metadata: run_metadata: 165 rows where experiment.platform = "BGISEQ" and tissue

165 rows where experiment.platform = "BGISEQ" and tissue_curation = "Whole Organism"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
28093	28093	SRR26196850	SRX21908248	SRS18993956	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:38868197		elipsa mutant clutch 4	GSM7808262	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa mutant clutch 4	Standard processing by BGI.p HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM7808262	GSM7808262: elipsa mutant clutch 4; Danio rerio; RNA Seq	GSM7808262 r1	GSM7808262	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504		ElipsaMUT4_1.fq.gz ElipsaMUT4_2.fq.gz	fastq fastq	4536153000.0	22680765.0	GSM7808262 r1	0:100 1:100	A:1194964224;C:1059904764;G:1074108947;T:1207175065;N:0	100	100	1194964224	1059904764	1074108947	1207175065	0	SRX21908248	SRS18993956	SRA1721841	NTNU	NTNU	2	0.93991	0.94735	0.10392	0.10318	0.66434	0.66344	0.48911	0.49311	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28094	28094	SRR26196851	SRX21908247	SRS18993955	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:38868197		elipsa mutant clutch 3	GSM7808261	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa mutant clutch 3	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM7808261	GSM7808261: elipsa mutant clutch 3; Danio rerio; RNA Seq	GSM7808261 r1	GSM7808261	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504		ElipsaMUT3_1.fq.gz ElipsaMUT3_2.fq.gz	fastq fastq	4547581600.0	22737908.0	GSM7808261 r1	0:100 1:100	A:1183476304;C:1077021222;G:1092963681;T:1194120393;N:0	100	100	1183476304	1077021222	1092963681	1194120393	0	SRX21908247	SRS18993955	SRA1721841	NTNU	NTNU	2	0.95029	0.95874	0.09085	0.09059	0.66856	0.66722	0.48534	0.48545	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28095	28095	SRR26196852	SRX21908246	SRS18993954	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:38868197		elipsa mutant clutch 2	GSM7808260	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa mutant clutch 2	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM7808260	GSM7808260: elipsa mutant clutch 2; Danio rerio; RNA Seq	GSM7808260 r1	GSM7808260	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504		ElipsaMUT2_1.fq.gz ElipsaMUT2_2.fq.gz	fastq fastq	4544444600.0	22722223.0	GSM7808260 r1	0:100 1:100	A:1186329827;C:1072965608;G:1087757513;T:1197391652;N:0	100	100	1186329827	1072965608	1087757513	1197391652	0	SRX21908246	SRS18993954	SRA1721841	NTNU	NTNU	2	0.94545	0.95403	0.09705	0.09653	0.66576	0.66466	0.47893	0.47882	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28096	28096	SRR26196853	SRX21908245	SRS18993953	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:38868197		elipsa mutant clutch 1	GSM7808259	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa mutant clutch 1	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM7808259	GSM7808259: elipsa mutant clutch 1; Danio rerio; RNA Seq	GSM7808259 r1	GSM7808259	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504		ElipsaMUT1_1.fq.gz ElipsaMUT1_2.fq.gz	fastq fastq	4561346400.0	22806732.0	GSM7808259 r1	0:100 1:100	A:1192227498;C:1073309826;G:1091718946;T:1204090130;N:0	100	100	1192227498	1073309826	1091718946	1204090130	0	SRX21908245	SRS18993953	SRA1721841	NTNU	NTNU	2	0.94079	0.94928	0.09838	0.09859	0.67093	0.66975	0.47837	0.4824	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28097	28097	SRR26196854	SRX21908244	SRS18993950	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:38868197		elipsa control clutch 4	GSM7808258	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa control clutch 4	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM7808258	GSM7808258: elipsa control clutch 4; Danio rerio; RNA Seq	GSM7808258 r1	GSM7808258	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504		ElipsaCTRL4_1.fq.gz ElipsaCTRL4_2.fq.gz	fastq fastq	4534543600.0	22672718.0	GSM7808258 r1	0:100 1:100	A:1195456125;C:1060510332;G:1073683545;T:1204893598;N:0	100	100	1195456125	1060510332	1073683545	1204893598	0	SRX21908244	SRS18993950	SRA1721841	NTNU	NTNU	2	0.94686	0.95523	0.0948	0.09459	0.66259	0.66093	0.49251	0.49154	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28098	28098	SRR26196855	SRX21908243	SRS18993952	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:38868197		elipsa control clutch 3	GSM7808257	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa control clutch 3	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM7808257	GSM7808257: elipsa control clutch 3; Danio rerio; RNA Seq	GSM7808257 r1	GSM7808257	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504		ElipsaCTRL3_1.fq.gz ElipsaCTRL3_2.fq.gz	fastq fastq	4546464800.0	22732324.0	GSM7808257 r1	0:100 1:100	A:1192169234;C:1070218166;G:1081895902;T:1202181498;N:0	100	100	1192169234	1070218166	1081895902	1202181498	0	SRX21908243	SRS18993952	SRA1721841	NTNU	NTNU	2	0.94937	0.95815	0.09867	0.09825	0.66574	0.66478	0.49056	0.48959	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28099	28099	SRR26196856	SRX21908242	SRS18993951	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:38868197		elipsa control clutch 2	GSM7808256	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa control clutch 2	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM7808256	GSM7808256: elipsa control clutch 2; Danio rerio; RNA Seq	GSM7808256 r1	GSM7808256	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504		ElipsaCTRL2_1.fq.gz ElipsaCTRL2_2.fq.gz	fastq fastq	4557679200.0	22788396.0	GSM7808256 r1	0:100 1:100	A:1184954651;C:1080955864;G:1098377272;T:1193391413;N:0	100	100	1184954651	1080955864	1098377272	1193391413	0	SRX21908242	SRS18993951	SRA1721841	NTNU	NTNU	2	0.94378	0.95076	0.0855	0.0847	0.66604	0.66342	0.48858	0.48404	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
28100	28100	SRR26196857	SRX21908241	SRS18993949	SRP463504	PRJNA1021586	Ciliogenesis defects post neurulation impact brain development and neuronal activity in larval zebrafish	GSE244171	Transcriptome Analysis	Cilia are slender hair like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system primary cilia contribute to signaling and sensory perception while motile cilia facilitate cerebrospinal fluid flow. Here we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects post neurulation affects neurogenesis and brain morphology especially in the cerebellum and lead to altered gene expression profiles. Using whole brain calcium imaging we measured reduced light evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models. Overall design: To analyse the impact of cilia loss on gene expression we performed RNA sequencing analysis of 4 dpf elipsa mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:38868197		elipsa control clutch 1	GSM7808255	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	elipsa control clutch 1	Standard processing by BGI. HISAT to align the clean reads to the reference genome. Bowtie2 to align the clean reads to the reference genes. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: The count matrix includes genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor. Supplementary files format and content: excel file containing fold changes	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM7808255	GSM7808255: elipsa control clutch 1; Danio rerio; RNA Seq	GSM7808255 r1	GSM7808255	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology using the Dr Tom data visualization and analysis platform provided by BGI. standard procedure performed by BGI		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP463504		ElipsaCTRL1_1.fq.gz ElipsaCTRL1_2.fq.gz	fastq fastq	4566618600.0	22833093.0	GSM7808255 r1	0:100 1:100	A:1193092402;C:1076659586;G:1094193492;T:1202673120;N:0	100	100	1193092402	1076659586	1094193492	1202673120	0	SRX21908241	SRS18993949	SRA1721841	NTNU	NTNU	2	0.94269	0.94899	0.09816	0.09712	0.66991	0.66925	0.47671	0.46995	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Unknown	2023-09-27	Larval	Larval	Whole Organism	All anatomical structures
30075	30075	SRR27700027	SRX23366859	SRS20229171	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:39798091		Smh mutant clutch 4	GSM8031712	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh mutant clutch 4	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM8031712	GSM8031712: Smh mutant clutch 4; Danio rerio; RNA Seq	GSM8031712 r1	GSM8031712	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459		SmhMUT4_1.fq.gz SmhMUT4_2.fq.gz	fastq fastq	4550057400.0	22750287.0	GSM8031712 r1	0:100 1:100	A:1198976754;C:1064190197;G:1077491671;T:1209398778;N:0	100	100	1198976754	1064190197	1077491671	1209398778	0	SRX23366859	SRS20229171	SRA1790727	NTNU	NTNU	2	0.94285	0.95266	0.101	0.10096	0.66145	0.65989	0.48209	0.47768	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30076	30076	SRR27700028	SRX23366858	SRS20229175	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:39798091		Smh mutant clutch 3	GSM8031711	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh mutant clutch 3	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM8031711	GSM8031711: Smh mutant clutch 3; Danio rerio; RNA Seq	GSM8031711 r1	GSM8031711	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459		SmhMUT3_1.fq.gz SmhMUT3_2.fq.gz	fastq fastq	4545452600.0	22727263.0	GSM8031711 r1	0:100 1:100	A:1188958937;C:1071903723;G:1087032258;T:1197557682;N:0	100	100	1188958937	1071903723	1087032258	1197557682	0	SRX23366858	SRS20229175	SRA1790727	NTNU	NTNU	2	0.94501	0.95409	0.09005	0.08947	0.66149	0.66062	0.46824	0.48019	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30077	30077	SRR27700029	SRX23366857	SRS20229173	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:39798091		Smh mutant clutch 2	GSM8031710	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh mutant clutch 2	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM8031710	GSM8031710: Smh mutant clutch 2; Danio rerio; RNA Seq	GSM8031710 r1	GSM8031710	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459		SmhMUT2_1.fq.gz SmhMUT2_2.fq.gz	fastq fastq	4548042000.0	22740210.0	GSM8031710 r1	0:100 1:100	A:1184618587;C:1077947166;G:1089628929;T:1195847318;N:0	100	100	1184618587	1077947166	1089628929	1195847318	0	SRX23366857	SRS20229173	SRA1790727	NTNU	NTNU	2	0.94502	0.95416	0.09209	0.092	0.66407	0.66214	0.48538	0.48509	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30078	30078	SRR27700030	SRX23366856	SRS20229174	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:39798091		Smh mutant clutch 1	GSM8031709	source name:whole larvae\|tissue:whole larvae\|genotype: / \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh mutant clutch 1	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype: / \|treatment:no treatment	GSM8031709	GSM8031709: Smh mutant clutch 1; Danio rerio; RNA Seq	GSM8031709 r1	GSM8031709	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459		SmhMUT1_1.fq.gz SmhMUT1_2.fq.gz	fastq fastq	4544759600.0	22723798.0	GSM8031709 r1	0:100 1:100	A:1194011331;C:1066502346;G:1077923006;T:1206322917;N:0	100	100	1194011331	1066502346	1077923006	1206322917	0	SRX23366856	SRS20229174	SRA1790727	NTNU	NTNU	2	0.945	0.95433	0.09733	0.09796	0.66034	0.65951	0.477	0.47705	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30079	30079	SRR27700031	SRX23366855	SRS20229172	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:39798091		Smh control clutch 4	GSM8031708	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh control clutch 4	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM8031708	GSM8031708: Smh control clutch 4; Danio rerio; RNA Seq	GSM8031708 r1	GSM8031708	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459		SmhCTRL4_1.fq.gz SmhCTRL4_2.fq.gz	fastq fastq	4536141000.0	22680705.0	GSM8031708 r1	0:100 1:100	A:1196842043;C:1059535727;G:1071488375;T:1208274855;N:0	100	100	1196842043	1059535727	1071488375	1208274855	0	SRX23366855	SRS20229172	SRA1790727	NTNU	NTNU	2	0.94102	0.95093	0.09453	0.09431	0.66403	0.6631	0.49804	0.49818	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30080	30080	SRR27700032	SRX23366854	SRS20229170	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:39798091		Smh control clutch 3	GSM8031707	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh control clutch 3	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM8031707	GSM8031707: Smh control clutch 3; Danio rerio; RNA Seq	GSM8031707 r1	GSM8031707	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459		SmhCTRL3_1.fq.gz SmhCTRL3_2.fq.gz	fastq fastq	4543416000.0	22717080.0	GSM8031707 r1	0:100 1:100	A:1189755812;C:1071666785;G:1082665579;T:1199327824;N:0	100	100	1189755812	1071666785	1082665579	1199327824	0	SRX23366854	SRS20229170	SRA1790727	NTNU	NTNU	2	0.94571	0.95506	0.08989	0.09005	0.6632	0.66107	0.49631	0.49649	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30081	30081	SRR27700033	SRX23366853	SRS20229169	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:39798091		Smh control clutch 2	GSM8031706	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh control clutch 2	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM8031706	GSM8031706: Smh control clutch 2; Danio rerio; RNA Seq	GSM8031706 r1	GSM8031706	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459		SmhCTRL2_2.fq.gz SmhCTRL2_1.fq.gz	fastq fastq	4536576000.0	22682880.0	GSM8031706 r1	0:100 1:100	A:1180961957;C:1074391564;G:1088552770;T:1192669709;N:0	100	100	1180961957	1074391564	1088552770	1192669709	0	SRX23366853	SRS20229169	SRA1790727	NTNU	NTNU	2	0.94324	0.95313	0.08618	0.08685	0.66399	0.66216	0.49362	0.49644	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
30082	30082	SRR27700034	SRX23366852	SRS20229168	SRP485459	PRJNA1068100	Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain	GSE254006	Transcriptome Analysis	The brain uses a specialized system to transport cerebrospinal fluid CSF consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system we identify that loss of ciliary motility does not alter progenitor proliferation brain morphology or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.		pubmed:39798091		Smh control clutch 1	GSM8031705	source name:whole larvae\|tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment\|geo loc name:missing\|collection date:missing	Smh control clutch 1	The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters： sensitive no discordant no mixed I 1 X 1000 p 8 rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version：v2.2.5 Parameters： q sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map the clean reads to the reference gene sequence transcriptome and then RSEM Version：v1.2.8 Parameters： p 8 forward prob 0 paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx	whole larvae		To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI’s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		tissue:whole larvae\|genotype:mixture wt and +/ \|treatment:no treatment	GSM8031705	GSM8031705: Smh control clutch 1; Danio rerio; RNA Seq	GSM8031705 r1	GSM8031705	1	To isolate RNA for sequencing 30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200μL chloroform and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4°C. post centrifugation the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10μL Dnase+ 70μL RDD buffer per tube for 45 minutes at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30 seconds. This step was repeated twice and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column 30μL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke v1.5.2 using the parameters Parameters l 15 q 0.2 n 0.05. The Hierarchical Indexing for S…		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP485459		SmhCTRL1_1.fq.gz SmhCTRL1_2.fq.gz	fastq fastq	4546026800.0	22730134.0	GSM8031705 r1	0:100 1:100	A:1201447089;C:1060722844;G:1073012718;T:1210844149;N:0	100	100	1201447089	1060722844	1073012718	1210844149	0	SRX23366852	SRS20229168	SRA1790727	NTNU	NTNU	2	0.94554	0.95419	0.09192	0.09168	0.66436	0.66222	0.4762	0.48114	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2024-01-23	Larval	Larval	Whole Organism	All anatomical structures
34182	34182	SRR31399561	SRX26768859	SRS23256160	SRP546207	PRJNA1188114	Reduced EIF6 dosage attenuates TP53 activation in models of Shwachman Diamond syndrome	GSE282310	Transcriptome Analysis	Shwachman Diamond syndrome SDS is characterized by neutropenia exocrine pancreatic insufficiency and bony abnormalities with an increased risk of myeloid neoplasia. Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects. We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models confirmed in patient derived tissues and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression 5 25% of the wildtype levels that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS EIF6 TP53 and cellular stress responses offer promising insights into SDS pathogenesis somatic genetic rescue and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 / or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 / and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39 we used EBSeq R package for differentially expressed gene detection between eif6 / and eif6+/+ fold change > 2 and P < 0.05.				eif6 3	GSM8641203	source name:whole larvae\|tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 KO\|geo loc name:missing\|collection date:missing	eif6 3	Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally reads were removed if they: 1 lacked a 3’ adapter sequence 2 were 5’ 3’ adapter ligation products 3 were 5’ 5’ adapter ligation products 4 were shorter than 18 nt or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters: f N 0 M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values	whole larvae	5 dpf	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 KO	GSM8641203	GSM8641203: eif6 3; Danio rerio; RNA Seq	GSM8641203 r1	GSM8641203	1	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP546207		eif6_3_1.fq.gz eif6_3_2.fq.gz	fastq fastq	6955801200.0	34779006.0	GSM8641203 r1	0:100 1:100	A:1784502248;C:1653592398;G:1716091635;T:1801614919;N:0	100	100	1784502248	1653592398	1716091635	1801614919	0	SRX26768859	SRS23256160	SRA2017777	Cleveland Clinic	Cleveland Clinic												B	B	biological fallback assumption	bgi	bgi	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2024-11-19	Larval	Larval	Whole Organism	All anatomical structures
34183	34183	SRR31399562	SRX26768858	SRS23256161	SRP546207	PRJNA1188114	Reduced EIF6 dosage attenuates TP53 activation in models of Shwachman Diamond syndrome	GSE282310	Transcriptome Analysis	Shwachman Diamond syndrome SDS is characterized by neutropenia exocrine pancreatic insufficiency and bony abnormalities with an increased risk of myeloid neoplasia. Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects. We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models confirmed in patient derived tissues and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression 5 25% of the wildtype levels that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS EIF6 TP53 and cellular stress responses offer promising insights into SDS pathogenesis somatic genetic rescue and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 / or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 / and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39 we used EBSeq R package for differentially expressed gene detection between eif6 / and eif6+/+ fold change > 2 and P < 0.05.				eif6 2	GSM8641202	source name:whole larvae\|tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 KO\|geo loc name:missing\|collection date:missing	eif6 2	Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally reads were removed if they: 1 lacked a 3’ adapter sequence 2 were 5’ 3’ adapter ligation products 3 were 5’ 5’ adapter ligation products 4 were shorter than 18 nt or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters: f N 0 M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values	whole larvae	5 dpf	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 KO	GSM8641202	GSM8641202: eif6 2; Danio rerio; RNA Seq	GSM8641202 r1	GSM8641202	1	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP546207		eif6_2_1.fq.gz eif6_2_2.fq.gz	fastq fastq	6968721400.0	34843607.0	GSM8641202 r1	0:100 1:100	A:1798630009;C:1650901437;G:1708195694;T:1810994260;N:0	100	100	1798630009	1650901437	1708195694	1810994260	0	SRX26768858	SRS23256161	SRA2017777	Cleveland Clinic	Cleveland Clinic												B	B	biological fallback assumption	bgi	bgi	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2024-11-19	Larval	Larval	Whole Organism	All anatomical structures
34184	34184	SRR31399563	SRX26768857	SRS23256159	SRP546207	PRJNA1188114	Reduced EIF6 dosage attenuates TP53 activation in models of Shwachman Diamond syndrome	GSE282310	Transcriptome Analysis	Shwachman Diamond syndrome SDS is characterized by neutropenia exocrine pancreatic insufficiency and bony abnormalities with an increased risk of myeloid neoplasia. Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects. We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models confirmed in patient derived tissues and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression 5 25% of the wildtype levels that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS EIF6 TP53 and cellular stress responses offer promising insights into SDS pathogenesis somatic genetic rescue and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 / or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 / and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39 we used EBSeq R package for differentially expressed gene detection between eif6 / and eif6+/+ fold change > 2 and P < 0.05.				eif6 1	GSM8641201	source name:whole larvae\|tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 KO\|geo loc name:missing\|collection date:missing	eif6 1	Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally reads were removed if they: 1 lacked a 3’ adapter sequence 2 were 5’ 3’ adapter ligation products 3 were 5’ 5’ adapter ligation products 4 were shorter than 18 nt or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters: f N 0 M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values	whole larvae	5 dpf	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 KO	GSM8641201	GSM8641201: eif6 1; Danio rerio; RNA Seq	GSM8641201 r1	GSM8641201	1	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP546207		eif6_1_1.fq.gz eif6_1_2.fq.gz	fastq fastq	6976474200.0	34882371.0	GSM8641201 r1	0:100 1:100	A:1819387431;C:1630709320;G:1698463303;T:1827914146;N:0	100	100	1819387431	1630709320	1698463303	1827914146	0	SRX26768857	SRS23256159	SRA2017777	Cleveland Clinic	Cleveland Clinic												B	B	biological fallback assumption	bgi	bgi	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2024-11-19	Larval	Larval	Whole Organism	All anatomical structures
34185	34185	SRR31399564	SRX26768856	SRS23256158	SRP546207	PRJNA1188114	Reduced EIF6 dosage attenuates TP53 activation in models of Shwachman Diamond syndrome	GSE282310	Transcriptome Analysis	Shwachman Diamond syndrome SDS is characterized by neutropenia exocrine pancreatic insufficiency and bony abnormalities with an increased risk of myeloid neoplasia. Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects. We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models confirmed in patient derived tissues and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression 5 25% of the wildtype levels that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS EIF6 TP53 and cellular stress responses offer promising insights into SDS pathogenesis somatic genetic rescue and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 / or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 / and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39 we used EBSeq R package for differentially expressed gene detection between eif6 / and eif6+/+ fold change > 2 and P < 0.05.				wt3	GSM8641200	source name:whole larvae\|tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 wildtype\|geo loc name:missing\|collection date:missing	wt3	Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally reads were removed if they: 1 lacked a 3’ adapter sequence 2 were 5’ 3’ adapter ligation products 3 were 5’ 5’ adapter ligation products 4 were shorter than 18 nt or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters: f N 0 M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values	whole larvae	5 dpf	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 wildtype	GSM8641200	GSM8641200: wt3; Danio rerio; RNA Seq	GSM8641200 r1	GSM8641200	1	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP546207		wt3_1.fq.gz wt3_2.fq.gz	fastq fastq	6990771600.0	34953858.0	GSM8641200 r1	0:100 1:100	A:1823561732;C:1639273273;G:1691098287;T:1836838308;N:0	100	100	1823561732	1639273273	1691098287	1836838308	0	SRX26768856	SRS23256158	SRA2017777	Cleveland Clinic	Cleveland Clinic												B	B	biological fallback assumption	bgi	bgi	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2024-11-19	Larval	Larval	Whole Organism	All anatomical structures
34186	34186	SRR31399565	SRX26768855	SRS23256157	SRP546207	PRJNA1188114	Reduced EIF6 dosage attenuates TP53 activation in models of Shwachman Diamond syndrome	GSE282310	Transcriptome Analysis	Shwachman Diamond syndrome SDS is characterized by neutropenia exocrine pancreatic insufficiency and bony abnormalities with an increased risk of myeloid neoplasia. Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects. We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models confirmed in patient derived tissues and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression 5 25% of the wildtype levels that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS EIF6 TP53 and cellular stress responses offer promising insights into SDS pathogenesis somatic genetic rescue and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 / or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 / and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39 we used EBSeq R package for differentially expressed gene detection between eif6 / and eif6+/+ fold change > 2 and P < 0.05.				wt2	GSM8641199	source name:whole larvae\|tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 wildtype\|geo loc name:missing\|collection date:missing	wt2	Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally reads were removed if they: 1 lacked a 3’ adapter sequence 2 were 5’ 3’ adapter ligation products 3 were 5’ 5’ adapter ligation products 4 were shorter than 18 nt or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters: f N 0 M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values	whole larvae	5 dpf	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 wildtype	GSM8641199	GSM8641199: wt2; Danio rerio; RNA Seq	GSM8641199 r1	GSM8641199	1	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP546207		wt2_1.fq.gz wt2_2.fq.gz	fastq fastq	6996780600.0	34983903.0	GSM8641199 r1	0:100 1:100	A:1819793027;C:1646550105;G:1701161650;T:1829275818;N:0	100	100	1819793027	1646550105	1701161650	1829275818	0	SRX26768855	SRS23256157	SRA2017777	Cleveland Clinic	Cleveland Clinic												B	B	biological fallback assumption	bgi	bgi	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2024-11-19	Larval	Larval	Whole Organism	All anatomical structures
34187	34187	SRR31399566	SRX26768854	SRS23256156	SRP546207	PRJNA1188114	Reduced EIF6 dosage attenuates TP53 activation in models of Shwachman Diamond syndrome	GSE282310	Transcriptome Analysis	Shwachman Diamond syndrome SDS is characterized by neutropenia exocrine pancreatic insufficiency and bony abnormalities with an increased risk of myeloid neoplasia. Almost all cases of SDS result from biallelic mutations in SBDS. SBDS interacts with EFL1 to displace EIF6 from the 60S ribosomal subunit. Released EIF6 permits the assembly of ribosomal large and small subunits in the cytoplasm. Decreased EIF6 levels due to haploinsufficiency or missense mutations which lead to decreased protein expression may provide a somatic genetic rescue and anti leukemic effects. We observed accumulation of EIF6 protein in sbds knockout KO zebrafish models confirmed in patient derived tissues and correlated with changes in ribosome proteins and TP53 pathways. The mechanism of action for this adaptive response is unknown. To address this we generated an eif6 zebrafish KO line which do not survive past 10 dpf We also created two mutants with low Eif6 expression 5 25% of the wildtype levels that can survive until maturity. We bred them with sbds null strains and analyzed their phenotype and biochemical properties. Low Eif6 levels reduced Tp53 pathway activation but did not rescue neutropenia in Sbds deficient zebrafish. Further studies elucidating the interplay between SBDS EIF6 TP53 and cellular stress responses offer promising insights into SDS pathogenesis somatic genetic rescue and therapeutic strategies. Overall design: RNA was extracted from pools of 8–9 individually genotyped larvae at 10 dpf using TRIzol. Three pools of eif6 / or wildtype from the same clutch were compared. RNA quality was determined by Bioanalyzer Agilent and eif6 mRNA expression was measured by RT qPCR. RNA Seq library preparation and sequencing and mapping of 3 pools of eif6 / and 3 pools of eif6+/+ were performed by the Beijing Genome Institute 4. Based on the FPKM values 39 we used EBSeq R package for differentially expressed gene detection between eif6 / and eif6+/+ fold change > 2 and P < 0.05.				wt1	GSM8641198	source name:whole larvae\|tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 wildtype\|geo loc name:missing\|collection date:missing	wt1	Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high quality reads. Finally reads were removed if they: 1 lacked a 3’ adapter sequence 2 were 5’ 3’ adapter ligation products 3 were 5’ 5’ adapter ligation products 4 were shorter than 18 nt or 5 contained only As homopolymers. High quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters: f N 0 M 10. Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: csv file. FPKM values and p and q values	whole larvae	5 dpf	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		tissue:whole larvae\|cell line:5 dpf\|genotype:eif6 wildtype	GSM8641198	GSM8641198: wt1; Danio rerio; RNA Seq	GSM8641198 r1	GSM8641198	1	RNA was harvested using TRIzol following the manufacturer's instructions. Total RNA was submitted to BGI for small RNA seq library construction and deep sequencing. BGISeq 500 sequencing platform		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP546207		wt1_1.fq.gz wt1_2.fq.gz	fastq fastq	6976844600.0	34884223.0	GSM8641198 r1	0:100 1:100	A:1807619362;C:1649374675;G:1693243894;T:1826606669;N:0	100	100	1807619362	1649374675	1693243894	1826606669	0	SRX26768854	SRS23256156	SRA2017777	Cleveland Clinic	Cleveland Clinic												B	B	biological fallback assumption	bgi	bgi	unknown	small_rna	unknown	bulk	unknown	unknown	United States	2024-11-19	Larval	Larval	Whole Organism	All anatomical structures
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
60445	60445	SRR12272862	SRX8777892	SRS7048444	SRP272672	PRJNA647444	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA	PRJNA647444	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C2	C2 C2 2 4	replicate:biological replicate 2\|strain:AB\|isolate:C2\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:100ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C2C220200712	C2C220200712	RNA seq of zebrafish in different conditions			miRNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500	SRP272672	loader:fastq load.py	C2_C2_2_4.fq	fastq	542610936.0	21965958.0	C2 C2 2 4.fq.gz	0:24.70	A:95221617;C:122628624;G:167025611;T:157730855;N:4229	24		95221617	122628624	167025611	157730855	4229	SRX8777892	SRS7048444	SRA1101037	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.8119		0.10745		0.85717		0.51338		22		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-08-05	Undetermined	Embryo	Whole Organism	All anatomical structures
60446	60446	SRR12272863	SRX8777891	SRS7048443	SRP272672	PRJNA647444	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA	PRJNA647444	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C2	C2 C2 1 4	replicate:biological replicate 1\|strain:AB\|isolate:C2\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:100ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C2C220200711	C2C220200711	RNA seq of zebrafish in different conditions			miRNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500	SRP272672	loader:fastq load.py	C2_C2_1_4.fq	fastq	542847476.0	22614181.0	C2 C2 1 4.fq.gz	0:24.00	A:99999101;C:125407906;G:162383758;T:155055099;N:1612	24		99999101	125407906	162383758	155055099	1612	SRX8777891	SRS7048443	SRA1101037	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.84327		0.10491		0.83256		0.52046		19		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-08-05	Undetermined	Embryo	Whole Organism	All anatomical structures
60447	60447	SRR12272864	SRX8777890	SRS7048442	SRP272672	PRJNA647444	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA	PRJNA647444	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C1	C1 C1 2 4	replicate:biological replicate 2\|strain:AB\|isolate:C1\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:1ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C1C120200712	C1C120200712	RNA seq of zebrafish in different conditions			miRNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500	SRP272672	loader:fastq load.py	C1_C1_2_4.fq	fastq	570918284.0	22577002.0	C1 C1 2 4.fq.gz	0:25.29	A:100121235;C:130480588;G:178656113;T:161652765;N:7583	25		100121235	130480588	178656113	161652765	7583	SRX8777890	SRS7048442	SRA1101037	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.85096		0.12542		0.82873		0.51535		22		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-08-05	Undetermined	Embryo	Whole Organism	All anatomical structures
60448	60448	SRR12272865	SRX8777889	SRS7048441	SRP272672	PRJNA647444	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA	PRJNA647444	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C1	C1 C1 1 4	replicate:biological replicate 1\|strain:AB\|isolate:C1\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:1ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C1C120200711	C1C120200711	RNA seq of zebrafish in different conditions			miRNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500	SRP272672	loader:fastq load.py	C1_C1_1_4.fq	fastq	545089417.0	22812164.0	C1 C1 1 4.fq.gz	0:23.89	A:99851844;C:125314095;G:166401335;T:153521167;N:976	23		99851844	125314095	166401335	153521167	976	SRX8777889	SRS7048441	SRA1101037	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.84602		0.11725		0.83159		0.51353		19		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-08-05	Undetermined	Embryo	Whole Organism	All anatomical structures
60449	60449	SRR12272866	SRX8777888	SRS7048440	SRP272672	PRJNA647444	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA	PRJNA647444	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C0	C0 C0 2 4	replicate:biological replicate 2\|strain:AB\|isolate:C0\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:0ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C0C020200712	C0C020200712	RNA seq of zebrafish in different conditions			miRNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500	SRP272672	loader:fastq load.py	C0_C0_2_4.fq	fastq	527443144.0	23174740.0	C0 C0 2 4.fq.gz	0:22.76	A:102368401;C:120843229;G:151690193;T:152540806;N:515	22		102368401	120843229	151690193	152540806	515	SRX8777888	SRS7048440	SRA1101037	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.83063		0.08114		0.85169		0.50894		16		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-08-05	Undetermined	Embryo	Whole Organism	All anatomical structures
60450	60450	SRR12272867	SRX8777887	SRS7048439	SRP272672	PRJNA647444	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA	PRJNA647444	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C0	C0 C0 1 4	replicate:biological replicate 1\|strain:AB\|isolate:C0\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:0ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C0C020200711	C0C020200711	RNA seq of zebrafish in different conditions			miRNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500	SRP272672	loader:fastq load.py	C0_C0_1_4.fq	fastq	511759408.0	22673361.0	C0 C0 1 4.fq.gz	0:22.57	A:100879182;C:120237907;G:142799495;T:147842595;N:229	22		100879182	120237907	142799495	147842595	229	SRX8777887	SRS7048439	SRA1101037	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.83904		0.0823		0.84741		0.49929		22		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-08-05	Undetermined	Embryo	Whole Organism	All anatomical structures
60496	60496	SRR12328853	SRX8829078	SRS7048444	SRP273655	PRJNA648800	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA	PRJNA648800	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C2	C2 C2 2 4	replicate:biological replicate 2\|strain:AB\|isolate:C2\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:100ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C2C220200712	C2C220200712	RNA seq of zebrafish in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP273655		C2_C2_2_4_1.fq.gz C2_C2_2_4_2.fq.gz	fastq fastq	6974294600.0	69742946.0	C2 C2 2 4 1.fq.gz	0:100 1:100	A:2057162032;C:1418016219;G:1425580374;T:2073535975;N:0	100	100	2057162032	1418016219	1425580374	2073535975	0	SRX8829078	SRS7048444	SRA1103962	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.93171		0.17455		0.71626		0.54961		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-07-27	Undetermined	Embryo	Whole Organism	All anatomical structures
60497	60497	SRR12328854	SRX8829077	SRS7048443	SRP273655	PRJNA648800	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA	PRJNA648800	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C2	C2 C2 1 4	replicate:biological replicate 1\|strain:AB\|isolate:C2\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:100ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C2C220200711	C2C220200711	RNA seq of zebrafish in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP273655		C2_C2_1_4_2.fq.gz C2_C2_1_4_1.fq.gz	fastq fastq	6942905200.0	69429052.0	C2 C2 1 4 1.fq.gz	0:100 1:100	A:2025129308;C:1433430820;G:1434784226;T:2049560846;N:0	100	100	2025129308	1433430820	1434784226	2049560846	0	SRX8829077	SRS7048443	SRA1103962	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.93211		0.16662		0.71001		0.53674		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-07-27	Undetermined	Embryo	Whole Organism	All anatomical structures
60498	60498	SRR12328855	SRX8829076	SRS7048442	SRP273655	PRJNA648800	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA	PRJNA648800	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C1	C1 C1 2 4	replicate:biological replicate 2\|strain:AB\|isolate:C1\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:1ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C1C120200712	C1C120200712	RNA seq of zebrafish in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP273655		C1_C1_2_4_1.fq.gz C1_C1_2_4_2.fq.gz	fastq fastq	6973657600.0	69736576.0	C1 C1 2 4 1.fq.gz	0:100 1:100	A:2050440259;C:1423350359;G:1423015668;T:2076851314;N:0	100	100	2050440259	1423350359	1423015668	2076851314	0	SRX8829076	SRS7048442	SRA1103962	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.92911		0.1877		0.72025		0.58085		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-07-27	Undetermined	Embryo	Whole Organism	All anatomical structures
60499	60499	SRR12328856	SRX8829075	SRS7048441	SRP273655	PRJNA648800	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA	PRJNA648800	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C1	C1 C1 1 4	replicate:biological replicate 1\|strain:AB\|isolate:C1\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:1ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C1C120200711	C1C120200711	RNA seq of zebrafish in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP273655		C1_C1_1_4_1.fq.gz C1_C1_1_4_2.fq.gz	fastq fastq	6746729200.0	67467292.0	C1 C1 1 4 1.fq.gz	0:100 1:100	A:2004203843;C:1356765594;G:1357760526;T:2027999237;N:0	100	100	2004203843	1356765594	1357760526	2027999237	0	SRX8829075	SRS7048441	SRA1103962	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.92733		0.19903		0.72228		0.59259		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-07-27	Undetermined	Embryo	Whole Organism	All anatomical structures
60500	60500	SRR12328857	SRX8829074	SRS7048440	SRP273655	PRJNA648800	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA	PRJNA648800	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C0	C0 C0 2 4	replicate:biological replicate 2\|strain:AB\|isolate:C0\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:0ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C0C020200712	C0C020200712	RNA seq of zebrafish in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP273655		C0_C0_2_4_1.fq.gz C0_C0_2_4_2.fq.gz	fastq fastq	6924724800.0	69247248.0	C0 C0 2 4 1.fq.gz	0:100 1:100	A:1974618038;C:1471821932;G:1482725702;T:1995559128;N:0	100	100	1974618038	1471821932	1482725702	1995559128	0	SRX8829074	SRS7048440	SRA1103962	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.93473		0.14676		0.69649		0.50413		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-07-27	Undetermined	Embryo	Whole Organism	All anatomical structures
60501	60501	SRR12328858	SRX8829073	SRS7048439	SRP273655	PRJNA648800	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA	PRJNA648800	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C0	C0 C0 1 4	replicate:biological replicate 1\|strain:AB\|isolate:C0\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:0ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C0C020200711	C0C020200711	RNA seq of zebrafish in different conditions			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP273655		C0_C0_1_4_1.fq.gz C0_C0_1_4_2.fq.gz	fastq fastq	6899505600.0	68995056.0	C0 C0 1 4 1.fq.gz	0:100 1:100	A:1957459931;C:1477351919;G:1482435319;T:1982258431;N:0	100	100	1957459931	1477351919	1482435319	1982258431	0	SRX8829073	SRS7048439	SRA1103962	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.93567		0.14057		0.6883		0.48707		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-07-27	Undetermined	Embryo	Whole Organism	All anatomical structures
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
65984	65984	SRR15859821	SRX12150937	SRS10130028	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			levonorgestrel treatment at high concentration treatment	LNG H 1	AN	strain:not collected2\|isolate:whole fish13\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 1'\|BioSampleModel:Model organism or animal									LNG H 1	BM	BM	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		50_1_R1.clean.fq.gz 50_1_R2.clean.fq.gz	fastq fastq	6850889266.0	22893917.0	50 1 R1.clean.fq.gz	0:149.83 1:149.42	A:1908972876;C:1556853849;G:1559240564;T:1825804841;N:17136	149	149	1908972876	1556853849	1559240564	1825804841	17136	SRX12150937	SRS10130028	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93957	0.92386	0.09467	0.08944	0.66582	0.67142	0.50349	0.499	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65985	65985	SRR15859822	SRX12150936	SRS10130027	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			levonorgestrel treatment at low concentration treatment	LNG L 4	M	strain:not collected2\|isolate:whole fish12\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 4'\|BioSampleModel:Model organism or animal									LNG L 4	BL	BL	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		5_4_R1.clean.fq.gz 5_4_R2.clean.fq.gz	fastq fastq	6757301758.0	22579367.0	5 4 R1.clean.fq.gz	0:149.83 1:149.44	A:1886236851;C:1526321374;G:1529138861;T:1815587663;N:17009	149	149	1886236851	1526321374	1529138861	1815587663	17009	SRX12150936	SRS10130027	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93955	0.92322	0.09955	0.0937	0.66612	0.67056	0.4936	0.50296	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65986	65986	SRR15859823	SRX12150935	SRS10130026	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			levonorgestrel treatment at low concentration treatment	LNG L 3	AL	strain:not collected2\|isolate:whole fish11\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 3 prime\|BioSampleModel:Model organism or animal									LNG L 3	BK	BK	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		5_3_R1.clean.fq.gz 5_3_R2.clean.fq.gz	fastq fastq	6942028867.0	23178890.0	5 3 R1.clean.fq.gz	0:149.82 1:149.68	A:1895507796;C:1573477638;G:1599422601;T:1873160988;N:459844	149	149	1895507796	1573477638	1599422601	1873160988	459844	SRX12150935	SRS10130026	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.92261	0.9213	0.10308	0.10394	0.67298	0.67677	0.50615	0.5026	150	145	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65987	65987	SRR15859824	SRX12150934	SRS10130025	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Solvent control	SC2	AC	strain:not collected2\|isolate:whole fish2\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 2'\|BioSampleModel:Model organism or animal									SC2	BB	BB	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		SC_2_R1.clean.fq.gz SC_2_R2.clean.fq.gz	fastq fastq	6847074418.0	22905359.0	SC 2 R1.clean.fq.gz	0:149.58 1:149.35	A:1835075664;C:1586631096;G:1607651961;T:1817247855;N:467842	149	149	1835075664	1586631096	1607651961	1817247855	467842	SRX12150934	SRS10130025	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93172	0.93195	0.07691	0.0771	0.67265	0.67665	0.48862	0.49579	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65988	65988	SRR15859825	SRX12150933	SRS10130024	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Solvent control	SC1	AB	strain:not collected2\|isolate:whole fish1\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 1'\|BioSampleModel:Model organism or animal									SC1	BA	BA	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		SC_1_R1.clean.fq.gz SC_1_R2.clean.fq.gz	fastq fastq	7101595814.0	23743270.0	SC 1 R1.clean.fq.gz	0:149.65 1:149.45	A:1888007422;C:1656304946;G:1683234514;T:1873563589;N:485343	149	149	1888007422	1656304946	1683234514	1873563589	485343	SRX12150933	SRS10130024	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93193	0.93408	0.08101	0.08156	0.6744	0.67785	0.49761	0.49038	150	149	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65989	65989	SRR15859826	SRX12150932	SRS10130023	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			levonorgestrel treatment at low concentration treatment	LNG L 2	AK	strain:not collected2\|isolate:whole fish10\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 2'\|BioSampleModel:Model organism or animal									LNG L 2	BJ	BJ	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		5_2_R1.clean.fq.gz 5_2_R2.clean.fq.gz	fastq fastq	6978116268.0	23316955.0	5 2 R1.clean.fq.gz	0:149.72 1:149.55	A:1877413088;C:1609547451;G:1632121199;T:1858563731;N:470799	149	149	1877413088	1609547451	1632121199	1858563731	470799	SRX12150932	SRS10130023	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93086	0.93049	0.08702	0.08712	0.68357	0.68844	0.49793	0.48668	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65990	65990	SRR15859827	SRX12150931	SRS10130022	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			levonorgestrel treatment at low concentration treatment	LNG L 1	AJ	strain:not collected2\|isolate:whole fish9\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 1'\|BioSampleModel:Model organism or animal									LNG L 1	BI	BI	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		5_1_R1.clean.fq.gz 5_1_R2.clean.fq.gz	fastq fastq	6306082896.0	21075245.0	5 1 R1.clean.fq.gz	0:149.70 1:149.52	A:1679788198;C:1469939151;G:1489873755;T:1666053801;N:427991	149	149	1679788198	1469939151	1489873755	1666053801	427991	SRX12150931	SRS10130022	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93145	0.93206	0.08123	0.08188	0.67951	0.68432	0.48499	0.48763	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65991	65991	SRR15859828	SRX12150930	SRS10130021	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			dydrogesterone treatment	DDG 4	AI	strain:not collected2\|isolate:whole fish8\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 4'\|BioSampleModel:Model organism or animal									DDG 4	BH	BH	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_4_R1.clean.fq.gz 100_4_R2.clean.fq.gz	fastq fastq	7014679884.0	23437449.0	100 4 R1.clean.fq.gz	0:149.72 1:149.57	A:1882114669;C:1625037935;G:1641102139;T:1865959279;N:465862	149	149	1882114669	1625037935	1641102139	1865959279	465862	SRX12150930	SRS10130021	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93236	0.93264	0.08797	0.08919	0.67574	0.67965	0.50279	0.495	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65992	65992	SRR15859829	SRX12150929	SRS10130019	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			dydrogesterone treatment	DDG 3	AH	strain:not collected2\|isolate:whole fish7\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 3 prime\|BioSampleModel:Model organism or animal									DDG 3	BG	BG	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_3_R1.clean.fq.gz 100_3_R2.clean.fq.gz	fastq fastq	7000790030.0	23371313.0	100 3 R1.clean.fq.gz	0:149.83 1:149.72	A:1906942833;C:1592634521;G:1609492258;T:1891245267;N:475151	149	149	1906942833	1592634521	1609492258	1891245267	475151	SRX12150929	SRS10130019	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.92801	0.92781	0.09747	0.09744	0.66517	0.66776	0.50246	0.49531	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65993	65993	SRR15859830	SRX12150928	SRS10130020	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			dydrogesterone treatment	DDG 2	AG	strain:not collected2\|isolate:whole fish6\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 2'\|BioSampleModel:Model organism or animal									DDG 2	BF	BF	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_2_R1.clean.fq.gz 100_2_R2.clean.fq.gz	fastq fastq	7075813310.0	23625836.0	100 2 R1.clean.fq.gz	0:149.82 1:149.68	A:1918796036;C:1619755625;G:1637664383;T:1899135516;N:461750	149	149	1918796036	1619755625	1637664383	1899135516	461750	SRX12150928	SRS10130020	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.92935	0.92868	0.08886	0.08912	0.65717	0.6621	0.4843	0.49415	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65994	65994	SRR15859831	SRX12150927	SRS10130018	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			dydrogesterone treatment	DDG 1	AF	strain:not collected2\|isolate:whole fish5\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 1'\|BioSampleModel:Model organism or animal									DDG 1	BE	BE	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_1_R1.clean.fq.gz 100_1_R2.clean.fq.gz	fastq fastq	6740898004.0	22511996.0	100 1 R1.clean.fq.gz	0:149.79 1:149.65	A:1828418830;C:1542362815;G:1564205385;T:1805464983;N:445991	149	149	1828418830	1542362815	1564205385	1805464983	445991	SRX12150927	SRS10130018	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.92893	0.92836	0.08577	0.08614	0.67639	0.68077	0.48573	0.49544	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65995	65995	SRR15859832	SRX12150926	SRS10130016	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Solvent control	SC4	AE	strain:not collected2\|isolate:whole fish4\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 4'\|BioSampleModel:Model organism or animal									SC4	BD	BD	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		SC_4_R1.clean.fq.gz SC_4_R2.clean.fq.gz	fastq fastq	6051468288.0	20209797.0	SC 4 R1.clean.fq.gz	0:149.80 1:149.63	A:1652651735;C:1373191643;G:1392749062;T:1632474997;N:400851	149	149	1652651735	1373191643	1392749062	1632474997	400851	SRX12150926	SRS10130016	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.92672	0.92501	0.09038	0.09121	0.66259	0.66565	0.49636	0.49698	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65996	65996	SRR15859833	SRX12150925	SRS10130017	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Levonorgestrel at high concentration and dydrogesterone mixturestreatment	DDG+LNG H 1	AY	strain:not collected2\|isolate:whole fish24\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 4'\|BioSampleModel:Model organism or animal									DDG+LNG H 1	BX	BX	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_50_4_R1.clean.fq.gz 100_50_4_R2.clean.fq.gz	fastq fastq	6861007764.0	22938186.0	100 50 4 R1.clean.fq.gz	0:149.76 1:149.35	A:1881600852;C:1578987219;G:1582313999;T:1818088269;N:17425	149	149	1881600852	1578987219	1582313999	1818088269	17425	SRX12150925	SRS10130017	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93777	0.92424	0.09796	0.0931	0.66182	0.66746	0.49608	0.49787	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65997	65997	SRR15859834	SRX12150924	SRS10130015	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Levonorgestrel at high concentration and dydrogesterone mixtures treatment	DDG+LNG H 1	AX	strain:not collected2\|isolate:whole fish23\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 3 prime\|BioSampleModel:Model organism or animal									DDG+LNG H 1	BW	BW	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_50_3_R1.clean.fq.gz 100_50_3_R2.clean.fq.gz	fastq fastq	6448167527.0	21546554.0	100 50 3 R1.clean.fq.gz	0:149.84 1:149.43	A:1776900923;C:1483436670;G:1478517308;T:1709296399;N:16227	149	149	1776900923	1483436670	1478517308	1709296399	16227	SRX12150924	SRS10130015	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.94114	0.92751	0.08812	0.0842	0.66557	0.67052	0.49525	0.49796	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65998	65998	SRR15859835	SRX12150923	SRS10130014	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Levonorgestrel at high concentration and dydrogesterone mixtures treatment	DDG+LNG H 1	AW	strain:not collected2\|isolate:whole fish22\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 2'\|BioSampleModel:Model organism or animal									DDG+LNG H 1	BV	BV	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_50_2_R1.clean.fq.gz 100_50_2_R2.clean.fq.gz	fastq fastq	6097050612.0	20374795.0	100 50 2 R1.clean.fq.gz	0:149.83 1:149.42	A:1697937652;C:1387399999;G:1387536896;T:1624160680;N:15385	149	149	1697937652	1387399999	1387536896	1624160680	15385	SRX12150923	SRS10130014	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93921	0.92457	0.09156	0.08703	0.677	0.68268	0.51381	0.51338	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
65999	65999	SRR15859836	SRX12150922	SRS10130013	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Levonorgestrel at high concentration and dydrogesterone mixtures treatment	DDG+LNG H 1	AV	strain:not collected2\|isolate:whole fish21\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 1'\|BioSampleModel:Model organism or animal									DDG+LNG H 1	BU	BU	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_50_1_R1.clean.fq.gz 100_50_1_R2.clean.fq.gz	fastq fastq	6200464490.0	20718210.0	100 50 1 R1.clean.fq.gz	0:149.84 1:149.44	A:1722773998;C:1411958803;G:1410364088;T:1655351787;N:15814	149	149	1722773998	1411958803	1410364088	1655351787	15814	SRX12150922	SRS10130013	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.94019	0.92317	0.09428	0.08799	0.66192	0.66813	0.50339	0.50384	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66000	66000	SRR15859837	SRX12150921	SRS10130012	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Solvent control	SC3	AD	strain:not collected2\|isolate:whole fish3\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 3 prime\|BioSampleModel:Model organism or animal									SC3	BC	BC	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		SC_3_R1.clean.fq.gz SC_3_R2.clean.fq.gz	fastq fastq	6744019219.0	22522868.0	SC 3 R1.clean.fq.gz	0:149.81 1:149.62	A:1832736009;C:1540439892;G:1560536404;T:1809859936;N:446978	149	149	1832736009	1540439892	1560536404	1809859936	446978	SRX12150921	SRS10130012	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.92908	0.92831	0.08407	0.08413	0.66748	0.67332	0.49151	0.50363	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66001	66001	SRR15859838	SRX12150920	SRS10130011	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Levonorgestrel at low concentration and dydrogesterone mixtures treatment	DDG+LNG L 4	AU	strain:not collected2\|isolate:whole fish20\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 4'\|BioSampleModel:Model organism or animal									DDG+LNG L 4	BT	BT	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_5_4_R1.clean.fq.gz 100_5_4_R2.clean.fq.gz	fastq fastq	6698715338.0	22386760.0	100 5 4 R1.clean.fq.gz	0:149.82 1:149.41	A:1854944489;C:1532319316;G:1533554376;T:1777880466;N:16691	149	149	1854944489	1532319316	1533554376	1777880466	16691	SRX12150920	SRS10130011	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.93948	0.92423	0.09198	0.08752	0.66967	0.67513	0.49914	0.49616	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66002	66002	SRR15859839	SRX12150919	SRS10130010	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Levonorgestrel at low concentration and dydrogesterone mixtures treatment	DDG+LNG L 3	AT	strain:not collected2\|isolate:whole fish19\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 3 prime\|BioSampleModel:Model organism or animal									DDG+LNG L 3	BS	BS	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_5_3_R1.clean.fq.gz 100_5_3_R2.clean.fq.gz	fastq fastq	6731263096.0	22494392.0	100 5 3 R1.clean.fq.gz	0:149.82 1:149.42	A:1853865687;C:1546635036;G:1549005691;T:1781740007;N:16675	149	149	1853865687	1546635036	1549005691	1781740007	16675	SRX12150919	SRS10130010	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.94161	0.92699	0.09368	0.08881	0.67146	0.67671	0.49075	0.4916	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66003	66003	SRR15859840	SRX12150918	SRS10130009	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Levonorgestrel at low concentration and dydrogesterone mixtures treatment	DDG+LNG L 2	AS	strain:not collected2\|isolate:whole fish18\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 2'\|BioSampleModel:Model organism or animal									DDG+LNG L 2	BR	BR	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_5_2_R1.clean.fq.gz 100_5_2_R2.clean.fq.gz	fastq fastq	6856677730.0	22942302.0	100 5 2 R1.clean.fq.gz	0:149.63 1:149.23	A:1861833177;C:1593702006;G:1601437245;T:1799688067;N:17235	149	149	1861833177	1593702006	1601437245	1799688067	17235	SRX12150918	SRS10130009	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.94226	0.93085	0.08471	0.08039	0.67677	0.68191	0.48927	0.47969	150	148	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66004	66004	SRR15859841	SRX12150917	SRS10130007	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			Levonorgestrel at low concentration and dydrogesterone mixtures treatment	DDG+LNG L 1	AR	strain:not collected2\|isolate:whole fish17\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 1'\|BioSampleModel:Model organism or animal									DDG+LNG L 1	BQ	BQ	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		100_5_1_R1.clean.fq.gz 100_5_1_R2.clean.fq.gz	fastq fastq	6734596961.0	22519168.0	100 5 1 R1.clean.fq.gz	0:149.72 1:149.34	A:1835515639;C:1562058332;G:1561380426;T:1775625709;N:16855	149	149	1835515639	1562058332	1561380426	1775625709	16855	SRX12150917	SRS10130007	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.94108	0.92768	0.09123	0.08716	0.66967	0.6747	0.50584	0.50347	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66005	66005	SRR15859842	SRX12150916	SRS10130006	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			levonorgestrel treatment at high concentration treatment	LNG H 4	AQ	strain:not collected2\|isolate:whole fish16\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 4'\|BioSampleModel:Model organism or animal									LNG H 4	BP	BP	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		50_4_R1.clean.fq.gz 50_4_R2.clean.fq.gz	fastq fastq	7033955938.0	23502039.0	50 4 R1.clean.fq.gz	0:149.84 1:149.46	A:1939982949;C:1612770444;G:1610988374;T:1870196531;N:17640	149	149	1939982949	1612770444	1610988374	1870196531	17640	SRX12150916	SRS10130006	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.94099	0.92749	0.09644	0.09215	0.67261	0.67838	0.49766	0.49584	150	149	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66006	66006	SRR15859843	SRX12150915	SRS10130008	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			levonorgestrel treatment at high concentration treatment	LNG H 3	AP	strain:not collected2\|isolate:whole fish15\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 3 prime\|BioSampleModel:Model organism or animal									LNG H 3	BO	BO	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		50_3_R1.clean.fq.gz 50_3_R2.clean.fq.gz	fastq fastq	5819952570.0	19444342.0	50 3 R1.clean.fq.gz	0:149.86 1:149.46	A:1615559082;C:1328350353;G:1325535770;T:1550492661;N:14704	149	149	1615559082	1328350353	1325535770	1550492661	14704	SRX12150915	SRS10130008	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.9397	0.92495	0.09375	0.08838	0.669	0.67338	0.50535	0.5146	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
66007	66007	SRR15859844	SRX12150914	SRS10130005	SRP336743	PRJNA760976	Danio rerio strain:AB Transcriptome or Gene expression	PRJNA760976	Transcriptome Analysis	we investigated the effects of progestins on gonadal differentiation and sex determination in zebrafish			levonorgestrel treatment at high concentration treatment	LNG H 2	AO	strain:not collected2\|isolate:whole fish14\|breed:not collected\|cultivar:not applicable3\|ecotype:not applicable4\|age:4 weeks\|dev stage:not applicable5\|sex:missing\|tissue:whole fish\|replicate:'replicate = biological replicate 2'\|BioSampleModel:Model organism or animal									LNG H 2	BN	BN	zebraifsh exposure			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP336743		50_2_R1.clean.fq.gz 50_2_R2.clean.fq.gz	fastq fastq	5888497480.0	19673249.0	50 2 R1.clean.fq.gz	0:149.84 1:149.47	A:1638307115;C:1337036459;G:1335389572;T:1577749137;N:15197	149	149	1638307115	1337036459	1335389572	1577749137	15197	SRX12150914	SRS10130005	SRA1291484	South China Normal University\|School of Environment	South China Normal University	2	0.9395	0.92471	0.09382	0.08964	0.66785	0.67144	0.50388	0.5077	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-09-12	Larval	Larval	Whole Organism	All anatomical structures
67043	67043	SRR17017805	SRX13207904	SRS11133999	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.		pubmed:35114580		Aldh 2.1 / KO la3	GSM5701222	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	Aldh 2.1 / KO la3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	GSM5701222	GSM5701222: Aldh 2.1 / KO la3; Danio rerio; RNA Seq	GSM5701222 r1	GSM5701222	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444		3-KOla3_1.fq.gz 3-KOla3_2.fq.gz	fastq fastq	4974883400.0	49748834.0	GSM5701222 r1	0:100 1:100	A:1325503000;C:1131322113;G:1183075417;T:1334982870;N:0	100	100	1325503000	1131322113	1183075417	1334982870	0	SRX13207904	SRS11133999	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95156		0.10103		0.68917		0.50967		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67044	67044	SRR17017806	SRX13207903	SRS11133998	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.		pubmed:35114580		Aldh 2.1 / KO la2	GSM5701221	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	Aldh 2.1 / KO la2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	GSM5701221	GSM5701221: Aldh 2.1 / KO la2; Danio rerio; RNA Seq	GSM5701221 r1	GSM5701221	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444		2-KOla2_1.fq.gz 2-KOla2_2.fq.gz	fastq fastq	4993502200.0	49935022.0	GSM5701221 r1	0:100 1:100	A:1337290403;C:1130744731;G:1181303599;T:1344163467;N:0	100	100	1337290403	1130744731	1181303599	1344163467	0	SRX13207903	SRS11133998	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95056		0.09273		0.69207		0.5213		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67045	67045	SRR17017807	SRX13207902	SRS11133997	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.		pubmed:35114580		Aldh 2.1 / KO la1	GSM5701220	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	Aldh 2.1 / KO la1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	GSM5701220	GSM5701220: Aldh 2.1 / KO la1; Danio rerio; RNA Seq	GSM5701220 r1	GSM5701220	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444		1-KOla1_1.fq.gz 1-KOla1_2.fq.gz	fastq fastq	4982824800.0	49828248.0	GSM5701220 r1	0:100 1:100	A:1318751230;C:1142967126;G:1194575929;T:1326530515;N:0	100	100	1318751230	1142967126	1194575929	1326530515	0	SRX13207902	SRS11133997	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95468		0.09398		0.67917		0.50026		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67046	67046	SRR17017808	SRX13207901	SRS11133996	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.		pubmed:35114580		Aldh 2.1 +/+ WT la6	GSM5701229	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	Aldh 2.1 +/+ WT la6	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	GSM5701229	GSM5701229: Aldh 2.1 +/+ WT la6; Danio rerio; RNA Seq	GSM5701229 r1	GSM5701229	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444		10-WTla6_1.fq.gz 10-WTla6_2.fq.gz	fastq fastq	4990544400.0	49905444.0	GSM5701229 r1	0:100 1:100	A:1342332744;C:1123081871;G:1174336584;T:1350793201;N:0	100	100	1342332744	1123081871	1174336584	1350793201	0	SRX13207901	SRS11133996	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.94932		0.10692		0.69246		0.5131		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67047	67047	SRR17017809	SRX13207900	SRS11133995	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.		pubmed:35114580		Aldh 2.1 +/+ WT la5	GSM5701228	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	Aldh 2.1 +/+ WT la5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	GSM5701228	GSM5701228: Aldh 2.1 +/+ WT la5; Danio rerio; RNA Seq	GSM5701228 r1	GSM5701228	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444		9-WTla5_1.fq.gz 9-WTla5_2.fq.gz	fastq fastq	4990444600.0	49904446.0	GSM5701228 r1	0:100 1:100	A:1347054785;C:1118741393;G:1169087601;T:1355560821;N:0	100	100	1347054785	1118741393	1169087601	1355560821	0	SRX13207900	SRS11133995	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.94929		0.10427		0.69925		0.51838		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67048	67048	SRR17017810	SRX13207899	SRS11133994	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.		pubmed:35114580		Aldh 2.1 +/+ WT la3	GSM5701227	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	Aldh 2.1 +/+ WT la3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	GSM5701227	GSM5701227: Aldh 2.1 +/+ WT la3; Danio rerio; RNA Seq	GSM5701227 r1	GSM5701227	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444		8-WTla3_1.fq.gz 8-WTla3_2.fq.gz	fastq fastq	4986064600.0	49860646.0	GSM5701227 r1	0:100 1:100	A:1358143440;C:1107981393;G:1154357851;T:1365581916;N:0	100	100	1358143440	1107981393	1154357851	1365581916	0	SRX13207899	SRS11133994	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95037		0.10323		0.69499		0.54725		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67049	67049	SRR17017811	SRX13207898	SRS11133993	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.		pubmed:35114580		Aldh 2.1 +/+ WT la2	GSM5701226	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	Aldh 2.1 +/+ WT la2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	GSM5701226	GSM5701226: Aldh 2.1 +/+ WT la2; Danio rerio; RNA Seq	GSM5701226 r1	GSM5701226	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444		7-WTla2_1.fq.gz 7-WTla2_2.fq.gz	fastq fastq	4977068600.0	49770686.0	GSM5701226 r1	0:100 1:100	A:1341174868;C:1117869236;G:1167898570;T:1350125926;N:0	100	100	1341174868	1117869236	1167898570	1350125926	0	SRX13207898	SRS11133993	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.94822		0.11063		0.69514		0.51197		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67050	67050	SRR17017812	SRX13207897	SRS11133992	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.		pubmed:35114580		Aldh 2.1 +/+ WT la1	GSM5701225	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	Aldh 2.1 +/+ WT la1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:WT	GSM5701225	GSM5701225: Aldh 2.1 +/+ WT la1; Danio rerio; RNA Seq	GSM5701225 r1	GSM5701225	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444		6-WTla1_1.fq.gz 6-WTla1_2.fq.gz	fastq fastq	4937740400.0	49377404.0	GSM5701225 r1	0:100 1:100	A:1322363529;C:1116877989;G:1169055598;T:1329443284;N:0	100	100	1322363529	1116877989	1169055598	1329443284	0	SRX13207897	SRS11133992	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.95215		0.10081		0.69534		0.51784		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67051	67051	SRR17017813	SRX13207896	SRS11133991	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.		pubmed:35114580		Aldh 2.1 / KO la6	GSM5701224	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	Aldh 2.1 / KO la6	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	GSM5701224	GSM5701224: Aldh 2.1 / KO la6; Danio rerio; RNA Seq	GSM5701224 r1	GSM5701224	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444		5-KOla6_1.fq.gz 5-KOla6_2.fq.gz	fastq fastq	4875673200.0	48756732.0	GSM5701224 r1	0:100 1:100	A:1325527276;C:1084173307;G:1132675639;T:1333296978;N:0	100	100	1325527276	1084173307	1132675639	1333296978	0	SRX13207896	SRS11133991	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.94517		0.10711		0.69548		0.47813		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67052	67052	SRR17017814	SRX13207895	SRS11133990	SRP347444	PRJNA782975	Accumulation of Acetaldehyde in aldh2.1 / Zebrafish Causes Increased Retinal Angiogenesis and Impaired Glucose Homeostasis	GSE189416	Transcriptome Analysis	In conclusion the data have identified acetaldehyde as the preferred substrate for Aldh2.1's detoxification ability. In zebrafish acetaldehyde induces impaired glucose metabolism by blocking gene expression of glucokinase and glucose 6 phosphatase. Moreover Stress activated protein Kinases JNK and p38 MAPK were activated by elevated endogenous acetaldehyde leading to increased angiogenesis and vasodilatory effects in aldh2.1 / zebrafish mutants. Overall design: Characterization of aldh2.1 knockout zebrafish mutants regarding effects on reactive metabolite detoxification metabolomics genomics and organ health especially vascular health.		pubmed:35114580		Aldh 2.1 / KO la5	GSM5701223	source name:whole larvae\|developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	Aldh 2.1 / KO la5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	whole larvae		Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Embryos / larvae were held and raised in egg water at 28.5 °C for 120 hours with no extra treatment.	developmental stage:larvae 120hpf\|tissue:whole larvae\|genotype:aldh2.1 knockout	GSM5701223	GSM5701223: Aldh 2.1 / KO la5; Danio rerio; RNA Seq	GSM5701223 r1	GSM5701223	1	Embryo / larvae samples were anaesthetized with 0.0003 % tricaine at 120 hpf collected and snap frozen in liquid nitrogen in a clutch of 50. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP347444		4-KOla5_1.fq.gz 4-KOla5_2.fq.gz	fastq fastq	4965270200.0	49652702.0	GSM5701223 r1	0:100 1:100	A:1348940910;C:1104562620;G:1155269060;T:1356497610;N:0	100	100	1348940910	1104562620	1155269060	1356497610	0	SRX13207895	SRS11133990	SRA1492011	ZMF, University Heidelberg	ZMF, University Heidelberg	1	0.94849		0.11019		0.69988		0.53589		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2021-11-23	Larval	Larval	Whole Organism	All anatomical structures
67884	67884	SRR17868935	SRX14028691	SRS11864778	SRP358022	PRJNA793391	Effects of acute exposure to nano silver on zebrafish larvae	PRJNA793391	Other	Sliver nanoparticles AgNPs are widely used for industry agriculture and medicals which potentially result in adverse effects for human health and aquatic environment. In this present study we investigated the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.					C4 1	strain:danio rerio AgNPs4\|breed:zebrafish10\|age:3 day\|sex:pooled male and female\|tissue:fish\|BioSampleModel:Model organism or animal									DANIO RERIO 4 1	AG 4 1	AG 4 1	treatment7			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP358022		C4-1_1.fq.gz C4-1_2.fq.gz	fastq fastq	6830916900.0	45539446.0	C4 1 1.fq.gz	0:150 1:150	A:2011586443;C:1405775454;G:1388504965;T:2024992696;N:57342	150	150	2011586443	1405775454	1388504965	2024992696	57342	SRX14028691	SRS11864778	SRA1350965	Center for Neuroscience\|Shantou university	Center for Neuroscience	1	0.92344		0.21929		0.71043		0.46315		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-03	Larval	Larval	Whole Organism	All anatomical structures
67885	67885	SRR17868936	SRX14028690	SRS11864777	SRP358022	PRJNA793391	Effects of acute exposure to nano silver on zebrafish larvae	PRJNA793391	Other	Sliver nanoparticles AgNPs are widely used for industry agriculture and medicals which potentially result in adverse effects for human health and aquatic environment. In this present study we investigated the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.					C2 3	strain:danio rerio AgNPs2\|breed:zebrafish9\|age:3 day\|sex:pooled male and female\|tissue:fish\|BioSampleModel:Model organism or animal									DANIO RERIO 2 3	AG 2 3	AG 2 3	treatment6			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP358022		C2-3_1.fq.gz C2-3_2.fq.gz	fastq fastq	6782959200.0	45219728.0	C2 3 1.fq.gz	0:150 1:150	A:1949560199;C:1443524899;G:1428814233;T:1960921903;N:137966	150	150	1949560199	1443524899	1428814233	1960921903	137966	SRX14028690	SRS11864777	SRA1350965	Center for Neuroscience\|Shantou university	Center for Neuroscience	1	0.93181		0.17739		0.6927		0.50528		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-03	Larval	Larval	Whole Organism	All anatomical structures
67886	67886	SRR17868937	SRX14028689	SRS11864776	SRP358022	PRJNA793391	Effects of acute exposure to nano silver on zebrafish larvae	PRJNA793391	Other	Sliver nanoparticles AgNPs are widely used for industry agriculture and medicals which potentially result in adverse effects for human health and aquatic environment. In this present study we investigated the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.					C2 2	strain:danio rerio AgNPs2\|breed:zebrafish8\|age:3 day\|sex:pooled male and female\|tissue:fish\|BioSampleModel:Model organism or animal									DANIO RERIO 2 2	AG 2 2	AG 2 2	treatment5			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP358022		C2-2_1.fq.gz C2-2_2.fq.gz	fastq fastq	6817863300.0	45452422.0	C2 2 1.fq.gz	0:150 1:150	A:1964890519;C:1446826412;G:1428708103;T:1977297439;N:140827	150	150	1964890519	1446826412	1428708103	1977297439	140827	SRX14028689	SRS11864776	SRA1350965	Center for Neuroscience\|Shantou university	Center for Neuroscience	1	0.93045		0.17846		0.69116		0.48565		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-03	Larval	Larval	Whole Organism	All anatomical structures
67887	67887	SRR17868938	SRX14028688	SRS11864774	SRP358022	PRJNA793391	Effects of acute exposure to nano silver on zebrafish larvae	PRJNA793391	Other	Sliver nanoparticles AgNPs are widely used for industry agriculture and medicals which potentially result in adverse effects for human health and aquatic environment. In this present study we investigated the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.					C2 1	strain:danio rerio AgNPs2\|breed:zebrafish7\|age:3 day\|sex:pooled male and female\|tissue:fish\|BioSampleModel:Model organism or animal									DANIO RERIO 2 1	AG 2 1	AG 2 1	treatment4			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP358022		C2-1_1.fq.gz C2-1_2.fq.gz	fastq fastq	6795911700.0	45306078.0	C2 1 1.fq.gz	0:150 1:150	A:1910936263;C:1486390531;G:1471463982;T:1927036309;N:84615	150	150	1910936263	1486390531	1471463982	1927036309	84615	SRX14028688	SRS11864774	SRA1350965	Center for Neuroscience\|Shantou university	Center for Neuroscience	1	0.93638		0.14847		0.6814		0.46864		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-03	Larval	Larval	Whole Organism	All anatomical structures
67888	67888	SRR17868939	SRX14028687	SRS11864775	SRP358022	PRJNA793391	Effects of acute exposure to nano silver on zebrafish larvae	PRJNA793391	Other	Sliver nanoparticles AgNPs are widely used for industry agriculture and medicals which potentially result in adverse effects for human health and aquatic environment. In this present study we investigated the illumine high throughput RNA sequencing revealed the transcriptome profiling of zebrafish larvae post AgNPs treatment for 72 h.					C1 3	strain:danio rerio AgNPs1\|breed:zebrafish6\|age:3 day\|sex:pooled male and female\|tissue:fish\|BioSampleModel:Model organism or animal									DANIO RERIO 1 3	AG 1 3	AG 1 3	treatment3			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP358022		C1-3_1.fq.gz C1-3_2.fq.gz	fastq fastq	6788960100.0	45259734.0	C1 3 1.fq.gz	0:150 1:150	A:1883226902;C:1511814926;G:1492397960;T:1901504019;N:16293	150	150	1883226902	1511814926	1492397960	1901504019	16293	SRX14028687	SRS11864775	SRA1350965	Center for Neuroscience\|Shantou university	Center for Neuroscience	1	0.94253		0.12673		0.67623		0.49289		150		B		usable mapping rate	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2022-02-03	Larval	Larval	Whole Organism	All anatomical structures

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