metadata: run_metadata: 123 rows where experiment.library_selection = "cDNA", experiment.platform = "BGISEQ" and tissue_curation

123 rows where experiment.library_selection = "cDNA", experiment.platform = "BGISEQ" and tissue_curation_coarse = "All anatomical structures"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
28093	28093	SRR26196850	SRX21908248	SRS18993956	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:38868197	elipsa mutant clutch 4	GSM7808262	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa mutant clutch 4	Standard processing by BGI.p HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM7808262	GSM7808262: elipsa mutant clutch 4; Danio rerio; RNA Seq	GSM7808262 r1	GSM7808262	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504	ElipsaMUT4_1.fq.gz ElipsaMUT4_2.fq.gz	fastq fastq	4536153000.0	22680765.0	GSM7808262 r1	0:100 1:100	A:1194964224;C:1059904764;G:1074108947;T:1207175065;N:0	100	100	1194964224	1059904764	1074108947	1207175065	0	SRX21908248	SRS18993956	SRA1721841	NTNU	NTNU	2	0.93991	0.94735	0.10392	0.10318	0.66434	0.66344	0.48911	0.49311	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28094	28094	SRR26196851	SRX21908247	SRS18993955	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:38868197	elipsa mutant clutch 3	GSM7808261	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa mutant clutch 3	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM7808261	GSM7808261: elipsa mutant clutch 3; Danio rerio; RNA Seq	GSM7808261 r1	GSM7808261	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504	ElipsaMUT3_1.fq.gz ElipsaMUT3_2.fq.gz	fastq fastq	4547581600.0	22737908.0	GSM7808261 r1	0:100 1:100	A:1183476304;C:1077021222;G:1092963681;T:1194120393;N:0	100	100	1183476304	1077021222	1092963681	1194120393	0	SRX21908247	SRS18993955	SRA1721841	NTNU	NTNU	2	0.95029	0.95874	0.09085	0.09059	0.66856	0.66722	0.48534	0.48545	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28095	28095	SRR26196852	SRX21908246	SRS18993954	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:38868197	elipsa mutant clutch 2	GSM7808260	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa mutant clutch 2	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM7808260	GSM7808260: elipsa mutant clutch 2; Danio rerio; RNA Seq	GSM7808260 r1	GSM7808260	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504	ElipsaMUT2_1.fq.gz ElipsaMUT2_2.fq.gz	fastq fastq	4544444600.0	22722223.0	GSM7808260 r1	0:100 1:100	A:1186329827;C:1072965608;G:1087757513;T:1197391652;N:0	100	100	1186329827	1072965608	1087757513	1197391652	0	SRX21908246	SRS18993954	SRA1721841	NTNU	NTNU	2	0.94545	0.95403	0.09705	0.09653	0.66576	0.66466	0.47893	0.47882	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28096	28096	SRR26196853	SRX21908245	SRS18993953	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:38868197	elipsa mutant clutch 1	GSM7808259	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa mutant clutch 1	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM7808259	GSM7808259: elipsa mutant clutch 1; Danio rerio; RNA Seq	GSM7808259 r1	GSM7808259	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504	ElipsaMUT1_1.fq.gz ElipsaMUT1_2.fq.gz	fastq fastq	4561346400.0	22806732.0	GSM7808259 r1	0:100 1:100	A:1192227498;C:1073309826;G:1091718946;T:1204090130;N:0	100	100	1192227498	1073309826	1091718946	1204090130	0	SRX21908245	SRS18993953	SRA1721841	NTNU	NTNU	2	0.94079	0.94928	0.09838	0.09859	0.67093	0.66975	0.47837	0.4824	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28097	28097	SRR26196854	SRX21908244	SRS18993950	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:38868197	elipsa control clutch 4	GSM7808258	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa control clutch 4	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM7808258	GSM7808258: elipsa control clutch 4; Danio rerio; RNA Seq	GSM7808258 r1	GSM7808258	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504	ElipsaCTRL4_1.fq.gz ElipsaCTRL4_2.fq.gz	fastq fastq	4534543600.0	22672718.0	GSM7808258 r1	0:100 1:100	A:1195456125;C:1060510332;G:1073683545;T:1204893598;N:0	100	100	1195456125	1060510332	1073683545	1204893598	0	SRX21908244	SRS18993950	SRA1721841	NTNU	NTNU	2	0.94686	0.95523	0.0948	0.09459	0.66259	0.66093	0.49251	0.49154	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28098	28098	SRR26196855	SRX21908243	SRS18993952	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:38868197	elipsa control clutch 3	GSM7808257	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa control clutch 3	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM7808257	GSM7808257: elipsa control clutch 3; Danio rerio; RNA Seq	GSM7808257 r1	GSM7808257	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504	ElipsaCTRL3_1.fq.gz ElipsaCTRL3_2.fq.gz	fastq fastq	4546464800.0	22732324.0	GSM7808257 r1	0:100 1:100	A:1192169234;C:1070218166;G:1081895902;T:1202181498;N:0	100	100	1192169234	1070218166	1081895902	1202181498	0	SRX21908243	SRS18993952	SRA1721841	NTNU	NTNU	2	0.94937	0.95815	0.09867	0.09825	0.66574	0.66478	0.49056	0.48959	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28099	28099	SRR26196856	SRX21908242	SRS18993951	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:38868197	elipsa control clutch 2	GSM7808256	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa control clutch 2	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM7808256	GSM7808256: elipsa control clutch 2; Danio rerio; RNA Seq	GSM7808256 r1	GSM7808256	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504	ElipsaCTRL2_1.fq.gz ElipsaCTRL2_2.fq.gz	fastq fastq	4557679200.0	22788396.0	GSM7808256 r1	0:100 1:100	A:1184954651;C:1080955864;G:1098377272;T:1193391413;N:0	100	100	1184954651	1080955864	1098377272	1193391413	0	SRX21908242	SRS18993951	SRA1721841	NTNU	NTNU	2	0.94378	0.95076	0.0855	0.0847	0.66604	0.66342	0.48858	0.48404	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28100	28100	SRR26196857	SRX21908241	SRS18993949	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:38868197	elipsa control clutch 1	GSM7808255	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa control clutch 1	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM7808255	GSM7808255: elipsa control clutch 1; Danio rerio; RNA Seq	GSM7808255 r1	GSM7808255	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504	ElipsaCTRL1_1.fq.gz ElipsaCTRL1_2.fq.gz	fastq fastq	4566618600.0	22833093.0	GSM7808255 r1	0:100 1:100	A:1193092402;C:1076659586;G:1094193492;T:1202673120;N:0	100	100	1193092402	1076659586	1094193492	1202673120	0	SRX21908241	SRS18993949	SRA1721841	NTNU	NTNU	2	0.94269	0.94899	0.09816	0.09712	0.66991	0.66925	0.47671	0.46995	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
30075	30075	SRR27700027	SRX23366859	SRS20229171	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:39798091	Smh mutant clutch 4	GSM8031712	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh mutant clutch 4	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM8031712	GSM8031712: Smh mutant clutch 4; Danio rerio; RNA Seq	GSM8031712 r1	GSM8031712	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459	SmhMUT4_1.fq.gz SmhMUT4_2.fq.gz	fastq fastq	4550057400.0	22750287.0	GSM8031712 r1	0:100 1:100	A:1198976754;C:1064190197;G:1077491671;T:1209398778;N:0	100	100	1198976754	1064190197	1077491671	1209398778	0	SRX23366859	SRS20229171	SRA1790727	NTNU	NTNU	2	0.94285	0.95266	0.101	0.10096	0.66145	0.65989	0.48209	0.47768	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30076	30076	SRR27700028	SRX23366858	SRS20229175	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:39798091	Smh mutant clutch 3	GSM8031711	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh mutant clutch 3	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM8031711	GSM8031711: Smh mutant clutch 3; Danio rerio; RNA Seq	GSM8031711 r1	GSM8031711	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459	SmhMUT3_1.fq.gz SmhMUT3_2.fq.gz	fastq fastq	4545452600.0	22727263.0	GSM8031711 r1	0:100 1:100	A:1188958937;C:1071903723;G:1087032258;T:1197557682;N:0	100	100	1188958937	1071903723	1087032258	1197557682	0	SRX23366858	SRS20229175	SRA1790727	NTNU	NTNU	2	0.94501	0.95409	0.09005	0.08947	0.66149	0.66062	0.46824	0.48019	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30077	30077	SRR27700029	SRX23366857	SRS20229173	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:39798091	Smh mutant clutch 2	GSM8031710	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh mutant clutch 2	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM8031710	GSM8031710: Smh mutant clutch 2; Danio rerio; RNA Seq	GSM8031710 r1	GSM8031710	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459	SmhMUT2_1.fq.gz SmhMUT2_2.fq.gz	fastq fastq	4548042000.0	22740210.0	GSM8031710 r1	0:100 1:100	A:1184618587;C:1077947166;G:1089628929;T:1195847318;N:0	100	100	1184618587	1077947166	1089628929	1195847318	0	SRX23366857	SRS20229173	SRA1790727	NTNU	NTNU	2	0.94502	0.95416	0.09209	0.092	0.66407	0.66214	0.48538	0.48509	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30078	30078	SRR27700030	SRX23366856	SRS20229174	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:39798091	Smh mutant clutch 1	GSM8031709	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh mutant clutch 1	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM8031709	GSM8031709: Smh mutant clutch 1; Danio rerio; RNA Seq	GSM8031709 r1	GSM8031709	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459	SmhMUT1_1.fq.gz SmhMUT1_2.fq.gz	fastq fastq	4544759600.0	22723798.0	GSM8031709 r1	0:100 1:100	A:1194011331;C:1066502346;G:1077923006;T:1206322917;N:0	100	100	1194011331	1066502346	1077923006	1206322917	0	SRX23366856	SRS20229174	SRA1790727	NTNU	NTNU	2	0.945	0.95433	0.09733	0.09796	0.66034	0.65951	0.477	0.47705	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30079	30079	SRR27700031	SRX23366855	SRS20229172	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:39798091	Smh control clutch 4	GSM8031708	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh control clutch 4	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM8031708	GSM8031708: Smh control clutch 4; Danio rerio; RNA Seq	GSM8031708 r1	GSM8031708	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459	SmhCTRL4_1.fq.gz SmhCTRL4_2.fq.gz	fastq fastq	4536141000.0	22680705.0	GSM8031708 r1	0:100 1:100	A:1196842043;C:1059535727;G:1071488375;T:1208274855;N:0	100	100	1196842043	1059535727	1071488375	1208274855	0	SRX23366855	SRS20229172	SRA1790727	NTNU	NTNU	2	0.94102	0.95093	0.09453	0.09431	0.66403	0.6631	0.49804	0.49818	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30080	30080	SRR27700032	SRX23366854	SRS20229170	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:39798091	Smh control clutch 3	GSM8031707	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh control clutch 3	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM8031707	GSM8031707: Smh control clutch 3; Danio rerio; RNA Seq	GSM8031707 r1	GSM8031707	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459	SmhCTRL3_1.fq.gz SmhCTRL3_2.fq.gz	fastq fastq	4543416000.0	22717080.0	GSM8031707 r1	0:100 1:100	A:1189755812;C:1071666785;G:1082665579;T:1199327824;N:0	100	100	1189755812	1071666785	1082665579	1199327824	0	SRX23366854	SRS20229170	SRA1790727	NTNU	NTNU	2	0.94571	0.95506	0.08989	0.09005	0.6632	0.66107	0.49631	0.49649	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30081	30081	SRR27700033	SRX23366853	SRS20229169	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:39798091	Smh control clutch 2	GSM8031706	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh control clutch 2	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM8031706	GSM8031706: Smh control clutch 2; Danio rerio; RNA Seq	GSM8031706 r1	GSM8031706	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459	SmhCTRL2_2.fq.gz SmhCTRL2_1.fq.gz	fastq fastq	4536576000.0	22682880.0	GSM8031706 r1	0:100 1:100	A:1180961957;C:1074391564;G:1088552770;T:1192669709;N:0	100	100	1180961957	1074391564	1088552770	1192669709	0	SRX23366853	SRS20229169	SRA1790727	NTNU	NTNU	2	0.94324	0.95313	0.08618	0.08685	0.66399	0.66216	0.49362	0.49644	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30082	30082	SRR27700034	SRX23366852	SRS20229168	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:39798091	Smh control clutch 1	GSM8031705	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh control clutch 1	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM8031705	GSM8031705: Smh control clutch 1; Danio rerio; RNA Seq	GSM8031705 r1	GSM8031705	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459	SmhCTRL1_1.fq.gz SmhCTRL1_2.fq.gz	fastq fastq	4546026800.0	22730134.0	GSM8031705 r1	0:100 1:100	A:1201447089;C:1060722844;G:1073012718;T:1210844149;N:0	100	100	1201447089	1060722844	1073012718	1210844149	0	SRX23366852	SRS20229168	SRA1790727	NTNU	NTNU	2	0.94554	0.95419	0.09192	0.09168	0.66436	0.66222	0.4762	0.48114	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
34182	34182	SRR31399561	SRX26768859	SRS23256160	SRP546207	PRJNA1188114	Reduced EIF6 dosage attenuates TP53 activation in models of Shwachman Diamond syndrome	GSE282310	Transcriptome Analysis	Shwachman Diamond syndrome SDS is characterized by neutropenia exocrine pancreatic insufficiency and bony abnormalities with an increased risk of myeloid neoplasia. Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects. We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models confirmed in patient derived tissues and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression 5 25% of the wildtype levels that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS EIF6 TP53 and cellular stress responses offer promising insights into SDS pathogenesis somatic genetic rescue and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 / or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 / and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39 we used EBSeq R package for differentially expressed gene detection between eif6 / and eif6+/+ fold change > 2 and P < 0.05.			eif6 3	GSM8641203	source name:whole larvae\|tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 KO\|geo loc name:missing\|collection date:missing	eif6 3	Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally reads were removed if they: 1 lacked a 3’ adapter sequence 2 were 5’ 3’ adapter ligation products 3 were 5’ 5’ adapter ligation products 4 were shorter than 18 nt or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters: f N 0 M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values	whole larvae	5 dpf	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 KO	GSM8641203	GSM8641203: eif6 3; Danio rerio; RNA Seq	GSM8641203 r1	GSM8641203	1	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP546207	eif6_3_1.fq.gz eif6_3_2.fq.gz	fastq fastq	6955801200.0	34779006.0	GSM8641203 r1	0:100 1:100	A:1784502248;C:1653592398;G:1716091635;T:1801614919;N:0	100	100	1784502248	1653592398	1716091635	1801614919	0	SRX26768859	SRS23256160	SRA2017777	Cleveland Clinic	Cleveland Clinic												B	B	biological fallback assumption	bgi	bgi	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2024-11-19	Larval	Larval	Whole Organism	All anatomical structures
34183	34183	SRR31399562	SRX26768858	SRS23256161	SRP546207	PRJNA1188114	Reduced EIF6 dosage attenuates TP53 activation in models of Shwachman Diamond syndrome	GSE282310	Transcriptome Analysis	Shwachman Diamond syndrome SDS is characterized by neutropenia exocrine pancreatic insufficiency and bony abnormalities with an increased risk of myeloid neoplasia. Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects. We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models confirmed in patient derived tissues and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression 5 25% of the wildtype levels that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS EIF6 TP53 and cellular stress responses offer promising insights into SDS pathogenesis somatic genetic rescue and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 / or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 / and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39 we used EBSeq R package for differentially expressed gene detection between eif6 / and eif6+/+ fold change > 2 and P < 0.05.			eif6 2	GSM8641202	source name:whole larvae\|tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 KO\|geo loc name:missing\|collection date:missing	eif6 2	Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally reads were removed if they: 1 lacked a 3’ adapter sequence 2 were 5’ 3’ adapter ligation products 3 were 5’ 5’ adapter ligation products 4 were shorter than 18 nt or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters: f N 0 M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values	whole larvae	5 dpf	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 KO	GSM8641202	GSM8641202: eif6 2; Danio rerio; RNA Seq	GSM8641202 r1	GSM8641202	1	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP546207	eif6_2_1.fq.gz eif6_2_2.fq.gz	fastq fastq	6968721400.0	34843607.0	GSM8641202 r1	0:100 1:100	A:1798630009;C:1650901437;G:1708195694;T:1810994260;N:0	100	100	1798630009	1650901437	1708195694	1810994260	0	SRX26768858	SRS23256161	SRA2017777	Cleveland Clinic	Cleveland Clinic												B	B	biological fallback assumption	bgi	bgi	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2024-11-19	Larval	Larval	Whole Organism	All anatomical structures
34184	34184	SRR31399563	SRX26768857	SRS23256159	SRP546207	PRJNA1188114	Reduced EIF6 dosage attenuates TP53 activation in models of Shwachman Diamond syndrome	GSE282310	Transcriptome Analysis	Shwachman Diamond syndrome SDS is characterized by neutropenia exocrine pancreatic insufficiency and bony abnormalities with an increased risk of myeloid neoplasia. Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects. We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models confirmed in patient derived tissues and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression 5 25% of the wildtype levels that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS EIF6 TP53 and cellular stress responses offer promising insights into SDS pathogenesis somatic genetic rescue and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 / or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 / and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39 we used EBSeq R package for differentially expressed gene detection between eif6 / and eif6+/+ fold change > 2 and P < 0.05.			eif6 1	GSM8641201	source name:whole larvae\|tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 KO\|geo loc name:missing\|collection date:missing	eif6 1	Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally reads were removed if they: 1 lacked a 3’ adapter sequence 2 were 5’ 3’ adapter ligation products 3 were 5’ 5’ adapter ligation products 4 were shorter than 18 nt or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters: f N 0 M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values	whole larvae	5 dpf	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 KO	GSM8641201	GSM8641201: eif6 1; Danio rerio; RNA Seq	GSM8641201 r1	GSM8641201	1	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP546207	eif6_1_1.fq.gz eif6_1_2.fq.gz	fastq fastq	6976474200.0	34882371.0	GSM8641201 r1	0:100 1:100	A:1819387431;C:1630709320;G:1698463303;T:1827914146;N:0	100	100	1819387431	1630709320	1698463303	1827914146	0	SRX26768857	SRS23256159	SRA2017777	Cleveland Clinic	Cleveland Clinic												B	B	biological fallback assumption	bgi	bgi	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2024-11-19	Larval	Larval	Whole Organism	All anatomical structures
34185	34185	SRR31399564	SRX26768856	SRS23256158	SRP546207	PRJNA1188114	Reduced EIF6 dosage attenuates TP53 activation in models of Shwachman Diamond syndrome	GSE282310	Transcriptome Analysis	Shwachman Diamond syndrome SDS is characterized by neutropenia exocrine pancreatic insufficiency and bony abnormalities with an increased risk of myeloid neoplasia. Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects. We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models confirmed in patient derived tissues and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression 5 25% of the wildtype levels that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS EIF6 TP53 and cellular stress responses offer promising insights into SDS pathogenesis somatic genetic rescue and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 / or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 / and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39 we used EBSeq R package for differentially expressed gene detection between eif6 / and eif6+/+ fold change > 2 and P < 0.05.			wt3	GSM8641200	source name:whole larvae\|tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 wildtype\|geo loc name:missing\|collection date:missing	wt3	Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally reads were removed if they: 1 lacked a 3’ adapter sequence 2 were 5’ 3’ adapter ligation products 3 were 5’ 5’ adapter ligation products 4 were shorter than 18 nt or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters: f N 0 M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values	whole larvae	5 dpf	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 wildtype	GSM8641200	GSM8641200: wt3; Danio rerio; RNA Seq	GSM8641200 r1	GSM8641200	1	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP546207	wt3_1.fq.gz wt3_2.fq.gz	fastq fastq	6990771600.0	34953858.0	GSM8641200 r1	0:100 1:100	A:1823561732;C:1639273273;G:1691098287;T:1836838308;N:0	100	100	1823561732	1639273273	1691098287	1836838308	0	SRX26768856	SRS23256158	SRA2017777	Cleveland Clinic	Cleveland Clinic												B	B	biological fallback assumption	bgi	bgi	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2024-11-19	Larval	Larval	Whole Organism	All anatomical structures
34186	34186	SRR31399565	SRX26768855	SRS23256157	SRP546207	PRJNA1188114	Reduced EIF6 dosage attenuates TP53 activation in models of Shwachman Diamond syndrome	GSE282310	Transcriptome Analysis	Shwachman Diamond syndrome SDS is characterized by neutropenia exocrine pancreatic insufficiency and bony abnormalities with an increased risk of myeloid neoplasia. Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects. We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models confirmed in patient derived tissues and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression 5 25% of the wildtype levels that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS EIF6 TP53 and cellular stress responses offer promising insights into SDS pathogenesis somatic genetic rescue and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 / or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 / and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39 we used EBSeq R package for differentially expressed gene detection between eif6 / and eif6+/+ fold change > 2 and P < 0.05.			wt2	GSM8641199	source name:whole larvae\|tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 wildtype\|geo loc name:missing\|collection date:missing	wt2	Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally reads were removed if they: 1 lacked a 3’ adapter sequence 2 were 5’ 3’ adapter ligation products 3 were 5’ 5’ adapter ligation products 4 were shorter than 18 nt or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters: f N 0 M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values	whole larvae	5 dpf	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 wildtype	GSM8641199	GSM8641199: wt2; Danio rerio; RNA Seq	GSM8641199 r1	GSM8641199	1	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP546207	wt2_1.fq.gz wt2_2.fq.gz	fastq fastq	6996780600.0	34983903.0	GSM8641199 r1	0:100 1:100	A:1819793027;C:1646550105;G:1701161650;T:1829275818;N:0	100	100	1819793027	1646550105	1701161650	1829275818	0	SRX26768855	SRS23256157	SRA2017777	Cleveland Clinic	Cleveland Clinic												B	B	biological fallback assumption	bgi	bgi	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2024-11-19	Larval	Larval	Whole Organism	All anatomical structures
34187	34187	SRR31399566	SRX26768854	SRS23256156	SRP546207	PRJNA1188114	Reduced EIF6 dosage attenuates TP53 activation in models of Shwachman Diamond syndrome	GSE282310	Transcriptome Analysis	Shwachman Diamond syndrome SDS is characterized by neutropenia exocrine pancreatic insufficiency and bony abnormalities with an increased risk of myeloid neoplasia. Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects. We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models confirmed in patient derived tissues and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression 5 25% of the wildtype levels that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS EIF6 TP53 and cellular stress responses offer promising insights into SDS pathogenesis somatic genetic rescue and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 / or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 / and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39 we used EBSeq R package for differentially expressed gene detection between eif6 / and eif6+/+ fold change > 2 and P < 0.05.			wt1	GSM8641198	source name:whole larvae\|tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 wildtype\|geo loc name:missing\|collection date:missing	wt1	Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally reads were removed if they: 1 lacked a 3’ adapter sequence 2 were 5’ 3’ adapter ligation products 3 were 5’ 5’ adapter ligation products 4 were shorter than 18 nt or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters: f N 0 M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values	whole larvae	5 dpf	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 wildtype	GSM8641198	GSM8641198: wt1; Danio rerio; RNA Seq	GSM8641198 r1	GSM8641198	1	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP546207	wt1_1.fq.gz wt1_2.fq.gz	fastq fastq	6976844600.0	34884223.0	GSM8641198 r1	0:100 1:100	A:1807619362;C:1649374675;G:1693243894;T:1826606669;N:0	100	100	1807619362	1649374675	1693243894	1826606669	0	SRX26768854	SRS23256156	SRA2017777	Cleveland Clinic	Cleveland Clinic												B	B	biological fallback assumption	bgi	bgi	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2024-11-19	Larval	Larval	Whole Organism	All anatomical structures
50717	50717	SRR8257205	SRX5074433	SRS4088243	SRP171045	PRJNA507426	Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]	GSE123058	Transcriptome Analysis	The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development we found two distinct functions clearly separated in space and time. During early development p63 binds enhancers associated to neural genes where it limits Sox3 binding and reduces the expression of these neural genes. Indeed we show that p63 and Sox3 are co expressed in the neural plate border. Later in development p63 binds enhancers associated to epidermal genes and promotes their expression acting as a pioneer factor as it binds to non accessible chromatin and is required for its opening. Therefore our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants	parent bioproject:PRJNA507423	pubmed:31296872	RNAseq in zebrafish wild type embryos at 36hpf replicate 3	GSM3494529	tissue:whole embryo\|developmental stage:36hpf\|genotype:WT	RNAseq in zebrafish wild type embryos at 36hpf replicate 3	Reads were aligned against reference genome using STAR software and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo		RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were cultivated at 28°C in E3 medium until desired developmental stage	developmental stage:36hpf\|genotype:WT	GSM3494529	GSM3494529: RNAseq in zebrafish wild type embryos at 36hpf replicate 3; Danio rerio; RNA Seq	GSM3494529		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM3494529	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP171045	RNAseq_zebra_WT_36hpf_rep3.fq.gz	fastq	2560587500.0	51211750.0	GSM3494529 r1	0:50	A:719232941;C:550474431;G:576590260;T:714289868;N:0	50		719232941	550474431	576590260	714289868	0	SRX5074433	SRS4088243	SRA815839	GEO	CABD/CSIC	1	0.93981		0.10951		0.71388		0.48297		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2018-11-28	Pharyngula	Embryo	Whole Organism	All anatomical structures
50718	50718	SRR8257204	SRX5074432	SRS4088242	SRP171045	PRJNA507426	Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]	GSE123058	Transcriptome Analysis	The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development we found two distinct functions clearly separated in space and time. During early development p63 binds enhancers associated to neural genes where it limits Sox3 binding and reduces the expression of these neural genes. Indeed we show that p63 and Sox3 are co expressed in the neural plate border. Later in development p63 binds enhancers associated to epidermal genes and promotes their expression acting as a pioneer factor as it binds to non accessible chromatin and is required for its opening. Therefore our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants	parent bioproject:PRJNA507423	pubmed:31296872	RNAseq in zebrafish wild type embryos at 36hpf replicate 2	GSM3494528	tissue:whole embryo\|developmental stage:36hpf\|genotype:WT	RNAseq in zebrafish wild type embryos at 36hpf replicate 2	Reads were aligned against reference genome using STAR software and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo		RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were cultivated at 28°C in E3 medium until desired developmental stage	developmental stage:36hpf\|genotype:WT	GSM3494528	GSM3494528: RNAseq in zebrafish wild type embryos at 36hpf replicate 2; Danio rerio; RNA Seq	GSM3494528		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM3494528	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP171045	RNAseq_zebra_WT_36hpf_rep2.fq.gz	fastq	2775840750.0	55516815.0	GSM3494528 r1	0:50	A:783053027;C:587947172;G:603351259;T:801489292;N:0	50		783053027	587947172	603351259	801489292	0	SRX5074432	SRS4088242	SRA815839	GEO	CABD/CSIC	1	0.93386		0.11853		0.7007		0.48856		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2018-11-28	Pharyngula	Embryo	Whole Organism	All anatomical structures
50719	50719	SRR8257203	SRX5074431	SRS4088241	SRP171045	PRJNA507426	Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]	GSE123058	Transcriptome Analysis	The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development we found two distinct functions clearly separated in space and time. During early development p63 binds enhancers associated to neural genes where it limits Sox3 binding and reduces the expression of these neural genes. Indeed we show that p63 and Sox3 are co expressed in the neural plate border. Later in development p63 binds enhancers associated to epidermal genes and promotes their expression acting as a pioneer factor as it binds to non accessible chromatin and is required for its opening. Therefore our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants	parent bioproject:PRJNA507423	pubmed:31296872	RNAseq in zebrafish wild type embryos at 36hpf replicate 1	GSM3494527	tissue:whole embryo\|developmental stage:36hpf\|genotype:WT	RNAseq in zebrafish wild type embryos at 36hpf replicate 1	Reads were aligned against reference genome using STAR software and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo		RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were cultivated at 28°C in E3 medium until desired developmental stage	developmental stage:36hpf\|genotype:WT	GSM3494527	GSM3494527: RNAseq in zebrafish wild type embryos at 36hpf replicate 1; Danio rerio; RNA Seq	GSM3494527		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM3494527	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP171045	RNAseq_zebra_WT_36hpf_rep1.fq.gz	fastq	2638769750.0	52775395.0	GSM3494527 r1	0:50	A:749627286;C:556213831;G:574654547;T:758274086;N:0	50		749627286	556213831	574654547	758274086	0	SRX5074431	SRS4088241	SRA815839	GEO	CABD/CSIC	1	0.92992		0.12022		0.72174		0.49097		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2018-11-28	Pharyngula	Embryo	Whole Organism	All anatomical structures
50720	50720	SRR8257202	SRX5074430	SRS4088240	SRP171045	PRJNA507426	Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]	GSE123058	Transcriptome Analysis	The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development we found two distinct functions clearly separated in space and time. During early development p63 binds enhancers associated to neural genes where it limits Sox3 binding and reduces the expression of these neural genes. Indeed we show that p63 and Sox3 are co expressed in the neural plate border. Later in development p63 binds enhancers associated to epidermal genes and promotes their expression acting as a pioneer factor as it binds to non accessible chromatin and is required for its opening. Therefore our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants	parent bioproject:PRJNA507423	pubmed:31296872	RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 3	GSM3494526	tissue:whole embryo\|developmental stage:36hpf\|genotype:tp63 /	RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 3	Reads were aligned against reference genome using STAR software and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo		RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were cultivated at 28°C in E3 medium until desired developmental stage	developmental stage:36hpf\|genotype:tp63 /	GSM3494526	GSM3494526: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 3; Danio rerio; RNA Seq	GSM3494526		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM3494526	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP171045	RNAseq_zebra_p63mut_36hpf_rep3.fq.gz	fastq	2651169450.0	53023389.0	GSM3494526 r1	0:50	A:752539060;C:560162268;G:581624300;T:756843822;N:0	50		752539060	560162268	581624300	756843822	0	SRX5074430	SRS4088240	SRA815839	GEO	CABD/CSIC	1	0.94022		0.12949		0.70019		0.50336		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2018-11-28	Pharyngula	Embryo	Whole Organism	All anatomical structures
50721	50721	SRR8257201	SRX5074429	SRS4088239	SRP171045	PRJNA507426	Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]	GSE123058	Transcriptome Analysis	The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development we found two distinct functions clearly separated in space and time. During early development p63 binds enhancers associated to neural genes where it limits Sox3 binding and reduces the expression of these neural genes. Indeed we show that p63 and Sox3 are co expressed in the neural plate border. Later in development p63 binds enhancers associated to epidermal genes and promotes their expression acting as a pioneer factor as it binds to non accessible chromatin and is required for its opening. Therefore our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants	parent bioproject:PRJNA507423	pubmed:31296872	RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 2	GSM3494525	tissue:whole embryo\|developmental stage:36hpf\|genotype:tp63 /	RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 2	Reads were aligned against reference genome using STAR software and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo		RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were cultivated at 28°C in E3 medium until desired developmental stage	developmental stage:36hpf\|genotype:tp63 /	GSM3494525	GSM3494525: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 2; Danio rerio; RNA Seq	GSM3494525		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM3494525	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP171045	RNAseq_zebra_p63mut_36hpf_rep2.fq.gz	fastq	2821501700.0	56430034.0	GSM3494525 r1	0:50	A:795357588;C:599294949;G:620563224;T:806285939;N:0	50		795357588	599294949	620563224	806285939	0	SRX5074429	SRS4088239	SRA815839	GEO	CABD/CSIC	1	0.93671		0.12314		0.6957		0.48362		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2018-11-28	Pharyngula	Embryo	Whole Organism	All anatomical structures
50722	50722	SRR8257200	SRX5074428	SRS4088238	SRP171045	PRJNA507426	Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq]	GSE123058	Transcriptome Analysis	The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development we found two distinct functions clearly separated in space and time. During early development p63 binds enhancers associated to neural genes where it limits Sox3 binding and reduces the expression of these neural genes. Indeed we show that p63 and Sox3 are co expressed in the neural plate border. Later in development p63 binds enhancers associated to epidermal genes and promotes their expression acting as a pioneer factor as it binds to non accessible chromatin and is required for its opening. Therefore our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants	parent bioproject:PRJNA507423	pubmed:31296872	RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 1	GSM3494524	tissue:whole embryo\|developmental stage:36hpf\|genotype:tp63 /	RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 1	Reads were aligned against reference genome using STAR software and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo		RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were cultivated at 28°C in E3 medium until desired developmental stage	developmental stage:36hpf\|genotype:tp63 /	GSM3494524	GSM3494524: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 1; Danio rerio; RNA Seq	GSM3494524		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM3494524	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP171045	RNAseq_zebra_p63mut_36hpf_rep1.fq.gz	fastq	2592494100.0	51849882.0	GSM3494524 r1	0:50	A:730978948;C:550803197;G:572081489;T:738630466;N:0	50		730978948	550803197	572081489	738630466	0	SRX5074428	SRS4088238	SRA815839	GEO	CABD/CSIC	1	0.94035		0.11571		0.70796		0.49468		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2018-11-28	Pharyngula	Embryo	Whole Organism	All anatomical structures
52944	52944	SRR9609439	SRX6372833	SRS5033898	SRP212216	PRJNA551488	TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos	GSE133459	Transcriptome Analysis	In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.			PBCAB Replicate 3	GSM3909672	tissue:Whole Embryo\|Stage:12 hpf\|treatment:PBCAB	PBCAB Replicate 3	Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.	Whole Embryo	Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.	Stage:12 hpf\|treatment:PBCAB	GSM3909672	GSM3909672: PBCAB Replicate 3; Danio rerio; RNA Seq	GSM3909672		1	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	GEO Accession:GSM3909672	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP212216	PBCAB_12hpf_zebrafish_biological_replicate3.fq.gz	fastq	1283013300.0	25660266.0	GSM3909672 r1	0:50	A:339417002;C:304649204;G:297783450;T:341163644;N:0	50		339417002	304649204	297783450	341163644	0	SRX6372833	SRS5033898	SRA914500	GEO	Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School	1	0.94342		0.10559		0.72401		0.47431		50		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2019-06-27	Segmentation	Embryo	Whole Organism	All anatomical structures
52945	52945	SRR9609438	SRX6372832	SRS5033897	SRP212216	PRJNA551488	TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos	GSE133459	Transcriptome Analysis	In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.			PBCAB Replicate 2	GSM3909671	tissue:Whole Embryo\|Stage:12 hpf\|treatment:PBCAB	PBCAB Replicate 2	Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.	Whole Embryo	Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.	Stage:12 hpf\|treatment:PBCAB	GSM3909671	GSM3909671: PBCAB Replicate 2; Danio rerio; RNA Seq	GSM3909671		1	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	GEO Accession:GSM3909671	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP212216	PBCAB_12hpf_zebrafish_biological_replicate2.fq.gz	fastq	1282475700.0	25649514.0	GSM3909671 r1	0:50	A:339635626;C:302447093;G:295507893;T:344885088;N:0	50		339635626	302447093	295507893	344885088	0	SRX6372832	SRS5033897	SRA914500	GEO	Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School	1	0.94396		0.10502		0.71465		0.47566		50		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2019-06-27	Segmentation	Embryo	Whole Organism	All anatomical structures
52946	52946	SRR9609437	SRX6372831	SRS5033896	SRP212216	PRJNA551488	TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos	GSE133459	Transcriptome Analysis	In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.			PBCAB Replicate 1	GSM3909670	tissue:Whole Embryo\|Stage:12 hpf\|treatment:PBCAB	PBCAB Replicate 1	Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.	Whole Embryo	Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.	Stage:12 hpf\|treatment:PBCAB	GSM3909670	GSM3909670: PBCAB Replicate 1; Danio rerio; RNA Seq	GSM3909670		1	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	GEO Accession:GSM3909670	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP212216	PBCAB_12hpf_zebrafish_biological_replicate1.fq.gz	fastq	1147572700.0	22951454.0	GSM3909670 r1	0:50	A:300633532;C:273711082;G:268229512;T:304998574;N:0	50		300633532	273711082	268229512	304998574	0	SRX6372831	SRS5033896	SRA914500	GEO	Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School	1	0.94418		0.09965		0.72746		0.47644		50		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2019-06-27	Segmentation	Embryo	Whole Organism	All anatomical structures
52947	52947	SRR9609436	SRX6372830	SRS5033895	SRP212216	PRJNA551488	TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos	GSE133459	Transcriptome Analysis	In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.			NF YA DN Replicate 3	GSM3909669	tissue:Whole Embryo\|Stage:12 hpf\|treatment:NF YA DN	NF YA DN Replicate 3	Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.	Whole Embryo	Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.	Stage:12 hpf\|treatment:NF YA DN	GSM3909669	GSM3909669: NF YA DN Replicate 3; Danio rerio; RNA Seq	GSM3909669		1	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	GEO Accession:GSM3909669	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP212216	NFYADN_12hpf_zebrafish_biological_replicate3.fq.gz	fastq	1282414400.0	25648288.0	GSM3909669 r1	0:50	A:334687310;C:307161534;G:302070174;T:338495382;N:0	50		334687310	307161534	302070174	338495382	0	SRX6372830	SRS5033895	SRA914500	GEO	Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School	1	0.94359		0.09476		0.72529		0.47117		50		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2019-06-27	Segmentation	Embryo	Whole Organism	All anatomical structures
52948	52948	SRR9609435	SRX6372829	SRS5033894	SRP212216	PRJNA551488	TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos	GSE133459	Transcriptome Analysis	In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.			NF YA DN Replicate 2	GSM3909668	tissue:Whole Embryo\|Stage:12 hpf\|treatment:NF YA DN	NF YA DN Replicate 2	Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.	Whole Embryo	Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.	Stage:12 hpf\|treatment:NF YA DN	GSM3909668	GSM3909668: NF YA DN Replicate 2; Danio rerio; RNA Seq	GSM3909668		1	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	GEO Accession:GSM3909668	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP212216	NFYADN_12hpf_zebrafish_biological_replicate2.fq.gz	fastq	1281370000.0	25627400.0	GSM3909668 r1	0:50	A:335735118;C:306450529;G:298815464;T:340368889;N:0	50		335735118	306450529	298815464	340368889	0	SRX6372829	SRS5033894	SRA914500	GEO	Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School	1	0.94338		0.09412		0.7204		0.48662		50		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2019-06-27	Segmentation	Embryo	Whole Organism	All anatomical structures
52949	52949	SRR9609434	SRX6372828	SRS5033893	SRP212216	PRJNA551488	TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos	GSE133459	Transcriptome Analysis	In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.			NF YA DN Replicate 1	GSM3909667	tissue:Whole Embryo\|Stage:12 hpf\|treatment:NF YA DN	NF YA DN Replicate 1	Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.	Whole Embryo	Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.	Stage:12 hpf\|treatment:NF YA DN	GSM3909667	GSM3909667: NF YA DN Replicate 1; Danio rerio; RNA Seq	GSM3909667		1	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	GEO Accession:GSM3909667	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP212216	NFYADN_12hpf_zebrafish_biological_replicate1.fq.gz	fastq	1278504750.0	25570095.0	GSM3909667 r1	0:50	A:334370606;C:306252389;G:299065406;T:338816349;N:0	50		334370606	306252389	299065406	338816349	0	SRX6372828	SRS5033893	SRA914500	GEO	Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School	1	0.94373		0.09279		0.7191		0.48836		50		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2019-06-27	Segmentation	Embryo	Whole Organism	All anatomical structures
52950	52950	SRR9609433	SRX6372827	SRS5033892	SRP212216	PRJNA551488	TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos	GSE133459	Transcriptome Analysis	In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.			GFP Replicate 3	GSM3909666	tissue:Whole Embryo\|Stage:12 hpf\|treatment:GFP	GFP Replicate 3	Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.	Whole Embryo	Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.	Stage:12 hpf\|treatment:GFP	GSM3909666	GSM3909666: GFP Replicate 3; Danio rerio; RNA Seq	GSM3909666		1	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	GEO Accession:GSM3909666	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP212216	GFP_12hpf_zebrafish_biological_replicate3.fq.gz	fastq	1284828600.0	25696572.0	GSM3909666 r1	0:50	A:340467505;C:302914392;G:291984238;T:349462465;N:0	50		340467505	302914392	291984238	349462465	0	SRX6372827	SRS5033892	SRA914500	GEO	Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School	1	0.94288		0.0963		0.71713		0.4793		50		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2019-06-27	Segmentation	Embryo	Whole Organism	All anatomical structures
52951	52951	SRR9609432	SRX6372826	SRS5033891	SRP212216	PRJNA551488	TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos	GSE133459	Transcriptome Analysis	In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.			GFP Replicate 2	GSM3909665	tissue:Whole Embryo\|Stage:12 hpf\|treatment:GFP	GFP Replicate 2	Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.	Whole Embryo	Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.	Stage:12 hpf\|treatment:GFP	GSM3909665	GSM3909665: GFP Replicate 2; Danio rerio; RNA Seq	GSM3909665		1	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	GEO Accession:GSM3909665	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP212216	GFP_12hpf_zebrafish_biological_replicate2.fq.gz	fastq	1274433150.0	25488663.0	GSM3909665 r1	0:50	A:336050330;C:303141446;G:297353928;T:337887446;N:0	50		336050330	303141446	297353928	337887446	0	SRX6372826	SRS5033891	SRA914500	GEO	Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School	1	0.94266		0.0966		0.72476		0.47615		50		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2019-06-27	Segmentation	Embryo	Whole Organism	All anatomical structures
52952	52952	SRR9609431	SRX6372825	SRS5033890	SRP212216	PRJNA551488	TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos	GSE133459	Transcriptome Analysis	In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.			GFP Replicate 1	GSM3909664	tissue:Whole Embryo\|Stage:12 hpf\|treatment:GFP	GFP Replicate 1	Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.	Whole Embryo	Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.	Stage:12 hpf\|treatment:GFP	GSM3909664	GSM3909664: GFP Replicate 1; Danio rerio; RNA Seq	GSM3909664		1	Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.	GEO Accession:GSM3909664	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP212216	GFP_12hpf_zebrafish_biological_replicate1.fq.gz	fastq	1278273350.0	25565467.0	GSM3909664 r1	0:50	A:336762127;C:304299745;G:297929933;T:339281545;N:0	50		336762127	304299745	297929933	339281545	0	SRX6372825	SRS5033890	SRA914500	GEO	Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School	1	0.94207		0.09472		0.72642		0.47988		50		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2019-06-27	Segmentation	Embryo	Whole Organism	All anatomical structures
57168	57168	SRR11237928	SRX7849591	SRS6259054	SRP251591	PRJNA610302	Transcriptome analysis of wild type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development	GSE146394	Transcriptome Analysis	To study the function of zebrafish nuclear pores during early embryogenesis we generated maternal zygotic double mutant of nup85;nup133 MZnup85;nup133 using CRISPR/Cas9 and report the transcriptome wide changes in comparison to wild type WT embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal to zygotic transition. Overall design: mRNA profile of zebrafish WT and MZnup85;nup133 embryos at 4.3 hpf or at stage with dome morphology			MZ 7hpf Dome	GSM4379949	source name:whole mount embryo\|strain:AB\|tissue:whole mount embryo\|developmental stage:7 hpf nup85 / ;nup133 /	MZ 7hpf Dome	BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50 then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead B. et al. Nat. Methods 2012 and Li B. & Dewey C. N. BMC Bioinformatics 2011. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample	whole mount embryo		total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols		strain:AB\|tissue:whole mount embryo\|developmental stage:7 hpf nup85 / ;nup133 /	GSM4379949	GSM4379949: MZ 7hpf Dome; Danio rerio; RNA Seq	GSM4379949		1	total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols	GEO Accession:GSM4379949	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP251591	MZ_7h_Dome_1.fq.gz	fastq	1065702100.0	21314042.0	GSM4379949 r1	0:50 1:0	A:283324952;C:247492025;G:242059243;T:291819466;N:1006414	50	0	283324952	247492025	242059243	291819466	1006414	SRX7849591	SRS6259054	SRA1051151	GEO	School of life science, Tsinghua University	1	0.9445		0.07752		0.72565		0.4828		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2020-03-04	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
57169	57169	SRR11237927	SRX7849590	SRS6259053	SRP251591	PRJNA610302	Transcriptome analysis of wild type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development	GSE146394	Transcriptome Analysis	To study the function of zebrafish nuclear pores during early embryogenesis we generated maternal zygotic double mutant of nup85;nup133 MZnup85;nup133 using CRISPR/Cas9 and report the transcriptome wide changes in comparison to wild type WT embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal to zygotic transition. Overall design: mRNA profile of zebrafish WT and MZnup85;nup133 embryos at 4.3 hpf or at stage with dome morphology			MZ 4.3hpf 1k	GSM4379948	source name:whole mount embryo\|strain:AB\|tissue:whole mount embryo\|developmental stage:4.3 hpf nup85 / ;nup133 /	MZ 4.3hpf 1k	BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50 then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead B. et al. Nat. Methods 2012 and Li B. & Dewey C. N. BMC Bioinformatics 2011. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample	whole mount embryo		total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols		strain:AB\|tissue:whole mount embryo\|developmental stage:4.3 hpf nup85 / ;nup133 /	GSM4379948	GSM4379948: MZ 4.3hpf 1k; Danio rerio; RNA Seq	GSM4379948		1	total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols	GEO Accession:GSM4379948	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP251591	MZ_4.3h_1k_1.fq.gz	fastq	1059959500.0	21199190.0	GSM4379948 r1	0:50 1:0	A:278456455;C:249622199;G:244991579;T:285847713;N:1041554	50	0	278456455	249622199	244991579	285847713	1041554	SRX7849590	SRS6259053	SRA1051151	GEO	School of life science, Tsinghua University	1	0.94882		0.03659		0.74361		0.48435		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2020-03-04	Blastula	Embryo	Embryo Imprecise	All anatomical structures
57170	57170	SRR11237926	SRX7849589	SRS6259052	SRP251591	PRJNA610302	Transcriptome analysis of wild type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development	GSE146394	Transcriptome Analysis	To study the function of zebrafish nuclear pores during early embryogenesis we generated maternal zygotic double mutant of nup85;nup133 MZnup85;nup133 using CRISPR/Cas9 and report the transcriptome wide changes in comparison to wild type WT embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal to zygotic transition. Overall design: mRNA profile of zebrafish WT and MZnup85;nup133 embryos at 4.3 hpf or at stage with dome morphology			WT 4.3hpf Dome	GSM4379947	source name:whole mount embryo\|strain:AB\|tissue:whole mount embryo\|developmental stage:4.3 hpf type	WT 4.3hpf Dome	BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50 then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead B. et al. Nat. Methods 2012 and Li B. & Dewey C. N. BMC Bioinformatics 2011. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample	whole mount embryo		total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols		strain:AB\|tissue:whole mount embryo\|developmental stage:4.3 hpf type	GSM4379947	GSM4379947: WT 4.3hpf Dome; Danio rerio; RNA Seq	GSM4379947		1	total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols	GEO Accession:GSM4379947	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP251591	WT_4.3h_Dome_1.fq.gz	fastq	1058158950.0	21163179.0	GSM4379947 r1	0:50 1:0	A:279307143;C:247873321;G:244308380;T:285580565;N:1089541	50	0	279307143	247873321	244308380	285580565	1089541	SRX7849589	SRS6259052	SRA1051151	GEO	School of life science, Tsinghua University	1	0.94374		0.05294		0.74164		0.48705		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2020-03-04	Blastula	Embryo	Embryo Imprecise	All anatomical structures
59480	59480	SRR11922874	SRX8468588	SRS6769276	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo Aldh3a1 KO rep6	GSM4590772	source name:zebrafish embryo\|genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	zebrafish embryo Aldh3a1 KO rep6	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	GSM4590772	GSM4590772: zebrafish embryo Aldh3a1 KO rep6; Danio rerio; RNA Seq	GSM4590772		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590772	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	12_aldh3a1----homo-48hpf-6_1.fq.gz 12_aldh3a1----homo-48hpf-6_2.fq.gz	fastq fastq	4660603600.0	46606036.0	GSM4590772 r1	0:100 1:100	A:1396899993;C:924291840;G:902974172;T:1436437595;N:0	100	100	1396899993	924291840	902974172	1436437595	0	SRX8468588	SRS6769276	SRA1083013	GEO	ZMF, University Heidelberg	1	0.90281		0.2525		0.75943		0.62165		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59481	59481	SRR11922873	SRX8468587	SRS6769275	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo Aldh3a1 KO rep5	GSM4590771	source name:zebrafish embryo\|genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	zebrafish embryo Aldh3a1 KO rep5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	GSM4590771	GSM4590771: zebrafish embryo Aldh3a1 KO rep5; Danio rerio; RNA Seq	GSM4590771		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590771	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	11_aldh3a1----homo-48hpf-5_1.fq.gz 11_aldh3a1----homo-48hpf-5_2.fq.gz	fastq fastq	3919649800.0	39196498.0	GSM4590771 r1	0:100 1:100	A:1203194756;C:742776682;G:744133378;T:1229544984;N:0	100	100	1203194756	742776682	744133378	1229544984	0	SRX8468587	SRS6769275	SRA1083013	GEO	ZMF, University Heidelberg	1	0.86745		0.31349		0.76702		0.63864		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59482	59482	SRR11922872	SRX8468586	SRS6769274	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo Aldh3a1 KO rep4	GSM4590770	source name:zebrafish embryo\|genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	zebrafish embryo Aldh3a1 KO rep4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	GSM4590770	GSM4590770: zebrafish embryo Aldh3a1 KO rep4; Danio rerio; RNA Seq	GSM4590770		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590770	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	10_aldh3a1----homo-48hpf-4_2.fq.gz 10_aldh3a1----homo-48hpf-4_1.fq.gz	fastq fastq	4549625000.0	45496250.0	GSM4590770 r1	0:100 1:100	A:1345145181;C:925949636;G:905779914;T:1372750269;N:0	100	100	1345145181	925949636	905779914	1372750269	0	SRX8468586	SRS6769274	SRA1083013	GEO	ZMF, University Heidelberg	1	0.9117		0.23055		0.72545		0.50968		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59483	59483	SRR11922871	SRX8468585	SRS6769273	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo Aldh3a1 KO rep3	GSM4590769	source name:zebrafish embryo\|genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	zebrafish embryo Aldh3a1 KO rep3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	GSM4590769	GSM4590769: zebrafish embryo Aldh3a1 KO rep3; Danio rerio; RNA Seq	GSM4590769		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590769	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	9_aldh3a1----homo-48hpf-3_1.fq.gz 9_aldh3a1----homo-48hpf-3_2.fq.gz	fastq fastq	4194991600.0	41949916.0	GSM4590769 r1	0:100 1:100	A:1258296885;C:833884600;G:816600639;T:1286209476;N:0	100	100	1258296885	833884600	816600639	1286209476	0	SRX8468585	SRS6769273	SRA1083013	GEO	ZMF, University Heidelberg	1	0.89574		0.28139		0.73397		0.56688		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59484	59484	SRR11922870	SRX8468584	SRS6769272	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo Aldh3a1 KO rep2	GSM4590768	source name:zebrafish embryo\|genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	zebrafish embryo Aldh3a1 KO rep2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	GSM4590768	GSM4590768: zebrafish embryo Aldh3a1 KO rep2; Danio rerio; RNA Seq	GSM4590768		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590768	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	8_aldh3a1----homo-48hpf-2_1.fq.gz 8_aldh3a1----homo-48hpf-2_2.fq.gz	fastq fastq	5097901600.0	50979016.0	GSM4590768 r1	0:100 1:100	A:1487281075;C:1055394796;G:1035616985;T:1519608744;N:0	100	100	1487281075	1055394796	1035616985	1519608744	0	SRX8468584	SRS6769272	SRA1083013	GEO	ZMF, University Heidelberg	1	0.92556		0.18622		0.73026		0.5187		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59485	59485	SRR11922869	SRX8468583	SRS6769271	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo Aldh3a1 KO rep1	GSM4590767	source name:zebrafish embryo\|genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	zebrafish embryo Aldh3a1 KO rep1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	GSM4590767	GSM4590767: zebrafish embryo Aldh3a1 KO rep1; Danio rerio; RNA Seq	GSM4590767		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590767	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	7_aldh3a1----homo-48hpf-1_1.fq.gz 7_aldh3a1----homo-48hpf-1_2.fq.gz	fastq fastq	5075421000.0	50754210.0	GSM4590767 r1	0:100 1:100	A:1523744143;C:1008915874;G:985443760;T:1557317223;N:0	100	100	1523744143	1008915874	985443760	1557317223	0	SRX8468583	SRS6769271	SRA1083013	GEO	ZMF, University Heidelberg	1	0.90167		0.27915		0.75879		0.6673		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59486	59486	SRR11922868	SRX8468582	SRS6769270	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo wildtype rep5	GSM4590766	source name:zebrafish embryo\|genotype:WT\|tissue:embryo\|age:48 hpf	zebrafish embryo wildtype rep5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:WT\|tissue:embryo\|age:48 hpf	GSM4590766	GSM4590766: zebrafish embryo wildtype rep5; Danio rerio; RNA Seq	GSM4590766		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590766	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	6_aldh3a1+-+-wt-48hpf-R_1.fq.gz 6_aldh3a1+-+-wt-48hpf-R_2.fq.gz	fastq fastq	5097636600.0	50976366.0	GSM4590766 r1	0:100 1:100	A:1402424015;C:1146863463;G:1121174200;T:1427174922;N:0	100	100	1402424015	1146863463	1121174200	1427174922	0	SRX8468582	SRS6769270	SRA1083013	GEO	ZMF, University Heidelberg	1	0.95115		0.09816		0.69781		0.46194		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59487	59487	SRR11922867	SRX8468581	SRS6769269	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo wildtype rep4	GSM4590765	source name:zebrafish embryo\|genotype:WT\|tissue:embryo\|age:48 hpf	zebrafish embryo wildtype rep4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:WT\|tissue:embryo\|age:48 hpf	GSM4590765	GSM4590765: zebrafish embryo wildtype rep4; Danio rerio; RNA Seq	GSM4590765		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590765	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	4_aldh3a1+-+-wt-48hpf-4_1.fq.gz 4_aldh3a1+-+-wt-48hpf-4_2.fq.gz	fastq fastq	4847250800.0	48472508.0	GSM4590765 r1	0:100 1:100	A:1351516729;C:1070410976;G:1050113082;T:1375210013;N:0	100	100	1351516729	1070410976	1050113082	1375210013	0	SRX8468581	SRS6769269	SRA1083013	GEO	ZMF, University Heidelberg	1	0.94418		0.12404		0.69374		0.49948		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59488	59488	SRR11922866	SRX8468580	SRS6769268	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo wildtype rep3	GSM4590764	source name:zebrafish embryo\|genotype:WT\|tissue:embryo\|age:48 hpf	zebrafish embryo wildtype rep3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:WT\|tissue:embryo\|age:48 hpf	GSM4590764	GSM4590764: zebrafish embryo wildtype rep3; Danio rerio; RNA Seq	GSM4590764		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590764	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	3_aldh3a1+-+-wt-48hpf-3_1.fq.gz 3_aldh3a1+-+-wt-48hpf-3_2.fq.gz	fastq fastq	5083417400.0	50834174.0	GSM4590764 r1	0:100 1:100	A:1375006484;C:1168556107;G:1139277849;T:1400576960;N:0	100	100	1375006484	1168556107	1139277849	1400576960	0	SRX8468580	SRS6769268	SRA1083013	GEO	ZMF, University Heidelberg	1	0.95419		0.09201		0.69209		0.48244		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59489	59489	SRR11922865	SRX8468579	SRS6769267	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo wildtype rep2	GSM4590763	source name:zebrafish embryo\|genotype:WT\|tissue:embryo\|age:48 hpf	zebrafish embryo wildtype rep2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:WT\|tissue:embryo\|age:48 hpf	GSM4590763	GSM4590763: zebrafish embryo wildtype rep2; Danio rerio; RNA Seq	GSM4590763		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590763	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	2_aldh3a1+-+-wt-48hpf-2_1.fq.gz 2_aldh3a1+-+-wt-48hpf-2_2.fq.gz	fastq fastq	5089646400.0	50896464.0	GSM4590763 r1	0:100 1:100	A:1384714450;C:1161015785;G:1138313445;T:1405602720;N:0	100	100	1384714450	1161015785	1138313445	1405602720	0	SRX8468579	SRS6769267	SRA1083013	GEO	ZMF, University Heidelberg	1	0.95309		0.09301		0.69798		0.48524		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59490	59490	SRR11922864	SRX8468578	SRS6769266	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo wildtype rep1	GSM4590762	source name:zebrafish embryo\|genotype:WT\|tissue:embryo\|age:48 hpf	zebrafish embryo wildtype rep1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:WT\|tissue:embryo\|age:48 hpf	GSM4590762	GSM4590762: zebrafish embryo wildtype rep1; Danio rerio; RNA Seq	GSM4590762		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590762	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	1_aldh3a1+-+-wt-48hpf-1_1.fq.gz 1_aldh3a1+-+-wt-48hpf-1_2.fq.gz	fastq fastq	5098267400.0	50982674.0	GSM4590762 r1	0:100 1:100	A:1406329756;C:1147290302;G:1118206731;T:1426440611;N:0	100	100	1406329756	1147290302	1118206731	1426440611	0	SRX8468578	SRS6769266	SRA1083013	GEO	ZMF, University Heidelberg	1	0.95039		0.10482		0.69641		0.47979		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
60605	60605	SRR12435896	SRX8931591	SRS7187999	SRP277167	PRJNA656771	CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]	GSE156094	Transcriptome Analysis	CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino	parent bioproject:PRJNA656767	pubmed:34518536	RNA seq in zebrafish wild type embryos at 48hpf replicate 2	GSM4724538	tissue:whole embryo\|developmental stage:48 hpf\|genotype:WT	RNA seq in zebrafish wild type embryos at 48hpf replicate 2	Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo	Injection of tp53 morpholino was performed at 1 cell stage	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were grown at 28°C in E3 medium until desired developmental stage	developmental stage:48 hpf\|genotype:WT	GSM4724538	GSM4724538: RNA seq in zebrafish wild type embryos at 48hpf replicate 2; Danio rerio; RNA Seq	GSM4724538		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM4724538	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP277167	RNAseq_48h_wt_rep2_1.fq.gz	fastq	2857833100.0	57156662.0	GSM4724538 r1	0:50 1:0	A:833205284;C:613960566;G:684040839;T:726626411;N:0	50	0	833205284	613960566	684040839	726626411	0	SRX8931591	SRS7187999	SRA1111981	GEO	CABD, Universidad Pablo de Olavide-CSIC	1	0.94607		0.13254		0.683		0.47253		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2020-08-12	Hatching	Embryo	Whole Organism	All anatomical structures
60606	60606	SRR12435895	SRX8931590	SRS7187998	SRP277167	PRJNA656771	CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]	GSE156094	Transcriptome Analysis	CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino	parent bioproject:PRJNA656767	pubmed:34518536	RNA seq in zebrafish wild type embryos at 48hpf replicate 1	GSM4724537	tissue:whole embryo\|developmental stage:48 hpf\|genotype:WT	RNA seq in zebrafish wild type embryos at 48hpf replicate 1	Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo	Injection of tp53 morpholino was performed at 1 cell stage	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were grown at 28°C in E3 medium until desired developmental stage	developmental stage:48 hpf\|genotype:WT	GSM4724537	GSM4724537: RNA seq in zebrafish wild type embryos at 48hpf replicate 1; Danio rerio; RNA Seq	GSM4724537		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM4724537	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP277167	RNAseq_48h_wt_rep1_1.fq.gz	fastq	1780117200.0	35602344.0	GSM4724537 r1	0:50 1:0	A:515966090;C:381813611;G:432619671;T:449717828;N:0	50	0	515966090	381813611	432619671	449717828	0	SRX8931590	SRS7187998	SRA1111981	GEO	CABD, Universidad Pablo de Olavide-CSIC	1	0.95016		0.1291		0.68546		0.47379		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2020-08-12	Hatching	Embryo	Whole Organism	All anatomical structures
60607	60607	SRR12435894	SRX8931589	SRS7187997	SRP277167	PRJNA656771	CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]	GSE156094	Transcriptome Analysis	CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino	parent bioproject:PRJNA656767	pubmed:34518536	RNA seq in zebrafish wild type embryos at 48hpf injected with morpholino against tp53 replicate 2	GSM4724536	tissue:whole embryo\|developmental stage:48 hpf\|genotype:WT\|treatment:tp53 morpholino	RNA seq in zebrafish wild type embryos at 48hpf injected with morpholino against tp53 replicate 2	Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo	Injection of tp53 morpholino was performed at 1 cell stage	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were grown at 28°C in E3 medium until desired developmental stage	developmental stage:48 hpf\|genotype:WT\|treatment:tp53 morpholino	GSM4724536	GSM4724536: RNA seq in zebrafish wild type embryos at 48hpf injected with morpholino against tp53 replicate 2; Danio rerio; RNA Seq	GSM4724536		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM4724536	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP277167	RNAseq_48h_wt_p53MO_rep2_1.fq.gz	fastq	1604734300.0	32094686.0	GSM4724536 r1	0:50	A:420858899;C:372944640;G:386038616;T:424892145;N:0	50		420858899	372944640	386038616	424892145	0	SRX8931589	SRS7187997	SRA1111981	GEO	CABD, Universidad Pablo de Olavide-CSIC	1	0.9522		0.09133		0.68885		0.47214		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2020-08-12	Hatching	Embryo	Whole Organism	All anatomical structures
60608	60608	SRR12435893	SRX8931588	SRS7187996	SRP277167	PRJNA656771	CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]	GSE156094	Transcriptome Analysis	CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino	parent bioproject:PRJNA656767	pubmed:34518536	RNA seq in zebrafish wild type embryos at 48hpf injected with morpholino against tp53 replicate 1	GSM4724535	tissue:whole embryo\|developmental stage:48 hpf\|genotype:WT\|treatment:tp53 morpholino	RNA seq in zebrafish wild type embryos at 48hpf injected with morpholino against tp53 replicate 1	Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo	Injection of tp53 morpholino was performed at 1 cell stage	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were grown at 28°C in E3 medium until desired developmental stage	developmental stage:48 hpf\|genotype:WT\|treatment:tp53 morpholino	GSM4724535	GSM4724535: RNA seq in zebrafish wild type embryos at 48hpf injected with morpholino against tp53 replicate 1; Danio rerio; RNA Seq	GSM4724535		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM4724535	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP277167	RNAseq_48h_wt_p53MO_rep1_1.fq.gz	fastq	2384014500.0	47680290.0	GSM4724535 r1	0:50	A:625164876;C:552875690;G:576784849;T:629189085;N:0	50		625164876	552875690	576784849	629189085	0	SRX8931588	SRS7187996	SRA1111981	GEO	CABD, Universidad Pablo de Olavide-CSIC	1	0.94749		0.09167		0.67978		0.48327		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2020-08-12	Hatching	Embryo	Whole Organism	All anatomical structures
60609	60609	SRR12435892	SRX8931587	SRS7187995	SRP277167	PRJNA656771	CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]	GSE156094	Transcriptome Analysis	CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino	parent bioproject:PRJNA656767	pubmed:34518536	RNA seq in zebrafish ctcf mutant embryos at 48hpf replicate 2	GSM4724534	tissue:whole embryo\|developmental stage:48 hpf\|genotype:ctcf /	RNA seq in zebrafish ctcf mutant embryos at 48hpf replicate 2	Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo	Injection of tp53 morpholino was performed at 1 cell stage	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were grown at 28°C in E3 medium until desired developmental stage	developmental stage:48 hpf\|genotype:ctcf /	GSM4724534	GSM4724534: RNA seq in zebrafish ctcf mutant embryos at 48hpf replicate 2; Danio rerio; RNA Seq	GSM4724534		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM4724534	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP277167	RNAseq_48h_ctcf_rep2_1.fq.gz	fastq	2142745700.0	42854914.0	GSM4724534 r1	0:50 1:0	A:622717093;C:460353664;G:518363295;T:541311648;N:0	50	0	622717093	460353664	518363295	541311648	0	SRX8931587	SRS7187995	SRA1111981	GEO	CABD, Universidad Pablo de Olavide-CSIC	1	0.94287		0.14736		0.69199		0.47986		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2020-08-12	Hatching	Embryo	Whole Organism	All anatomical structures
60610	60610	SRR12435891	SRX8931586	SRS7187994	SRP277167	PRJNA656771	CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]	GSE156094	Transcriptome Analysis	CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino	parent bioproject:PRJNA656767	pubmed:34518536	RNA seq in zebrafish ctcf mutant embryos at 48hpf replicate 1	GSM4724533	tissue:whole embryo\|developmental stage:48 hpf\|genotype:ctcf /	RNA seq in zebrafish ctcf mutant embryos at 48hpf replicate 1	Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo	Injection of tp53 morpholino was performed at 1 cell stage	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were grown at 28°C in E3 medium until desired developmental stage	developmental stage:48 hpf\|genotype:ctcf /	GSM4724533	GSM4724533: RNA seq in zebrafish ctcf mutant embryos at 48hpf replicate 1; Danio rerio; RNA Seq	GSM4724533		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM4724533	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP277167	RNAseq_48h_ctcf_rep1_1.fq.gz	fastq	1858500400.0	37170008.0	GSM4724533 r1	0:50 1:0	A:544611701;C:398699344;G:449892006;T:465297349;N:0	50	0	544611701	398699344	449892006	465297349	0	SRX8931586	SRS7187994	SRA1111981	GEO	CABD, Universidad Pablo de Olavide-CSIC	1	0.94363		0.14349		0.69089		0.48114		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2020-08-12	Hatching	Embryo	Whole Organism	All anatomical structures
60611	60611	SRR12435890	SRX8931585	SRS7187993	SRP277167	PRJNA656771	CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]	GSE156094	Transcriptome Analysis	CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino	parent bioproject:PRJNA656767	pubmed:34518536	RNA seq in zebrafish ctcf mutant embryos at 48hpf injected with morpholino against tp53 replicate 2	GSM4724532	tissue:whole embryo\|developmental stage:48 hpf\|genotype:ctcf / \|treatment:tp53 morpholino	RNA seq in zebrafish ctcf mutant embryos at 48hpf injected with morpholino against tp53 replicate 2	Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo	Injection of tp53 morpholino was performed at 1 cell stage	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were grown at 28°C in E3 medium until desired developmental stage	developmental stage:48 hpf\|genotype:ctcf / \|treatment:tp53 morpholino	GSM4724532	GSM4724532: RNA seq in zebrafish ctcf mutant embryos at 48hpf injected with morpholino against tp53 replicate 2; Danio rerio; RNA Seq	GSM4724532		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM4724532	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP277167	RNAseq_48h_ctcf_p53MO_rep2_1.fq.gz	fastq	2622498950.0	52449979.0	GSM4724532 r1	0:50	A:683425987;C:612438973;G:639683260;T:686950730;N:0	50		683425987	612438973	639683260	686950730	0	SRX8931585	SRS7187993	SRA1111981	GEO	CABD, Universidad Pablo de Olavide-CSIC	1	0.94822		0.10163		0.69954		0.4758		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2020-08-12	Hatching	Embryo	Whole Organism	All anatomical structures
60612	60612	SRR12435889	SRX8931584	SRS7187992	SRP277167	PRJNA656771	CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]	GSE156094	Transcriptome Analysis	CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino	parent bioproject:PRJNA656767	pubmed:34518536	RNA seq in zebrafish ctcf mutant embryos at 48hpf injected with morpholino against tp53 replicate 1	GSM4724531	tissue:whole embryo\|developmental stage:48 hpf\|genotype:ctcf / \|treatment:tp53 morpholino	RNA seq in zebrafish ctcf mutant embryos at 48hpf injected with morpholino against tp53 replicate 1	Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo	Injection of tp53 morpholino was performed at 1 cell stage	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were grown at 28°C in E3 medium until desired developmental stage	developmental stage:48 hpf\|genotype:ctcf / \|treatment:tp53 morpholino	GSM4724531	GSM4724531: RNA seq in zebrafish ctcf mutant embryos at 48hpf injected with morpholino against tp53 replicate 1; Danio rerio; RNA Seq	GSM4724531		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM4724531	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP277167	RNAseq_48h_ctcf_p53MO_rep1_1.fq.gz	fastq	2421682100.0	48433642.0	GSM4724531 r1	0:50	A:625808320;C:568572947;G:596940410;T:630360423;N:0	50		625808320	568572947	596940410	630360423	0	SRX8931584	SRS7187992	SRA1111981	GEO	CABD, Universidad Pablo de Olavide-CSIC	1	0.94893		0.09731		0.71476		0.48546		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2020-08-12	Hatching	Embryo	Whole Organism	All anatomical structures
60613	60613	SRR12435888	SRX8931583	SRS7187991	SRP277167	PRJNA656771	CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]	GSE156094	Transcriptome Analysis	CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino	parent bioproject:PRJNA656767	pubmed:34518536	RNA seq in zebrafish wild type embryos at 24hpf replicate 2	GSM4724530	tissue:whole embryo\|developmental stage:24 hpf\|genotype:WT	RNA seq in zebrafish wild type embryos at 24hpf replicate 2	Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo	Injection of tp53 morpholino was performed at 1 cell stage	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were grown at 28°C in E3 medium until desired developmental stage	developmental stage:24 hpf\|genotype:WT	GSM4724530	GSM4724530: RNA seq in zebrafish wild type embryos at 24hpf replicate 2; Danio rerio; RNA Seq	GSM4724530		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM4724530	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP277167	RNAseq_24h_wt_rep2_1.fq.gz	fastq	2241073250.0	44821465.0	GSM4724530 r1	0:50	A:593435654;C:517470954;G:544866646;T:585299996;N:0	50		593435654	517470954	544866646	585299996	0	SRX8931583	SRS7187991	SRA1111981	GEO	CABD, Universidad Pablo de Olavide-CSIC	1	0.9534		0.07821		0.70331		0.47463		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2020-08-12	Pharyngula	Embryo	Whole Organism	All anatomical structures
60614	60614	SRR12435887	SRX8931582	SRS7187990	SRP277167	PRJNA656771	CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]	GSE156094	Transcriptome Analysis	CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino	parent bioproject:PRJNA656767	pubmed:34518536	RNA seq in zebrafish wild type embryos at 24hpf replicate 1	GSM4724529	tissue:whole embryo\|developmental stage:24 hpf\|genotype:WT	RNA seq in zebrafish wild type embryos at 24hpf replicate 1	Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo	Injection of tp53 morpholino was performed at 1 cell stage	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were grown at 28°C in E3 medium until desired developmental stage	developmental stage:24 hpf\|genotype:WT	GSM4724529	GSM4724529: RNA seq in zebrafish wild type embryos at 24hpf replicate 1; Danio rerio; RNA Seq	GSM4724529		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM4724529	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP277167	RNAseq_24h_wt_rep1_1.fq.gz	fastq	1206103900.0	24122078.0	GSM4724529 r1	0:50	A:329983157;C:268788282;G:289794374;T:316858580;N:679507	50		329983157	268788282	289794374	316858580	679507	SRX8931582	SRS7187990	SRA1111981	GEO	CABD, Universidad Pablo de Olavide-CSIC	1	0.94221		0.09615		0.69077		0.47405		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2020-08-12	Pharyngula	Embryo	Whole Organism	All anatomical structures
60615	60615	SRR12435886	SRX8931581	SRS7187989	SRP277167	PRJNA656771	CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]	GSE156094	Transcriptome Analysis	CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino	parent bioproject:PRJNA656767	pubmed:34518536	RNA seq in zebrafish ctcf mutant embryos at 24hpf replicate 2	GSM4724528	tissue:whole embryo\|developmental stage:24 hpf\|genotype:ctcf /	RNA seq in zebrafish ctcf mutant embryos at 24hpf replicate 2	Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo	Injection of tp53 morpholino was performed at 1 cell stage	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were grown at 28°C in E3 medium until desired developmental stage	developmental stage:24 hpf\|genotype:ctcf /	GSM4724528	GSM4724528: RNA seq in zebrafish ctcf mutant embryos at 24hpf replicate 2; Danio rerio; RNA Seq	GSM4724528		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM4724528	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP277167	RNAseq_24h_ctcf_rep2_1.fq.gz	fastq	2823674750.0	56473495.0	GSM4724528 r1	0:50	A:743759446;C:653943934;G:679405104;T:746566266;N:0	50		743759446	653943934	679405104	746566266	0	SRX8931581	SRS7187989	SRA1111981	GEO	CABD, Universidad Pablo de Olavide-CSIC	1	0.95027		0.08763		0.6984		0.487		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2020-08-12	Pharyngula	Embryo	Whole Organism	All anatomical structures
60616	60616	SRR12435885	SRX8931580	SRS7187988	SRP277167	PRJNA656771	CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq]	GSE156094	Transcriptome Analysis	CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino	parent bioproject:PRJNA656767	pubmed:34518536	RNA seq in zebrafish ctcf mutant embryos at 24hpf replicate 1	GSM4724527	tissue:whole embryo\|developmental stage:24 hpf\|genotype:ctcf /	RNA seq in zebrafish ctcf mutant embryos at 24hpf replicate 1	Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene	whole embryo	Injection of tp53 morpholino was performed at 1 cell stage	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	Embryos were grown at 28°C in E3 medium until desired developmental stage	developmental stage:24 hpf\|genotype:ctcf /	GSM4724527	GSM4724527: RNA seq in zebrafish ctcf mutant embryos at 24hpf replicate 1; Danio rerio; RNA Seq	GSM4724527		1	RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen	GEO Accession:GSM4724527	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP277167	RNAseq_24h_ctcf_rep1_1.fq.gz	fastq	2408631250.0	48172625.0	GSM4724527 r1	0:50	A:623761639;C:570722378;G:584932664;T:629214569;N:0	50		623761639	570722378	584932664	629214569	0	SRX8931580	SRS7187988	SRA1111981	GEO	CABD, Universidad Pablo de Olavide-CSIC	1	0.95366		0.07765		0.70023		0.47375		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Spain	2020-08-12	Pharyngula	Embryo	Whole Organism	All anatomical structures
61503	61503	SRR12780056	SRX9249644	SRS7482118	SRP286526	PRJNA667677	Bipartite histone H3 recognition by the PZP domain of PHF14 facilitates zygotic genome activation in zebrafish	GSE159087	Transcriptome Analysis	Standard and Phf14 MOs were injected into 1 cell stage embryos and when developed into sphere stage 4.7 hpf embryos were lysed for mRNA extraction for high through put sequencing based on BGISEQ in order to compare gene expression test at the whole genome level. Overall design: mRNA profiles of standard std MO 4.7h versus phf14 MO injected phf tMO 4.7h zebrash embryos at 4.7 hpf.			phf tMO 4.7h	GSM4819005	tissue:embryos\|strain:Tuebingen\|genotype/variation:phf14 MO injected\|developmental stage:4.7 hpf\|tissue/cell type:whole embryos	phf tMO 4.7h	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to zv9 whole genome using SOAPaligner/soap2 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from mortazavi et al. nature method 2008. Genome build: zv9 Supplementary files format and content: Excel files include RPKM values and read counts for each gene in the two samples	embryos	Embryos were injected with 5 ng standard or Phf14 morpholinos at xxx cell stage	Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Embryos were cultured in the holfretor water.	strain:Tuebingen\|genotype/variation:phf14 MO injected\|developmental stage:4.7 hpf\|tissue/cell type:whole embryos	GSM4819005	GSM4819005: phf tMO 4.7h; Danio rerio; RNA Seq	GSM4819005		1	Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4819005	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP286526	phf_tMO_4.7h.fq.gz	fastq	1169147800.0	23382956.0	GSM4819005 r1	0:50	A:311605612;C:272452820;G:269040332;T:316049036;N:0	50		311605612	272452820	269040332	316049036	0	SRX9249644	SRS7482118	SRA1139165	GEO	Haitao Li, School of medicine, Tsinghua University	1	0.94966		0.07252		0.73651		0.49931		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	China	2020-10-06	Blastula	Embryo	Embryo Imprecise	All anatomical structures
61504	61504	SRR12780055	SRX9249643	SRS7482117	SRP286526	PRJNA667677	Bipartite histone H3 recognition by the PZP domain of PHF14 facilitates zygotic genome activation in zebrafish	GSE159087	Transcriptome Analysis	Standard and Phf14 MOs were injected into 1 cell stage embryos and when developed into sphere stage 4.7 hpf embryos were lysed for mRNA extraction for high through put sequencing based on BGISEQ in order to compare gene expression test at the whole genome level. Overall design: mRNA profiles of standard std MO 4.7h versus phf14 MO injected phf tMO 4.7h zebrash embryos at 4.7 hpf.			std MO 4.7h	GSM4819004	tissue:embryos\|strain:Tuebingen\|genotype/variation:standard MO injected\|developmental stage:4.7 hpf\|tissue/cell type:whole embryos	std MO 4.7h	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to zv9 whole genome using SOAPaligner/soap2 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from mortazavi et al. nature method 2008. Genome build: zv9 Supplementary files format and content: Excel files include RPKM values and read counts for each gene in the two samples	embryos	Embryos were injected with 5 ng standard or Phf14 morpholinos at xxx cell stage	Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	Embryos were cultured in the holfretor water.	strain:Tuebingen\|genotype/variation:standard MO injected\|developmental stage:4.7 hpf\|tissue/cell type:whole embryos	GSM4819004	GSM4819004: std MO 4.7h; Danio rerio; RNA Seq	GSM4819004		1	Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4819004	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500	SRP286526	std_MO_4.7h.fq.gz	fastq	1169210150.0	23384203.0	GSM4819004 r1	0:50	A:311848924;C:271805947;G:268541126;T:317014153;N:0	50		311848924	271805947	268541126	317014153	0	SRX9249643	SRS7482117	SRA1139165	GEO	Haitao Li, School of medicine, Tsinghua University	1	0.94838		0.07833		0.74192		0.48213		50		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	China	2020-10-06	Blastula	Embryo	Embryo Imprecise	All anatomical structures
65852	65852	SRR15657174	SRX11954177	SRS9963999	SRP334492	PRJNA758398	Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]	GSE182945	Transcriptome Analysis	Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq.	parent bioproject:PRJNA758396		embryo Cu 0.156uM 96hpf	GSM5543529	tissue:embryo Cu 0.156uM 96hpf\|cell type:embryos at 96hpf whose parents were exposed to 0.156μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	embryo Cu 0.156uM 96hpf	Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample	embryo Cu 0.156uM 96hpf	50 60 embryos F1 from each group	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	embryos F1 cultured in normal water environment	cell type:embryos at 96hpf hours post fertilization\|treatment:embryos whose parents were exposed to 0.156μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	GSM5543529	GSM5543529: embryo Cu 0.156uM 96hpf; Danio rerio; RNA Seq	GSM5543529		1	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	GEO Accession:GSM5543529	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP334492	Cu_0.156uM_96hpf_R1.fastq.gz Cu_0.156uM_96hpf_R2.fastq.gz	fastq fastq	7167443000.0	71674430.0	GSM5543529 r1	0:100 1:100	A:1930084120;C:1646651059;G:1623549050;T:1966203424;N:955347	100	100	1930084120	1646651059	1623549050	1966203424	955347	SRX11954177	SRS9963999	SRA1284991	GEO	college of informatics, Huazhong Agricultural University	1	0.94339		0.113		0.6549		0.4857		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2021-08-27	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
65853	65853	SRR15657173	SRX11954176	SRS9963998	SRP334492	PRJNA758398	Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]	GSE182945	Transcriptome Analysis	Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq.	parent bioproject:PRJNA758396		embryo Cu 0.156uM 24hpf	GSM5543528	tissue:embryo Cu 0.156uM 24hpf\|cell type:embryos at 24hpf whose parents were exposed to 0.156μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	embryo Cu 0.156uM 24hpf	Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample	embryo Cu 0.156uM 24hpf	50 60 embryos F1 from each group	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	embryos F1 cultured in normal water environment	cell type:embryos at 24hpf hours post fertilization\|treatment:embryos whose parents were exposed to 0.156μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	GSM5543528	GSM5543528: embryo Cu 0.156uM 24hpf; Danio rerio; RNA Seq	GSM5543528		1	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	GEO Accession:GSM5543528	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP334492	Cu_0.156uM_24hpf_R1.fastq.gz Cu_0.156uM_24hpf_R2.fastq.gz	fastq fastq	7164832400.0	71648324.0	GSM5543528 r1	0:100 1:100	A:1929135591;C:1646939515;G:1617401036;T:1970900148;N:456110	100	100	1929135591	1646939515	1617401036	1970900148	456110	SRX11954176	SRS9963998	SRA1284991	GEO	college of informatics, Huazhong Agricultural University	1	0.94344		0.10713		0.68919		0.47118		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2021-08-27	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
65854	65854	SRR15657172	SRX11954175	SRS9963997	SRP334492	PRJNA758398	Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]	GSE182945	Transcriptome Analysis	Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq.	parent bioproject:PRJNA758396		embryo Cu 0.078uM 96hpf	GSM5543527	tissue:embryo Cu 0.078uM 96hpf\|cell type:embryos at 96hpf whose parents were exposed to 0.078μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	embryo Cu 0.078uM 96hpf	Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample	embryo Cu 0.078uM 96hpf	50 60 embryos F1 from each group	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	embryos F1 cultured in normal water environment	cell type:embryos at 96hpf hours post fertilization\|treatment:embryos whose parents were exposed to 0.078μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	GSM5543527	GSM5543527: embryo Cu 0.078uM 96hpf; Danio rerio; RNA Seq	GSM5543527		1	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	GEO Accession:GSM5543527	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP334492	Cu_0.078uM_96hpf_R1.fastq.gz Cu_0.078uM_96hpf_R2.fastq.gz	fastq fastq	7135774800.0	71357748.0	GSM5543527 r1	0:100 1:100	A:1928230196;C:1633490990;G:1605871113;T:1967776814;N:405687	100	100	1928230196	1633490990	1605871113	1967776814	405687	SRX11954175	SRS9963997	SRA1284991	GEO	college of informatics, Huazhong Agricultural University	1	0.94191		0.11803		0.65614		0.48225		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2021-08-27	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
65855	65855	SRR15657171	SRX11954174	SRS9963995	SRP334492	PRJNA758398	Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]	GSE182945	Transcriptome Analysis	Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq.	parent bioproject:PRJNA758396		embryo Cu 0.078uM 24hpf	GSM5543526	tissue:embryo Cu 0.078uM 24hpf\|cell type:embryos at 24hpf whose parents were exposed to 0.078μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	embryo Cu 0.078uM 24hpf	Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample	embryo Cu 0.078uM 24hpf	50 60 embryos F1 from each group	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	embryos F1 cultured in normal water environment	cell type:embryos at 24hpf hours post fertilization\|treatment:embryos whose parents were exposed to 0.078μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	GSM5543526	GSM5543526: embryo Cu 0.078uM 24hpf; Danio rerio; RNA Seq	GSM5543526		1	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	GEO Accession:GSM5543526	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP334492	Cu_0.078uM_24hpf_R1.fastq.gz Cu_0.078uM_24hpf_R2.fastq.gz	fastq fastq	6934019600.0	69340196.0	GSM5543526 r1	0:100 1:100	A:1865548284;C:1597354050;G:1569395022;T:1901304271;N:417973	100	100	1865548284	1597354050	1569395022	1901304271	417973	SRX11954174	SRS9963995	SRA1284991	GEO	college of informatics, Huazhong Agricultural University	1	0.94389		0.10356		0.68726		0.47794		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2021-08-27	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
65856	65856	SRR15657170	SRX11954173	SRS9963996	SRP334492	PRJNA758398	Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]	GSE182945	Transcriptome Analysis	Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq.	parent bioproject:PRJNA758396		embryo Control 96hpf	GSM5543525	tissue:embryo Control 96hpf\|cell type:embryos at 96hpf whose parents were exposed to normal water environment F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	embryo Control 96hpf	Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample	embryo Control 96hpf	50 60 embryos F1 from each group	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	embryos F1 cultured in normal water environment	cell type:embryos at 96hpf hours post fertilization\|treatment:embryos whose parents were exposed to normal water environment F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	GSM5543525	GSM5543525: embryo Control 96hpf; Danio rerio; RNA Seq	GSM5543525		1	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	GEO Accession:GSM5543525	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP334492	Control_96hpf_R1.fastq.gz Control_96hpf_R2.fastq.gz	fastq fastq	6698614400.0	66986144.0	GSM5543525 r1	0:100 1:100	A:1816763075;C:1526218454;G:1496202651;T:1858550518;N:879702	100	100	1816763075	1526218454	1496202651	1858550518	879702	SRX11954173	SRS9963996	SRA1284991	GEO	college of informatics, Huazhong Agricultural University	1	0.93836		0.12432		0.65504		0.47564		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2021-08-27	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
65857	65857	SRR15657169	SRX11954172	SRS9963994	SRP334492	PRJNA758398	Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]	GSE182945	Transcriptome Analysis	Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq.	parent bioproject:PRJNA758396		embryo Control 24hpf	GSM5543524	tissue:embryo Control 24hpf\|cell type:embryos at 24hpf whose parents were exposed to normal water environment F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	embryo Control 24hpf	Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample	embryo Control 24hpf	50 60 embryos F1 from each group	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	embryos F1 cultured in normal water environment	cell type:embryos at 24hpf hours post fertilization\|treatment:embryos whose parents were exposed to normal water environment F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	GSM5543524	GSM5543524: embryo Control 24hpf; Danio rerio; RNA Seq	GSM5543524		1	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	GEO Accession:GSM5543524	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP334492	Control_24hpf_R1.fastq.gz Control_24hpf_R2.fastq.gz	fastq fastq	6911559200.0	69115592.0	GSM5543524 r1	0:100 1:100	A:1858569189;C:1592355971;G:1564572369;T:1895593185;N:468486	100	100	1858569189	1592355971	1564572369	1895593185	468486	SRX11954172	SRS9963994	SRA1284991	GEO	college of informatics, Huazhong Agricultural University	1	0.93745		0.09795		0.69059		0.48209		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2021-08-27	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
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
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

Advanced export

JSON shape: default, array, newline-delimited

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");;