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology	1	0.86721		0.07253		0.69465		0.50499		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-04-27	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");;