metadata: run_metadata: 73 rows where devstage_curation_coarse = "Embryo" and experiment.platform = "DNBSEQ"

73 rows where devstage_curation_coarse = "Embryo" and experiment.platform = "DNBSEQ"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.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
34053	34053	SRR31034578	SRX26420033	SRS22939666	SRP539240	PRJNA1174234	Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A	GSE279773	Transcriptome Analysis	Prior to type 2 diabetes onset ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A we used the following animal and cell based models: transgenic zebrafish and inducible ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly following 4 weeks of high fat diet feeding and obesity mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells despite similar weight gain and insulin sensitivity. Taken together our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function inpart from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control dhps or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.		pubmed:39832654	eif5a1/2 morpholino 3	GSM8579963	source name:whole body\|tissue:whole body\|treatment:eif5a1/2 morpholino\|geo loc name:missing\|collection date:missing	eif5a1/2 morpholino 3	Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value	whole body	zebrafish were treated with morpholino and RNA was extracted 24 hours later	RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.		tissue:whole body\|treatment:eif5a1/2 morpholino	GSM8579963	GSM8579963: eif5a1/2 morpholino 3; Danio rerio; RNA Seq	GSM8579963 r1	GSM8579963	1	RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP539240		eIF5AMO3_1.fq.gz eIF5AMO3_2.fq.gz	fastq fastq	6591810600.0	21972702.0	GSM8579963 r1	0:150 1:150	A:1735827111;C:1561621052;G:1576813159;T:1717549278;N:0	150	150	1735827111	1561621052	1576813159	1717549278	0	SRX26420033	SRS22939666	SRA1993170	Medicine, University of Chicago	Medicine, University of Chicago												B	B	biological fallback assumption	bgi	bgi	3prime	poly_a	unknown	bulk	unknown	unknown	United States	2024-10-17	Undetermined	Embryo	Trunk	Surface Structure
34054	34054	SRR31034579	SRX26420032	SRS22939665	SRP539240	PRJNA1174234	Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A	GSE279773	Transcriptome Analysis	Prior to type 2 diabetes onset ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A we used the following animal and cell based models: transgenic zebrafish and inducible ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly following 4 weeks of high fat diet feeding and obesity mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells despite similar weight gain and insulin sensitivity. Taken together our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function inpart from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control dhps or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.		pubmed:39832654	eif5a1/2 morpholino 2	GSM8579962	source name:whole body\|tissue:whole body\|treatment:eif5a1/2 morpholino\|geo loc name:missing\|collection date:missing	eif5a1/2 morpholino 2	Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value	whole body	zebrafish were treated with morpholino and RNA was extracted 24 hours later	RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.		tissue:whole body\|treatment:eif5a1/2 morpholino	GSM8579962	GSM8579962: eif5a1/2 morpholino 2; Danio rerio; RNA Seq	GSM8579962 r1	GSM8579962	1	RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP539240		eIF5AMO2_1.fq.gz eIF5AMO2_2.fq.gz	fastq fastq	6615856500.0	22052855.0	GSM8579962 r1	0:150 1:150	A:1712890711;C:1594159797;G:1606364019;T:1702441973;N:0	150	150	1712890711	1594159797	1606364019	1702441973	0	SRX26420032	SRS22939665	SRA1993170	Medicine, University of Chicago	Medicine, University of Chicago												B	B	biological fallback assumption	bgi	bgi	3prime	poly_a	unknown	bulk	unknown	unknown	United States	2024-10-17	Undetermined	Embryo	Trunk	Surface Structure
34055	34055	SRR31034580	SRX26420031	SRS22939663	SRP539240	PRJNA1174234	Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A	GSE279773	Transcriptome Analysis	Prior to type 2 diabetes onset ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A we used the following animal and cell based models: transgenic zebrafish and inducible ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly following 4 weeks of high fat diet feeding and obesity mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells despite similar weight gain and insulin sensitivity. Taken together our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function inpart from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control dhps or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.		pubmed:39832654	eif5a1/2 morpholino 1	GSM8579961	source name:whole body\|tissue:whole body\|treatment:eif5a1/2 morpholino\|geo loc name:missing\|collection date:missing	eif5a1/2 morpholino 1	Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value	whole body	zebrafish were treated with morpholino and RNA was extracted 24 hours later	RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.		tissue:whole body\|treatment:eif5a1/2 morpholino	GSM8579961	GSM8579961: eif5a1/2 morpholino 1; Danio rerio; RNA Seq	GSM8579961 r1	GSM8579961	1	RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP539240		eIF5AMO1_1.fq.gz eIF5AMO1_2.fq.gz	fastq fastq	6172597200.0	20575324.0	GSM8579961 r1	0:150 1:150	A:1612632964;C:1473173555;G:1490511736;T:1596278945;N:0	150	150	1612632964	1473173555	1490511736	1596278945	0	SRX26420031	SRS22939663	SRA1993170	Medicine, University of Chicago	Medicine, University of Chicago												B	B	biological fallback assumption	bgi	bgi	3prime	poly_a	unknown	bulk	unknown	unknown	United States	2024-10-17	Undetermined	Embryo	Trunk	Surface Structure
34056	34056	SRR31034581	SRX26420030	SRS22939664	SRP539240	PRJNA1174234	Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A	GSE279773	Transcriptome Analysis	Prior to type 2 diabetes onset ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A we used the following animal and cell based models: transgenic zebrafish and inducible ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly following 4 weeks of high fat diet feeding and obesity mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells despite similar weight gain and insulin sensitivity. Taken together our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function inpart from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control dhps or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.		pubmed:39832654	dhps morpholino 3	GSM8579960	source name:whole body\|tissue:whole body\|treatment:dhps morpholino\|geo loc name:missing\|collection date:missing	dhps morpholino 3	Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value	whole body	zebrafish were treated with morpholino and RNA was extracted 24 hours later	RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.		tissue:whole body\|treatment:dhps morpholino	GSM8579960	GSM8579960: dhps morpholino 3; Danio rerio; RNA Seq	GSM8579960 r1	GSM8579960	1	RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP539240		DHPSMO3_1.fq.gz DHPSMO3_2.fq.gz	fastq fastq	6620802600.0	22069342.0	GSM8579960 r1	0:150 1:150	A:1736599369;C:1572800715;G:1587922794;T:1723479722;N:0	150	150	1736599369	1572800715	1587922794	1723479722	0	SRX26420030	SRS22939664	SRA1993170	Medicine, University of Chicago	Medicine, University of Chicago												B	B	biological fallback assumption	bgi	bgi	3prime	poly_a	unknown	bulk	unknown	unknown	United States	2024-10-17	Undetermined	Embryo	Trunk	Surface Structure
34057	34057	SRR31034582	SRX26420029	SRS22939659	SRP539240	PRJNA1174234	Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A	GSE279773	Transcriptome Analysis	Prior to type 2 diabetes onset ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A we used the following animal and cell based models: transgenic zebrafish and inducible ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly following 4 weeks of high fat diet feeding and obesity mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells despite similar weight gain and insulin sensitivity. Taken together our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function inpart from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control dhps or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.		pubmed:39832654	dhps morpholino 2	GSM8579959	source name:whole body\|tissue:whole body\|treatment:dhps morpholino\|geo loc name:missing\|collection date:missing	dhps morpholino 2	Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value	whole body	zebrafish were treated with morpholino and RNA was extracted 24 hours later	RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.		tissue:whole body\|treatment:dhps morpholino	GSM8579959	GSM8579959: dhps morpholino 2; Danio rerio; RNA Seq	GSM8579959 r1	GSM8579959	1	RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP539240		DHPSMO2_1.fq.gz DHPSMO2_2.fq.gz	fastq fastq	6582483600.0	21941612.0	GSM8579959 r1	0:150 1:150	A:1720509810;C:1570278366;G:1585433293;T:1706262131;N:0	150	150	1720509810	1570278366	1585433293	1706262131	0	SRX26420029	SRS22939659	SRA1993170	Medicine, University of Chicago	Medicine, University of Chicago												B	B	biological fallback assumption	bgi	bgi	3prime	poly_a	unknown	bulk	unknown	unknown	United States	2024-10-17	Undetermined	Embryo	Trunk	Surface Structure
34058	34058	SRR31034583	SRX26420028	SRS22939662	SRP539240	PRJNA1174234	Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A	GSE279773	Transcriptome Analysis	Prior to type 2 diabetes onset ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A we used the following animal and cell based models: transgenic zebrafish and inducible ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly following 4 weeks of high fat diet feeding and obesity mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells despite similar weight gain and insulin sensitivity. Taken together our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function inpart from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control dhps or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.		pubmed:39832654	dhps morpholino 1	GSM8579958	source name:whole body\|tissue:whole body\|treatment:dhps morpholino\|geo loc name:missing\|collection date:missing	dhps morpholino 1	Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value	whole body	zebrafish were treated with morpholino and RNA was extracted 24 hours later	RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.		tissue:whole body\|treatment:dhps morpholino	GSM8579958	GSM8579958: dhps morpholino 1; Danio rerio; RNA Seq	GSM8579958 r1	GSM8579958	1	RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP539240		DHPSMO1_1.fq.gz DHPSMO1_2.fq.gz	fastq fastq	6596391000.0	21987970.0	GSM8579958 r1	0:150 1:150	A:1725362753;C:1572510096;G:1586851982;T:1711666169;N:0	150	150	1725362753	1572510096	1586851982	1711666169	0	SRX26420028	SRS22939662	SRA1993170	Medicine, University of Chicago	Medicine, University of Chicago												B	B	biological fallback assumption	bgi	bgi	3prime	poly_a	unknown	bulk	unknown	unknown	United States	2024-10-17	Undetermined	Embryo	Trunk	Surface Structure
34059	34059	SRR31034584	SRX26420027	SRS22939661	SRP539240	PRJNA1174234	Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A	GSE279773	Transcriptome Analysis	Prior to type 2 diabetes onset ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A we used the following animal and cell based models: transgenic zebrafish and inducible ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly following 4 weeks of high fat diet feeding and obesity mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells despite similar weight gain and insulin sensitivity. Taken together our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function inpart from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control dhps or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.		pubmed:39832654	Control morpholino 3	GSM8579957	source name:whole body\|tissue:whole body\|treatment:Control morpholino\|geo loc name:missing\|collection date:missing	Control morpholino 3	Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value	whole body	zebrafish were treated with morpholino and RNA was extracted 24 hours later	RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.		tissue:whole body\|treatment:Control morpholino	GSM8579957	GSM8579957: Control morpholino 3; Danio rerio; RNA Seq	GSM8579957 r1	GSM8579957	1	RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP539240		CtrlMO3_1.fq.gz CtrlMO3_2.fq.gz	fastq fastq	6625089300.0	22083631.0	GSM8579957 r1	0:150 1:150	A:1728439807;C:1584339137;G:1602988513;T:1709321843;N:0	150	150	1728439807	1584339137	1602988513	1709321843	0	SRX26420027	SRS22939661	SRA1993170	Medicine, University of Chicago	Medicine, University of Chicago												B	B	biological fallback assumption	bgi	bgi	3prime	poly_a	unknown	bulk	unknown	unknown	United States	2024-10-17	Undetermined	Embryo	Trunk	Surface Structure
34060	34060	SRR31034585	SRX26420026	SRS22939658	SRP539240	PRJNA1174234	Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A	GSE279773	Transcriptome Analysis	Prior to type 2 diabetes onset ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A we used the following animal and cell based models: transgenic zebrafish and inducible ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly following 4 weeks of high fat diet feeding and obesity mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells despite similar weight gain and insulin sensitivity. Taken together our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function inpart from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control dhps or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.		pubmed:39832654	Control morpholino 2	GSM8579956	source name:whole body\|tissue:whole body\|treatment:Control morpholino\|geo loc name:missing\|collection date:missing	Control morpholino 2	Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value	whole body	zebrafish were treated with morpholino and RNA was extracted 24 hours later	RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.		tissue:whole body\|treatment:Control morpholino	GSM8579956	GSM8579956: Control morpholino 2; Danio rerio; RNA Seq	GSM8579956 r1	GSM8579956	1	RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP539240		CtrlMO2_1.fq.gz CtrlMO2_2.fq.gz	fastq fastq	6823000500.0	22743335.0	GSM8579956 r1	0:150 1:150	A:1777305843;C:1633379395;G:1649025317;T:1763289945;N:0	150	150	1777305843	1633379395	1649025317	1763289945	0	SRX26420026	SRS22939658	SRA1993170	Medicine, University of Chicago	Medicine, University of Chicago												B	B	biological fallback assumption	bgi	bgi	3prime	poly_a	unknown	bulk	unknown	unknown	United States	2024-10-17	Undetermined	Embryo	Trunk	Surface Structure
34061	34061	SRR31034586	SRX26420025	SRS22939660	SRP539240	PRJNA1174234	Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A	GSE279773	Transcriptome Analysis	Prior to type 2 diabetes onset ß cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that ß cell compensation requires the activity of deoxyhypusine synthase DHPS which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for ß cell compensation it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A we used the following animal and cell based models: transgenic zebrafish and inducible ß cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly following 4 weeks of high fat diet feeding and obesity mice lacking total eIF5A in ß cells had improved glucose tolerance compared to mice lacking DHPS in ß cells despite similar weight gain and insulin sensitivity. Taken together our data provide evidence that DHPS deficiency and obesity conditions impair ß cell function inpart from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which ß cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control dhps or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.		pubmed:39832654	Control morpholino 1	GSM8579955	source name:whole body\|tissue:whole body\|treatment:Control morpholino\|geo loc name:missing\|collection date:missing	Control morpholino 1	Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value	whole body	zebrafish were treated with morpholino and RNA was extracted 24 hours later	RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.		tissue:whole body\|treatment:Control morpholino	GSM8579955	GSM8579955: Control morpholino 1; Danio rerio; RNA Seq	GSM8579955 r1	GSM8579955	1	RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP539240		CtrlMO1_1.fq.gz CtrlMO1_2.fq.gz	fastq fastq	6625797900.0	22085993.0	GSM8579955 r1	0:150 1:150	A:1738695154;C:1575541452;G:1592240618;T:1719320676;N:0	150	150	1738695154	1575541452	1592240618	1719320676	0	SRX26420025	SRS22939660	SRA1993170	Medicine, University of Chicago	Medicine, University of Chicago												B	B	biological fallback assumption	bgi	bgi	3prime	poly_a	unknown	bulk	unknown	unknown	United States	2024-10-17	Undetermined	Embryo	Trunk	Surface Structure
64506	64506	SRR17299063	SRX13476323	SRS11373166	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 24hpf COL58	GSM5746868	source name:Zebrafish 24hpf sample1\|strain:AB\|age:24 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 24hpf COL58	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 24hpf sample1		Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:24 hours\|tissue:whole organism	GSM5746868	GSM5746868: Microwell seq datasets of Zebrafish 24hpf COL58; Danio rerio; RNA Seq	GSM5746868		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_24hpf_COL58.bam	bam	91823975304.0	527723996.0	GSM5746868 r1	0:24 1:150	A:27162173122;C:19911517883;G:21018214314;T:23663599459;N:68470526	24	150	27162173122	19911517883	21018214314	23663599459	68470526	SRX13476323	SRS11373166	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00273	0.74807	0.00242	0.067	0.99949	0.84889	0.32	0.62031	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-21	Pharyngula	Embryo	Whole Organism	All anatomical structures
64507	64507	SRR17299062	SRX13476322	SRS11373165	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 24hpf COL57	GSM5746867	source name:Zebrafish 24hpf sample1\|strain:AB\|age:24 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 24hpf COL57	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 24hpf sample1		Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:24 hours\|tissue:whole organism	GSM5746867	GSM5746867: Microwell seq datasets of Zebrafish 24hpf COL57; Danio rerio; RNA Seq	GSM5746867		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_24hpf_COL57.bam	bam	83668974276.0	480856174.0	GSM5746867 r1	0:24 1:150	A:24589284117;C:18203396283;G:19071978317;T:21739883658;N:64431901	24	150	24589284117	18203396283	19071978317	21739883658	64431901	SRX13476322	SRS11373165	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00288	0.75168	0.00269	0.07335	0.99969	0.84419	0.6	0.6312	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-21	Pharyngula	Embryo	Whole Organism	All anatomical structures
64508	64508	SRR17299061	SRX13476321	SRS11373164	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 24hpf COL56	GSM5746866	source name:Zebrafish 24hpf sample1\|strain:AB\|age:24 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 24hpf COL56	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 24hpf sample1		Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:24 hours\|tissue:whole organism	GSM5746866	GSM5746866: Microwell seq datasets of Zebrafish 24hpf COL56; Danio rerio; RNA Seq	GSM5746866		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_24hpf_COL56.bam	bam	86257073418.0	495730307.0	GSM5746866 r1	0:24 1:150	A:25447223471;C:18668491192;G:19647110520;T:22426583347;N:67664888	24	150	25447223471	18668491192	19647110520	22426583347	67664888	SRX13476321	SRS11373164	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00275	0.73434	0.00255	0.07548	0.99967	0.84325	0.4375	0.5398	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-21	Pharyngula	Embryo	Whole Organism	All anatomical structures
64509	64509	SRR17299060	SRX13476320	SRS11373163	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 24hpf COL55	GSM5746865	source name:Zebrafish 24hpf sample1\|strain:AB\|age:24 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 24hpf COL55	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 24hpf sample1		Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:24 hours\|tissue:whole organism	GSM5746865	GSM5746865: Microwell seq datasets of Zebrafish 24hpf COL55; Danio rerio; RNA Seq	GSM5746865		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_24hpf_COL55.bam	bam	90331122120.0	519144380.0	GSM5746865 r1	0:24 1:150	A:26895594483;C:19418243460;G:20453276913;T:23498626121;N:65381143	24	150	26895594483	19418243460	20453276913	23498626121	65381143	SRX13476320	SRS11373163	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00295	0.73613	0.00277	0.07262	0.99971	0.83926	0.66666	0.56101	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-21	Pharyngula	Embryo	Whole Organism	All anatomical structures
64510	64510	SRR17299059	SRX13476319	SRS11373162	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 24hpf COL53	GSM5746864	source name:Zebrafish 24hpf sample1\|strain:AB\|age:24 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 24hpf COL53	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 24hpf sample1		Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:24 hours\|tissue:whole organism	GSM5746864	GSM5746864: Microwell seq datasets of Zebrafish 24hpf COL53; Danio rerio; RNA Seq	GSM5746864		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_24hpf_COL53.bam	bam	89040837126.0	511728949.0	GSM5746864 r1	0:24 1:150	A:26403646377;C:19129690981;G:20273444200;T:23171059435;N:62996133	24	150	26403646377	19129690981	20273444200	23171059435	62996133	SRX13476319	SRS11373162	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00256	0.73401	0.00242	0.07541	0.99977	0.83731	0.36363	0.56119	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-21	Pharyngula	Embryo	Whole Organism	All anatomical structures
64511	64511	SRR17299058	SRX13476318	SRS11373161	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 24hpf COL52	GSM5746863	source name:Zebrafish 24hpf sample1\|strain:AB\|age:24 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 24hpf COL52	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 24hpf sample1		Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:24 hours\|tissue:whole organism	GSM5746863	GSM5746863: Microwell seq datasets of Zebrafish 24hpf COL52; Danio rerio; RNA Seq	GSM5746863		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_24hpf_COL52.bam	bam	92071528062.0	529146713.0	GSM5746863 r1	0:24 1:150	A:27250499787;C:19863195558;G:21006813218;T:23884436340;N:66583159	24	150	27250499787	19863195558	21006813218	23884436340	66583159	SRX13476318	SRS11373161	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00303	0.73044	0.00285	0.07319	0.99969	0.84118	0.6	0.55998	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-21	Pharyngula	Embryo	Whole Organism	All anatomical structures
64512	64512	SRR17299057	SRX13476317	SRS11373160	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 24hpf COL51	GSM5746862	source name:Zebrafish 24hpf sample1\|strain:AB\|age:24 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 24hpf COL51	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 24hpf sample1		Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:24 hours\|tissue:whole organism	GSM5746862	GSM5746862: Microwell seq datasets of Zebrafish 24hpf COL51; Danio rerio; RNA Seq	GSM5746862		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_24hpf_COL51.bam	bam	89393336592.0	513754808.0	GSM5746862 r1	0:24 1:150	A:26357157407;C:19229237017;G:20353675917;T:23391840285;N:61425966	24	150	26357157407	19229237017	20353675917	23391840285	61425966	SRX13476317	SRS11373160	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00318	0.74297	0.003	0.07874	0.99969	0.83481	0.6	0.58428	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-21	Pharyngula	Embryo	Whole Organism	All anatomical structures
64513	64513	SRR17299056	SRX13476316	SRS11373159	SRP324000	PRJNA737474	Construction the larval and adult zebrafish cell atlas at single cell resolution	GSE178150	Transcriptome Analysis	Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.	parent bioproject:PRJNA737471	pubmed:36229673	Microwell seq datasets of Zebrafish 24hpf COL50	GSM5746861	source name:Zebrafish 24hpf sample1\|strain:AB\|age:24 hours\|tissue:whole organism	Microwell seq datasets of Zebrafish 24hpf COL50	Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.	Zebrafish 24hpf sample1		Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol		strain:AB\|age:24 hours\|tissue:whole organism	GSM5746861	GSM5746861: Microwell seq datasets of Zebrafish 24hpf COL50; Danio rerio; RNA Seq	GSM5746861		1	Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP324000	assembly:GRCz11\|intentional duplicate	Zebrafish_24hpf_COL50.bam	bam	93180912216.0	535522484.0	GSM5746861 r1	0:24 1:150	A:27511179288;C:19943495783;G:21163186103;T:24482014463;N:81036579	24	150	27511179288	19943495783	21163186103	24482014463	81036579	SRX13476316	SRS11373159	SRA1244752	GEO	Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine	2	0.00287	0.73081	0.00269	0.08165	0.99969	0.83469	0.53333	0.56313	24	150	T	B	sc-like readlen	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2021-12-21	Pharyngula	Embryo	Whole Organism	All anatomical structures
68685	68685	SRR18173220	SRX14320215	SRS12136321	SRP361858	PRJNA811237	Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish	GSE197627	Transcriptome Analysis	Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as "5G". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.		pubmed:35434172	Control 48hpf Replicate 4	GSM5924083	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|developmental stage:48 hpf\|treatment:Control	Control 48hpf Replicate 4	SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.	Zebrafish embryonic total RNA	Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.	Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.		tissue:whole embryos\|developmental stage:48 hpf\|treatment:Control	GSM5924083	GSM5924083: Control 48hpf Replicate 4; Danio rerio; RNA Seq	GSM5924083 r1	GSM5924083	1	Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP361858		Control_48hpf_4_2.fq.gz Control_48hpf_4_1.fq.gz	fastq fastq	4893304000.0	48933040.0	GSM5924083 r1	0:100 1:100	A:1295107147;C:1131453899;G:1158231463;T:1307269653;N:1241838	100	100	1295107147	1131453899	1158231463	1307269653	1241838	SRX14320215	SRS12136321	SRA1379040	Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University	Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University	1	0.94011		0.0801		0.6927		0.48073		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-02-28	Hatching	Embryo	Whole Organism	All anatomical structures
68686	68686	SRR18173221	SRX14320214	SRS12136320	SRP361858	PRJNA811237	Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish	GSE197627	Transcriptome Analysis	Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as "5G". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.		pubmed:35434172	Control 48hpf Replicate 3	GSM5924082	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|developmental stage:48 hpf\|treatment:Control	Control 48hpf Replicate 3	SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.	Zebrafish embryonic total RNA	Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.	Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.		tissue:whole embryos\|developmental stage:48 hpf\|treatment:Control	GSM5924082	GSM5924082: Control 48hpf Replicate 3; Danio rerio; RNA Seq	GSM5924082 r1	GSM5924082	1	Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP361858		Control_48hpf_3_1.fq.gz Control_48hpf_3_2.fq.gz	fastq fastq	4673710400.0	46737104.0	GSM5924082 r1	0:100 1:100	A:1239135128;C:1079263067;G:1106439223;T:1248694558;N:178424	100	100	1239135128	1079263067	1106439223	1248694558	178424	SRX14320214	SRS12136320	SRA1379040	Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University	Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University	1	0.9388		0.09027		0.6896		0.47121		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-02-28	Hatching	Embryo	Whole Organism	All anatomical structures
68687	68687	SRR18173222	SRX14320213	SRS12136319	SRP361858	PRJNA811237	Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish	GSE197627	Transcriptome Analysis	Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as "5G". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.		pubmed:35434172	Control 48hpf Replicate 2	GSM5924081	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|developmental stage:48 hpf\|treatment:Control	Control 48hpf Replicate 2	SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.	Zebrafish embryonic total RNA	Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.	Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.		tissue:whole embryos\|developmental stage:48 hpf\|treatment:Control	GSM5924081	GSM5924081: Control 48hpf Replicate 2; Danio rerio; RNA Seq	GSM5924081 r1	GSM5924081	1	Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP361858		Control_48hpf_2_2.fq.gz Control_48hpf_2_1.fq.gz	fastq fastq	4669056600.0	46690566.0	GSM5924081 r1	0:100 1:100	A:1230949768;C:1083419632;G:1111527320;T:1243051944;N:107936	100	100	1230949768	1083419632	1111527320	1243051944	107936	SRX14320213	SRS12136319	SRA1379040	Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University	Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University	1	0.94517		0.08072		0.70084		0.47423		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-02-28	Hatching	Embryo	Whole Organism	All anatomical structures
68688	68688	SRR18173223	SRX14320212	SRS12136318	SRP361858	PRJNA811237	Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish	GSE197627	Transcriptome Analysis	Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as "5G". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.		pubmed:35434172	Control 48hpf Replicate 1	GSM5924080	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|developmental stage:48 hpf\|treatment:Control	Control 48hpf Replicate 1	SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.	Zebrafish embryonic total RNA	Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.	Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.		tissue:whole embryos\|developmental stage:48 hpf\|treatment:Control	GSM5924080	GSM5924080: Control 48hpf Replicate 1; Danio rerio; RNA Seq	GSM5924080 r1	GSM5924080	1	Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP361858		Control_48hpf_1_2.fq.gz Control_48hpf_1_1.fq.gz	fastq fastq	4710239800.0	47102398.0	GSM5924080 r1	0:100 1:100	A:1244163615;C:1092143032;G:1118126753;T:1255696249;N:110151	100	100	1244163615	1092143032	1118126753	1255696249	110151	SRX14320212	SRS12136318	SRA1379040	Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University	Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University	1	0.94203		0.08895		0.69335		0.46922		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-02-28	Hatching	Embryo	Whole Organism	All anatomical structures
68693	68693	SRR18173228	SRX14320207	SRS12136313	SRP361858	PRJNA811237	Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish	GSE197627	Transcriptome Analysis	Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as "5G". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.		pubmed:35434172	5G 48hpf Replicate 4	GSM5924075	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|developmental stage:48 hpf\|treatment:5G	5G 48hpf Replicate 4	SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.	Zebrafish embryonic total RNA	Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.	Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.		tissue:whole embryos\|developmental stage:48 hpf\|treatment:5G	GSM5924075	GSM5924075: 5G 48hpf Replicate 4; Danio rerio; RNA Seq	GSM5924075 r1	GSM5924075	1	Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP361858		5G_48hpf_4_2.fq.gz 5G_48hpf_4_1.fq.gz	fastq fastq	3960397600.0	39603976.0	GSM5924075 r1	0:100 1:100	A:1055375851;C:908722788;G:931610403;T:1063707959;N:980599	100	100	1055375851	908722788	931610403	1063707959	980599	SRX14320207	SRS12136313	SRA1379040	Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University	Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University	1	0.93498		0.09353		0.6884		0.48205		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-02-28	Hatching	Embryo	Whole Organism	All anatomical structures
68694	68694	SRR18173229	SRX14320206	SRS12136312	SRP361858	PRJNA811237	Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish	GSE197627	Transcriptome Analysis	Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as "5G". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.		pubmed:35434172	5G 48hpf Replicate 3	GSM5924074	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|developmental stage:48 hpf\|treatment:5G	5G 48hpf Replicate 3	SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.	Zebrafish embryonic total RNA	Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.	Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.		tissue:whole embryos\|developmental stage:48 hpf\|treatment:5G	GSM5924074	GSM5924074: 5G 48hpf Replicate 3; Danio rerio; RNA Seq	GSM5924074 r1	GSM5924074	1	Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP361858		5G_48hpf_3_1.fq.gz 5G_48hpf_3_2.fq.gz	fastq fastq	4666094000.0	46660940.0	GSM5924074 r1	0:100 1:100	A:1237561088;C:1075964364;G:1103985038;T:1248326386;N:257124	100	100	1237561088	1075964364	1103985038	1248326386	257124	SRX14320206	SRS12136312	SRA1379040	Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University	Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University	1	0.93689		0.09226		0.68655		0.46431		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-02-28	Hatching	Embryo	Whole Organism	All anatomical structures
68695	68695	SRR18173230	SRX14320205	SRS12136311	SRP361858	PRJNA811237	Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish	GSE197627	Transcriptome Analysis	Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as "5G". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.		pubmed:35434172	5G 48hpf Replicate 2	GSM5924073	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|developmental stage:48 hpf\|treatment:5G	5G 48hpf Replicate 2	SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.	Zebrafish embryonic total RNA	Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.	Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.		tissue:whole embryos\|developmental stage:48 hpf\|treatment:5G	GSM5924073	GSM5924073: 5G 48hpf Replicate 2; Danio rerio; RNA Seq	GSM5924073 r1	GSM5924073	1	Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP361858		5G_48hpf_2_1.fq.gz 5G_48hpf_2_2.fq.gz	fastq fastq	4687152000.0	46871520.0	GSM5924073 r1	0:100 1:100	A:1241838266;C:1082317123;G:1110355516;T:1252466907;N:174188	100	100	1241838266	1082317123	1110355516	1252466907	174188	SRX14320205	SRS12136311	SRA1379040	Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University	Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University	1	0.94454		0.08717		0.69122		0.47277		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-02-28	Hatching	Embryo	Whole Organism	All anatomical structures
68696	68696	SRR18173231	SRX14320204	SRS12136310	SRP361858	PRJNA811237	Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish	GSE197627	Transcriptome Analysis	Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as "5G". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.		pubmed:35434172	5G 48hpf Replicate 1	GSM5924072	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|developmental stage:48 hpf\|treatment:5G	5G 48hpf Replicate 1	SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.	Zebrafish embryonic total RNA	Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.	Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.		tissue:whole embryos\|developmental stage:48 hpf\|treatment:5G	GSM5924072	GSM5924072: 5G 48hpf Replicate 1; Danio rerio; RNA Seq	GSM5924072 r1	GSM5924072	1	Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP361858		5G_48hpf_1_1.fq.gz 5G_48hpf_1_2.fq.gz	fastq fastq	4703041000.0	47030410.0	GSM5924072 r1	0:100 1:100	A:1245130239;C:1085229448;G:1115856477;T:1256653090;N:171746	100	100	1245130239	1085229448	1115856477	1256653090	171746	SRX14320204	SRS12136310	SRA1379040	Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University	Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University	1	0.94571		0.0868		0.69798		0.47971		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-02-28	Hatching	Embryo	Whole Organism	All anatomical structures
72716	72716	SRR23093173	SRX19045602	SRS16462359	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	BigD 1 Replicate 4	GSM6936129	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	BigD 1 Replicate 4	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936129	GSM6936129: BigD 1 Replicate 4; Danio rerio; RNA Seq	GSM6936129 r1	GSM6936129	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		BigD-1-4_1.fq BigD-1-4_2.fq	fastq fastq	4755323200.0	47553232.0	GSM6936129 r1	0:100 1:100	A:1259475778;C:1103209979;G:1118288213;T:1274349230;N:0	100	100	1259475778	1103209979	1118288213	1274349230	0	SRX19045602	SRS16462359	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.94182		0.08223		0.69518		0.47067		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72717	72717	SRR23093174	SRX19045601	SRS16462358	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	BigD 1 Replicate 3	GSM6936128	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	BigD 1 Replicate 3	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936128	GSM6936128: BigD 1 Replicate 3; Danio rerio; RNA Seq	GSM6936128 r1	GSM6936128	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		BigD-1-3_2.fq BigD-1-3_1.fq	fastq fastq	4738473800.0	47384738.0	GSM6936128 r1	0:100 1:100	A:1230991342;C:1119773250;G:1142489795;T:1245219413;N:0	100	100	1230991342	1119773250	1142489795	1245219413	0	SRX19045601	SRS16462358	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.94511		0.07248		0.69749		0.47843		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72718	72718	SRR23093175	SRX19045600	SRS16462357	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	BigD 1 Replicate 2	GSM6936127	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	BigD 1 Replicate 2	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936127	GSM6936127: BigD 1 Replicate 2; Danio rerio; RNA Seq	GSM6936127 r1	GSM6936127	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		BigD-1-2_1.fq BigD-1-2_2.fq	fastq fastq	4745335600.0	47453356.0	GSM6936127 r1	0:100 1:100	A:1257788396;C:1100683810;G:1115523773;T:1271339621;N:0	100	100	1257788396	1100683810	1115523773	1271339621	0	SRX19045600	SRS16462357	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.94135		0.08664		0.69865		0.47343		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72719	72719	SRR23093176	SRX19045599	SRS16462356	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	BigD 1 Replicate 1	GSM6936126	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	BigD 1 Replicate 1	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936126	GSM6936126: BigD 1 Replicate 1; Danio rerio; RNA Seq	GSM6936126 r1	GSM6936126	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		BigD-1-1_2.fq BigD-1-1_1.fq	fastq fastq	4775819400.0	47758194.0	GSM6936126 r1	0:100 1:100	A:1262118404;C:1112939383;G:1129357162;T:1271404451;N:0	100	100	1262118404	1112939383	1129357162	1271404451	0	SRX19045599	SRS16462356	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.94154		0.09296		0.70084		0.47896		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72720	72720	SRR23093177	SRX19045598	SRS16462355	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	BigD 0 Replicate 4	GSM6936125	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	BigD 0 Replicate 4	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936125	GSM6936125: BigD 0 Replicate 4; Danio rerio; RNA Seq	GSM6936125 r1	GSM6936125	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		BigD-0-4_1.fq BigD-0-4_2.fq	fastq fastq	4738837400.0	47388374.0	GSM6936125 r1	0:100 1:100	A:1244831242;C:1110059895;G:1126083779;T:1257862484;N:0	100	100	1244831242	1110059895	1126083779	1257862484	0	SRX19045598	SRS16462355	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.94552		0.07745		0.69848		0.46383		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72721	72721	SRR23093178	SRX19045597	SRS16462354	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	BigD 0 Replicate 3	GSM6936124	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	BigD 0 Replicate 3	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936124	GSM6936124: BigD 0 Replicate 3; Danio rerio; RNA Seq	GSM6936124 r1	GSM6936124	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		BigD-0-3_1.fq BigD-0-3_2.fq	fastq fastq	4736351200.0	47363512.0	GSM6936124 r1	0:100 1:100	A:1240173237;C:1113150532;G:1131294144;T:1251733287;N:0	100	100	1240173237	1113150532	1131294144	1251733287	0	SRX19045597	SRS16462354	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.94653		0.0793		0.69201		0.46073		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72722	72722	SRR23093179	SRX19045596	SRS16462353	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	BigD 0 Replicate 2	GSM6936123	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	BigD 0 Replicate 2	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936123	GSM6936123: BigD 0 Replicate 2; Danio rerio; RNA Seq	GSM6936123 r1	GSM6936123	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		BigD-0-2_1.fq BigD-0-2_2.fq	fastq fastq	4775453400.0	47754534.0	GSM6936123 r1	0:100 1:100	A:1248380099;C:1123077801;G:1142524298;T:1261471202;N:0	100	100	1248380099	1123077801	1142524298	1261471202	0	SRX19045596	SRS16462353	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.94724		0.0772		0.69723		0.47889		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72723	72723	SRR23093180	SRX19045595	SRS16462352	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	BigD 0 Replicate 1	GSM6936122	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	BigD 0 Replicate 1	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936122	GSM6936122: BigD 0 Replicate 1; Danio rerio; RNA Seq	GSM6936122 r1	GSM6936122	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		BigD-0-1_1.fq BigD-0-1_2.fq	fastq fastq	4761071200.0	47610712.0	GSM6936122 r1	0:100 1:100	A:1270360983;C:1096308629;G:1109191368;T:1285210220;N:0	100	100	1270360983	1096308629	1109191368	1285210220	0	SRX19045595	SRS16462352	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.93762		0.10251		0.69083		0.4721		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72724	72724	SRR23093181	SRX19045594	SRS16462351	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	slincRosu3 1 Replicate 4	GSM6936121	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	slincRosu3 1 Replicate 4	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936121	GSM6936121: slincRosu3 1 Replicate 4; Danio rerio; RNA Seq	GSM6936121 r1	GSM6936121	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		sg6-1-4_1.fq sg6-1-4_2.fq	fastq fastq	4622482200.0	46224822.0	GSM6936121 r1	0:100 1:100	A:1245531002;C:1052822845;G:1064854322;T:1259274031;N:0	100	100	1245531002	1052822845	1064854322	1259274031	0	SRX19045594	SRS16462351	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.9312		0.11025		0.69739		0.481		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72725	72725	SRR23093182	SRX19045593	SRS16462350	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	slincRosu3 1 Replicate 3	GSM6936120	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	slincRosu3 1 Replicate 3	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936120	GSM6936120: slincRosu3 1 Replicate 3; Danio rerio; RNA Seq	GSM6936120 r1	GSM6936120	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		sg6-1-3_1.fq sg6-1-3_2.fq	fastq fastq	4604489600.0	46044896.0	GSM6936120 r1	0:100 1:100	A:1244947733;C:1043962852;G:1059753219;T:1255825796;N:0	100	100	1244947733	1043962852	1059753219	1255825796	0	SRX19045593	SRS16462350	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.92963		0.11585		0.69343		0.47368		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72726	72726	SRR23093183	SRX19045592	SRS16462349	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	slincRosu3 1 Replicate 2	GSM6936119	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	slincRosu3 1 Replicate 2	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936119	GSM6936119: slincRosu3 1 Replicate 2; Danio rerio; RNA Seq	GSM6936119 r1	GSM6936119	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		sg6-1-2_2.fq sg6-1-2_1.fq	fastq fastq	4431322600.0	44313226.0	GSM6936119 r1	0:100 1:100	A:1184420890;C:1018559466;G:1031360825;T:1196981419;N:0	100	100	1184420890	1018559466	1031360825	1196981419	0	SRX19045592	SRS16462349	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.93843		0.0986		0.69599		0.47758		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72727	72727	SRR23093184	SRX19045591	SRS16462348	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	slincRosu3 1 Replicate 1	GSM6936118	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	slincRosu3 1 Replicate 1	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936118	GSM6936118: slincRosu3 1 Replicate 1; Danio rerio; RNA Seq	GSM6936118 r1	GSM6936118	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		sg6-1-1_1.fq sg6-1-1_2.fq	fastq fastq	4396745400.0	43967454.0	GSM6936118 r1	0:100 1:100	A:1185074260;C:1001121172;G:1012401845;T:1198148123;N:0	100	100	1185074260	1001121172	1012401845	1198148123	0	SRX19045591	SRS16462348	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.93137		0.11121		0.69958		0.4756		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72728	72728	SRR23093185	SRX19045590	SRS16462347	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	slincRosu3 0 Replicate 4	GSM6936117	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	slincRosu3 0 Replicate 4	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936117	GSM6936117: slincRosu3 0 Replicate 4; Danio rerio; RNA Seq	GSM6936117 r1	GSM6936117	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		sg6-0-4_2.fq sg6-0-4_1.fq	fastq fastq	4648351000.0	46483510.0	GSM6936117 r1	0:100 1:100	A:1244006259;C:1067002816;G:1081782122;T:1255559803;N:0	100	100	1244006259	1067002816	1081782122	1255559803	0	SRX19045590	SRS16462347	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.93516		0.1013		0.70755		0.46381		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72729	72729	SRR23093186	SRX19045589	SRS16462346	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	slincRosu3 0 Replicate 3	GSM6936116	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	slincRosu3 0 Replicate 3	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936116	GSM6936116: slincRosu3 0 Replicate 3; Danio rerio; RNA Seq	GSM6936116 r1	GSM6936116	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		sg6-0-3_1.fq sg6-0-3_2.fq	fastq fastq	4621468200.0	46214682.0	GSM6936116 r1	0:100 1:100	A:1244328076;C:1053787175;G:1066438665;T:1256914284;N:0	100	100	1244328076	1053787175	1066438665	1256914284	0	SRX19045589	SRS16462346	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.93103		0.11076		0.69404		0.46175		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72730	72730	SRR23093187	SRX19045588	SRS16462345	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	slincRosu3 0 Replicate 2	GSM6936115	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	slincRosu3 0 Replicate 2	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936115	GSM6936115: slincRosu3 0 Replicate 2; Danio rerio; RNA Seq	GSM6936115 r1	GSM6936115	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		sg6-0-2_1.fq sg6-0-2_2.fq	fastq fastq	4637287600.0	46372876.0	GSM6936115 r1	0:100 1:100	A:1256523385;C:1049501445;G:1056556807;T:1274705963;N:0	100	100	1256523385	1049501445	1056556807	1274705963	0	SRX19045588	SRS16462345	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.92954		0.11594		0.69061		0.47895		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72731	72731	SRR23093188	SRX19045587	SRS16462344	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	slincRosu3 0 Replicate 1	GSM6936114	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	slincRosu3 0 Replicate 1	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936114	GSM6936114: slincRosu3 0 Replicate 1; Danio rerio; RNA Seq	GSM6936114 r1	GSM6936114	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		sg6-0-1_1.fq sg6-0-1_2.fq	fastq fastq	4602449600.0	46024496.0	GSM6936114 r1	0:100 1:100	A:1245544635;C:1042672437;G:1053397049;T:1260835479;N:0	100	100	1245544635	1042672437	1053397049	1260835479	0	SRX19045587	SRS16462344	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.92775		0.1179		0.6939		0.48034		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72732	72732	SRR23093189	SRX19045586	SRS16462343	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	WT 1 Replicate 4	GSM6936113	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	WT 1 Replicate 4	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936113	GSM6936113: WT 1 Replicate 4; Danio rerio; RNA Seq	GSM6936113 r1	GSM6936113	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		WT-1-4_1.fq WT-1-4_2.fq	fastq fastq	4757111000.0	47571110.0	GSM6936113 r1	0:100 1:100	A:1236859359;C:1126640135;G:1145893787;T:1247717719;N:0	100	100	1236859359	1126640135	1145893787	1247717719	0	SRX19045586	SRS16462343	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.95154		0.07197		0.70372		0.47356		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72733	72733	SRR23093190	SRX19045585	SRS16462342	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	WT 1 Replicate 3	GSM6936112	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	WT 1 Replicate 3	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936112	GSM6936112: WT 1 Replicate 3; Danio rerio; RNA Seq	GSM6936112 r1	GSM6936112	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		WT-1-3_1.fq WT-1-3_2.fq	fastq fastq	4793944800.0	47939448.0	GSM6936112 r1	0:100 1:100	A:1279690931;C:1098309519;G:1124616455;T:1291327895;N:0	100	100	1279690931	1098309519	1124616455	1291327895	0	SRX19045585	SRS16462342	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.94589		0.08413		0.7024		0.4773		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72734	72734	SRR23093191	SRX19045584	SRS16462341	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	WT 1 Replicate 2	GSM6936111	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	WT 1 Replicate 2	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936111	GSM6936111: WT 1 Replicate 2; Danio rerio; RNA Seq	GSM6936111 r1	GSM6936111	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		WT-1-2_1.fq WT-1-2_2.fq	fastq fastq	4615392200.0	46153922.0	GSM6936111 r1	0:100 1:100	A:1244196156;C:1050648528;G:1063942383;T:1256605133;N:0	100	100	1244196156	1050648528	1063942383	1256605133	0	SRX19045584	SRS16462341	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.93175		0.11429		0.68874		0.47472		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72735	72735	SRR23093192	SRX19045583	SRS16462340	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	WT 1 Replicate 1	GSM6936110	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	WT 1 Replicate 1	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936110	GSM6936110: WT 1 Replicate 1; Danio rerio; RNA Seq	GSM6936110 r1	GSM6936110	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		WT-1-1_1.fq WT-1-1_2.fq	fastq fastq	4612084800.0	46120848.0	GSM6936110 r1	0:100 1:100	A:1250315815;C:1042931084;G:1056483329;T:1262354572;N:0	100	100	1250315815	1042931084	1056483329	1262354572	0	SRX19045583	SRS16462340	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.93006		0.12132		0.69404		0.47744		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72736	72736	SRR23093193	SRX19045582	SRS16462339	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	WT 0 Replicate 4	GSM6936109	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	WT 0 Replicate 4	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936109	GSM6936109: WT 0 Replicate 4; Danio rerio; RNA Seq	GSM6936109 r1	GSM6936109	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		WT-0-4_1.fq WT-0-4_2.fq	fastq fastq	4627056800.0	46270568.0	GSM6936109 r1	0:100 1:100	A:1234346617;C:1067059379;G:1082149220;T:1243501584;N:0	100	100	1234346617	1067059379	1082149220	1243501584	0	SRX19045582	SRS16462339	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.93595		0.10611		0.71078		0.4733		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72737	72737	SRR23093194	SRX19045581	SRS16462338	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	WT 0 Replicate 3	GSM6936108	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	WT 0 Replicate 3	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936108	GSM6936108: WT 0 Replicate 3; Danio rerio; RNA Seq	GSM6936108 r1	GSM6936108	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		WT-0-3_1.fq WT-0-3_2.fq	fastq fastq	4599938000.0	45999380.0	GSM6936108 r1	0:100 1:100	A:1231676201;C:1055994444;G:1070031969;T:1242235386;N:0	100	100	1231676201	1055994444	1070031969	1242235386	0	SRX19045581	SRS16462338	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.93416		0.10542		0.69254		0.47784		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72738	72738	SRR23093195	SRX19045580	SRS16462337	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	WT 0 Replicate 2	GSM6936107	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	WT 0 Replicate 2	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936107	GSM6936107: WT 0 Replicate 2; Danio rerio; RNA Seq	GSM6936107 r1	GSM6936107	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		WT-0-2_1.fq WT-0-2_2.fq	fastq fastq	4629711000.0	46297110.0	GSM6936107 r1	0:100 1:100	A:1229906979;C:1072378508;G:1087363270;T:1240062243;N:0	100	100	1229906979	1072378508	1087363270	1240062243	0	SRX19045580	SRS16462337	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.93801		0.0965		0.69341		0.4638		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
72739	72739	SRR23093196	SRX19045579	SRS16462336	SRP417750	PRJNA924320	'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration	GSE222975	Transcriptome Analysis	transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE		pubmed:37220911	WT 0 Replicate 1	GSM6936106	source name:Zebrafish embryonic total RNA\|tissue:whole embryos\|geo loc name:missing\|collection date:missing	WT 0 Replicate 1	SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples.	Zebrafish embryonic total RNA		none provided		tissue:whole embryos	GSM6936106	GSM6936106: WT 0 Replicate 1; Danio rerio; RNA Seq	GSM6936106 r1	GSM6936106	1	none provided	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G50	SRP417750		WT-0-1_1.fq WT-0-1_2.fq	fastq fastq	4610038400.0	46100384.0	GSM6936106 r1	0:100 1:100	A:1230210147;C:1062445460;G:1076466688;T:1240916105;N:0	100	100	1230210147	1062445460	1076466688	1240916105	0	SRX19045579	SRS16462336	SRA1575131	SARL, Environmental Molecular Toxicology, Oregon State University	SARL, Environmental Molecular Toxicology, Oregon State University	1	0.93649		0.09807		0.70082		0.47723		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2023-01-16	Undetermined	Embryo	Whole Organism	All anatomical structures
74329	74329	SRR23635030	SRX19518333	SRS16905710	SRP425040	PRJNA939370	The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq]	GSE226182	Transcriptome Analysis	Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine “reader” Sall4 to specifically bind the bmp4 promoter thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Total RNAs were purified using TRIzol reagent Life Technologies 343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform.	parent bioproject:PRJNA939357	pubmed:38427557	KO replicate 2 bulk RNAseq	GSM7067524	source name:embryo\|tissue:embryo\|age:48 hpf\|genotype:tet2/3 double knock out\|geo loc name:missing\|collection date:missing	KO replicate 2 bulk RNAseq	Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression for each Sample	embryo		RNA was extracted by TRNzol method and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.		tissue:embryo\|age:48 hpf\|genotype:tet2/3 double knock out	GSM7067524	GSM7067524: KO replicate 2 bulk RNAseq; Danio rerio; RNA Seq	GSM7067524 r1	GSM7067524	1	RNA was extracted by TRNzol method and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	DNBSEQ	DNBSEQ-G400	SRP425040		KO2.fastq.gz	fastq	4188284200.0	41882842.0	GSM7067524 r1	0:100	A:1066992737;C:1011357361;G:1055554148;T:1041284278;N:13095676	100		1066992737	1011357361	1055554148	1041284278	13095676	SRX19518333	SRS16905710	SRA1597336	Yunnan University	Yunnan University	1	0.88647		0.07541		0.7237		0.47069		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures
74330	74330	SRR23635031	SRX19518332	SRS16905709	SRP425040	PRJNA939370	The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq]	GSE226182	Transcriptome Analysis	Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine “reader” Sall4 to specifically bind the bmp4 promoter thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Total RNAs were purified using TRIzol reagent Life Technologies 343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform.	parent bioproject:PRJNA939357	pubmed:38427557	KO replicate 1 bulk RNAseq	GSM7067523	source name:embryo\|tissue:embryo\|age:48 hpf\|genotype:tet2/3 double knock out\|geo loc name:missing\|collection date:missing	KO replicate 1 bulk RNAseq	Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression for each Sample	embryo		RNA was extracted by TRNzol method and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.		tissue:embryo\|age:48 hpf\|genotype:tet2/3 double knock out	GSM7067523	GSM7067523: KO replicate 1 bulk RNAseq; Danio rerio; RNA Seq	GSM7067523 r1	GSM7067523	1	RNA was extracted by TRNzol method and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	DNBSEQ	DNBSEQ-G400	SRP425040		KO1.fastq.gz	fastq	4181083400.0	41810834.0	GSM7067523 r1	0:100	A:1077414361;C:996554293;G:1053357384;T:1040649776;N:13107586	100		1077414361	996554293	1053357384	1040649776	13107586	SRX19518332	SRS16905709	SRA1597336	Yunnan University	Yunnan University	1	0.87685		0.07522		0.72699		0.48859		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures
74331	74331	SRR23635032	SRX19518331	SRS16905708	SRP425040	PRJNA939370	The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq]	GSE226182	Transcriptome Analysis	Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine “reader” Sall4 to specifically bind the bmp4 promoter thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Total RNAs were purified using TRIzol reagent Life Technologies 343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform.	parent bioproject:PRJNA939357	pubmed:38427557	WT replicate 2 bulk RNAseq	GSM7067522	source name:embryo\|tissue:embryo\|age:48 hpf\|genotype:wild type\|geo loc name:missing\|collection date:missing	WT replicate 2 bulk RNAseq	Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression for each Sample	embryo		RNA was extracted by TRNzol method and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.		tissue:embryo\|age:48 hpf\|genotype:wild type	GSM7067522	GSM7067522: WT replicate 2 bulk RNAseq; Danio rerio; RNA Seq	GSM7067522 r1	GSM7067522	1	RNA was extracted by TRNzol method and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	DNBSEQ	DNBSEQ-G400	SRP425040		WT2.fastq.gz	fastq	1435167700.0	14351677.0	GSM7067522 r1	0:100	A:371412640;C:334204906;G:351277070;T:371684263;N:6588821	100		371412640	334204906	351277070	371684263	6588821	SRX19518331	SRS16905708	SRA1597336	Yunnan University	Yunnan University	1	0.83841		0.15087		0.71417		0.50982		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures
74332	74332	SRR23635033	SRX19518330	SRS16905707	SRP425040	PRJNA939370	The TET BMP regulatory axis in pathogenesis of CFM [RNA Seq]	GSE226182	Transcriptome Analysis	Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine “reader” Sall4 to specifically bind the bmp4 promoter thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Total RNAs were purified using TRIzol reagent Life Technologies 343702. Libraries were constructed using a VAHTS Universal V8 RNA seq Library Prep Kit for MGI Vazyme according to the manufacturer's instructions and then sequenced on the MGISEQ 2000 platform.	parent bioproject:PRJNA939357	pubmed:38427557	WT replicate 1 bulk RNAseq	GSM7067521	source name:embryo\|tissue:embryo\|age:48 hpf\|genotype:wild type\|geo loc name:missing\|collection date:missing	WT replicate 1 bulk RNAseq	Sequence reads were mapped to GRCz11/danrer11 using STAR v2.7.10a Read count extraction were performed using RSEM v1.3.1 Reads normalization and differentially expressed gene calling were performed using DESeq2 v1.32.0 Assembly: danrer11 Supplementary files format and content: tab delimited text files include gene expression for each Sample	embryo		RNA was extracted by TRNzol method and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.		tissue:embryo\|age:48 hpf\|genotype:wild type	GSM7067521	GSM7067521: WT replicate 1 bulk RNAseq; Danio rerio; RNA Seq	GSM7067521 r1	GSM7067521	1	RNA was extracted by TRNzol method and 500ng of total RNA was used to construct sequencing library. RNA libraries for RNA Seq were prepared using the Vazyme RNA Seq library kit according to the manufacturer's protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	DNBSEQ	DNBSEQ-G400	SRP425040		WT1.fastq.gz	fastq	1961618800.0	19616188.0	GSM7067521 r1	0:100	A:518460045;C:447438337;G:477081234;T:509513188;N:9125996	100		518460045	447438337	477081234	509513188	9125996	SRX19518330	SRS16905707	SRA1597336	Yunnan University	Yunnan University	1	0.81315		0.14097		0.72342		0.50905		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures
74889	74889	SRR24100386	SRX19900535	SRS17254309	SRP431420	PRJNA953151	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during trunk development	GSE229162	Transcriptome Analysis	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during notochord and muscle development. Overall design: Gene expression analysis using RNA seq data from wild type zebrafish embryos and the tpcn2 mutant each with five biological replicates.		pubmed:38028019	Zebrafish embryos Strain: TPC2 mutant Stage: 17 18 somite Biol rep 5	GSM7156163	source name:Whole embryo\|tissue:Whole embryo\|genotype:TPC2 mutant\|developmental stage:17 18 somite stage\|geo loc name:missing\|collection date:missing	Zebrafish embryos Strain: TPC2 mutant Stage: 17 18 somite Biol rep 5	Performed adapter trimming with cutadapt v3.4 software with parameters: " minimum length=30 a A\{100\} A A\{100\} a CTGTCTCTTATACACATCT A CTGTCTCTTATACACATCT g AGATGTGTATAAGAGACAG G AGATGTGTATAAGAGACAG". Read alignment to mm10 using STAR v2.7 aligner with default settings and extra parameters " outSAMtype BAM SortedByCoordinate quantMode GeneCounts". Gene overlapping read counts and differentially expressed genes were calculated using DEseq2 v1.30.0. Assembly: danRer10 Genome Reference Consortium Zebrafish Build 10 Supplementary files format and content: all.tsv: Tab delimited text file includes raw counts. Supplementary files format and content: Treatment 1 vs Control.diffexp.tsv: Table of differential expression results for per gene calculated with DESeq2.	Whole embryo		RNA extraction was performed using RNAzol® according to the manufacturer’s instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	Embryos were collected from wild type ABTU and mutant TPC2 fish line and kept at 28 °C.	tissue:Whole embryo\|genotype:TPC2 mutant\|developmental stage:17 18 somite stage	GSM7156163	GSM7156163: Zebrafish embryos Strain: TPC2 mutant Stage: 17 18 somite Biol rep 5; Danio rerio; RNA Seq	GSM7156163 r1	GSM7156163	1	RNA extraction was performed using RNAzol® according to the manufacturer's instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP431420		V300083329_L01_10_1.fq.gz V300083329_L01_10_2.fq.gz	fastq fastq	5909038000.0	29545190.0	GSM7156163 r1	0:100 1:100	A:1623230733;C:1331545315;G:1343152861;T:1610987311;N:121780	100	100	1623230733	1331545315	1343152861	1610987311	121780	SRX19900535	SRS17254309	SRA1622257	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	2	0.91221	0.92929	0.10504	0.10961	0.72078	0.71875	0.49598	0.49947	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-04-06	Segmentation	Embryo	Whole Organism	All anatomical structures
74890	74890	SRR24100387	SRX19900534	SRS17254308	SRP431420	PRJNA953151	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during trunk development	GSE229162	Transcriptome Analysis	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during notochord and muscle development. Overall design: Gene expression analysis using RNA seq data from wild type zebrafish embryos and the tpcn2 mutant each with five biological replicates.		pubmed:38028019	Zebrafish embryos Strain: TPC2 mutant Stage: 17 18 somite Biol rep 4	GSM7156162	source name:Whole embryo\|tissue:Whole embryo\|genotype:TPC2 mutant\|developmental stage:17 18 somite stage\|geo loc name:missing\|collection date:missing	Zebrafish embryos Strain: TPC2 mutant Stage: 17 18 somite Biol rep 4	Performed adapter trimming with cutadapt v3.4 software with parameters: " minimum length=30 a A\{100\} A A\{100\} a CTGTCTCTTATACACATCT A CTGTCTCTTATACACATCT g AGATGTGTATAAGAGACAG G AGATGTGTATAAGAGACAG". Read alignment to mm10 using STAR v2.7 aligner with default settings and extra parameters " outSAMtype BAM SortedByCoordinate quantMode GeneCounts". Gene overlapping read counts and differentially expressed genes were calculated using DEseq2 v1.30.0. Assembly: danRer10 Genome Reference Consortium Zebrafish Build 10 Supplementary files format and content: all.tsv: Tab delimited text file includes raw counts. Supplementary files format and content: Treatment 1 vs Control.diffexp.tsv: Table of differential expression results for per gene calculated with DESeq2.	Whole embryo		RNA extraction was performed using RNAzol® according to the manufacturer’s instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	Embryos were collected from wild type ABTU and mutant TPC2 fish line and kept at 28 °C.	tissue:Whole embryo\|genotype:TPC2 mutant\|developmental stage:17 18 somite stage	GSM7156162	GSM7156162: Zebrafish embryos Strain: TPC2 mutant Stage: 17 18 somite Biol rep 4; Danio rerio; RNA Seq	GSM7156162 r1	GSM7156162	1	RNA extraction was performed using RNAzol® according to the manufacturer's instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP431420		V300083329_L01_9_1.fq.gz V300083329_L01_9_2.fq.gz	fastq fastq	7158980600.0	35794903.0	GSM7156162 r1	0:100 1:100	A:1968354520;C:1609788228;G:1624681203;T:1956008153;N:148496	100	100	1968354520	1609788228	1624681203	1956008153	148496	SRX19900534	SRS17254308	SRA1622257	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	2	0.91862	0.93327	0.10568	0.10926	0.72011	0.7178	0.49831	0.49497	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-04-06	Segmentation	Embryo	Whole Organism	All anatomical structures
74891	74891	SRR24100388	SRX19900533	SRS17254307	SRP431420	PRJNA953151	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during trunk development	GSE229162	Transcriptome Analysis	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during notochord and muscle development. Overall design: Gene expression analysis using RNA seq data from wild type zebrafish embryos and the tpcn2 mutant each with five biological replicates.		pubmed:38028019	Zebrafish embryos Strain: TPC2 mutant Stage: 17 18 somite Biol rep 3	GSM7156161	source name:Whole embryo\|tissue:Whole embryo\|genotype:TPC2 mutant\|developmental stage:17 18 somite stage\|geo loc name:missing\|collection date:missing	Zebrafish embryos Strain: TPC2 mutant Stage: 17 18 somite Biol rep 3	Performed adapter trimming with cutadapt v3.4 software with parameters: " minimum length=30 a A\{100\} A A\{100\} a CTGTCTCTTATACACATCT A CTGTCTCTTATACACATCT g AGATGTGTATAAGAGACAG G AGATGTGTATAAGAGACAG". Read alignment to mm10 using STAR v2.7 aligner with default settings and extra parameters " outSAMtype BAM SortedByCoordinate quantMode GeneCounts". Gene overlapping read counts and differentially expressed genes were calculated using DEseq2 v1.30.0. Assembly: danRer10 Genome Reference Consortium Zebrafish Build 10 Supplementary files format and content: all.tsv: Tab delimited text file includes raw counts. Supplementary files format and content: Treatment 1 vs Control.diffexp.tsv: Table of differential expression results for per gene calculated with DESeq2.	Whole embryo		RNA extraction was performed using RNAzol® according to the manufacturer’s instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	Embryos were collected from wild type ABTU and mutant TPC2 fish line and kept at 28 °C.	tissue:Whole embryo\|genotype:TPC2 mutant\|developmental stage:17 18 somite stage	GSM7156161	GSM7156161: Zebrafish embryos Strain: TPC2 mutant Stage: 17 18 somite Biol rep 3; Danio rerio; RNA Seq	GSM7156161 r1	GSM7156161	1	RNA extraction was performed using RNAzol® according to the manufacturer's instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP431420		V300083329_L01_8_1.fq.gz V300083329_L01_8_2.fq.gz	fastq fastq	6531770800.0	32658854.0	GSM7156161 r1	0:100 1:100	A:1793771000;C:1470976560;G:1484688544;T:1782200344;N:134352	100	100	1793771000	1470976560	1484688544	1782200344	134352	SRX19900533	SRS17254307	SRA1622257	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	2	0.91557	0.93175	0.10273	0.107	0.71952	0.71804	0.50709	0.50851	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-04-06	Segmentation	Embryo	Whole Organism	All anatomical structures
74892	74892	SRR24100389	SRX19900532	SRS17254306	SRP431420	PRJNA953151	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during trunk development	GSE229162	Transcriptome Analysis	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during notochord and muscle development. Overall design: Gene expression analysis using RNA seq data from wild type zebrafish embryos and the tpcn2 mutant each with five biological replicates.		pubmed:38028019	Zebrafish embryos Strain: TPC2 mutant Stage: 17 18 somite Biol rep 2	GSM7156160	source name:Whole embryo\|tissue:Whole embryo\|genotype:TPC2 mutant\|developmental stage:17 18 somite stage\|geo loc name:missing\|collection date:missing	Zebrafish embryos Strain: TPC2 mutant Stage: 17 18 somite Biol rep 2	Performed adapter trimming with cutadapt v3.4 software with parameters: " minimum length=30 a A\{100\} A A\{100\} a CTGTCTCTTATACACATCT A CTGTCTCTTATACACATCT g AGATGTGTATAAGAGACAG G AGATGTGTATAAGAGACAG". Read alignment to mm10 using STAR v2.7 aligner with default settings and extra parameters " outSAMtype BAM SortedByCoordinate quantMode GeneCounts". Gene overlapping read counts and differentially expressed genes were calculated using DEseq2 v1.30.0. Assembly: danRer10 Genome Reference Consortium Zebrafish Build 10 Supplementary files format and content: all.tsv: Tab delimited text file includes raw counts. Supplementary files format and content: Treatment 1 vs Control.diffexp.tsv: Table of differential expression results for per gene calculated with DESeq2.	Whole embryo		RNA extraction was performed using RNAzol® according to the manufacturer’s instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	Embryos were collected from wild type ABTU and mutant TPC2 fish line and kept at 28 °C.	tissue:Whole embryo\|genotype:TPC2 mutant\|developmental stage:17 18 somite stage	GSM7156160	GSM7156160: Zebrafish embryos Strain: TPC2 mutant Stage: 17 18 somite Biol rep 2; Danio rerio; RNA Seq	GSM7156160 r1	GSM7156160	1	RNA extraction was performed using RNAzol® according to the manufacturer's instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP431420		V300083329_L01_7_2.fq.gz V300083329_L01_7_1.fq.gz	fastq fastq	6855987000.0	34279935.0	GSM7156160 r1	0:100 1:100	A:1877835332;C:1550053152;G:1562891634;T:1865065844;N:141038	100	100	1877835332	1550053152	1562891634	1865065844	141038	SRX19900532	SRS17254306	SRA1622257	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	2	0.91324	0.93178	0.10397	0.1088	0.71904	0.71747	0.49646	0.49643	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-04-06	Segmentation	Embryo	Whole Organism	All anatomical structures
74893	74893	SRR24100390	SRX19900531	SRS17254304	SRP431420	PRJNA953151	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during trunk development	GSE229162	Transcriptome Analysis	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during notochord and muscle development. Overall design: Gene expression analysis using RNA seq data from wild type zebrafish embryos and the tpcn2 mutant each with five biological replicates.		pubmed:38028019	Zebrafish embryos Strain: TPC2 mutant Stage: 17 18 somite Biol rep 1	GSM7156159	source name:Whole embryo\|tissue:Whole embryo\|genotype:TPC2 mutant\|developmental stage:17 18 somite stage\|geo loc name:missing\|collection date:missing	Zebrafish embryos Strain: TPC2 mutant Stage: 17 18 somite Biol rep 1	Performed adapter trimming with cutadapt v3.4 software with parameters: " minimum length=30 a A\{100\} A A\{100\} a CTGTCTCTTATACACATCT A CTGTCTCTTATACACATCT g AGATGTGTATAAGAGACAG G AGATGTGTATAAGAGACAG". Read alignment to mm10 using STAR v2.7 aligner with default settings and extra parameters " outSAMtype BAM SortedByCoordinate quantMode GeneCounts". Gene overlapping read counts and differentially expressed genes were calculated using DEseq2 v1.30.0. Assembly: danRer10 Genome Reference Consortium Zebrafish Build 10 Supplementary files format and content: all.tsv: Tab delimited text file includes raw counts. Supplementary files format and content: Treatment 1 vs Control.diffexp.tsv: Table of differential expression results for per gene calculated with DESeq2.	Whole embryo		RNA extraction was performed using RNAzol® according to the manufacturer’s instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	Embryos were collected from wild type ABTU and mutant TPC2 fish line and kept at 28 °C.	tissue:Whole embryo\|genotype:TPC2 mutant\|developmental stage:17 18 somite stage	GSM7156159	GSM7156159: Zebrafish embryos Strain: TPC2 mutant Stage: 17 18 somite Biol rep 1; Danio rerio; RNA Seq	GSM7156159 r1	GSM7156159	1	RNA extraction was performed using RNAzol® according to the manufacturer's instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP431420		V300083329_L01_6_2.fq.gz V300083329_L01_6_1.fq.gz	fastq fastq	5942422000.0	29712110.0	GSM7156159 r1	0:100 1:100	A:1632350094;C:1339164685;G:1349845574;T:1620939701;N:121946	100	100	1632350094	1339164685	1349845574	1620939701	121946	SRX19900531	SRS17254304	SRA1622257	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	2	0.9125	0.93046	0.09915	0.10311	0.72161	0.71839	0.50048	0.50346	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-04-06	Segmentation	Embryo	Whole Organism	All anatomical structures
74894	74894	SRR24100391	SRX19900530	SRS17254305	SRP431420	PRJNA953151	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during trunk development	GSE229162	Transcriptome Analysis	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during notochord and muscle development. Overall design: Gene expression analysis using RNA seq data from wild type zebrafish embryos and the tpcn2 mutant each with five biological replicates.		pubmed:38028019	Zebrafish embryos Strain: ABTU Stage: 17 18 somite Biol rep 5	GSM7156158	source name:Whole embryo\|tissue:Whole embryo\|strain:ABTU\|genotype:WT\|developmental stage:17 18 somite stage\|geo loc name:missing\|collection date:missing	Zebrafish embryos Strain: ABTU Stage: 17 18 somite Biol rep 5	Performed adapter trimming with cutadapt v3.4 software with parameters: " minimum length=30 a A\{100\} A A\{100\} a CTGTCTCTTATACACATCT A CTGTCTCTTATACACATCT g AGATGTGTATAAGAGACAG G AGATGTGTATAAGAGACAG". Read alignment to mm10 using STAR v2.7 aligner with default settings and extra parameters " outSAMtype BAM SortedByCoordinate quantMode GeneCounts". Gene overlapping read counts and differentially expressed genes were calculated using DEseq2 v1.30.0. Assembly: danRer10 Genome Reference Consortium Zebrafish Build 10 Supplementary files format and content: all.tsv: Tab delimited text file includes raw counts. Supplementary files format and content: Treatment 1 vs Control.diffexp.tsv: Table of differential expression results for per gene calculated with DESeq2.	Whole embryo		RNA extraction was performed using RNAzol® according to the manufacturer’s instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	Embryos were collected from wild type ABTU and mutant TPC2 fish line and kept at 28 °C.	tissue:Whole embryo\|strain:ABTU\|genotype:WT\|developmental stage:17 18 somite stage	GSM7156158	GSM7156158: Zebrafish embryos Strain: ABTU Stage: 17 18 somite Biol rep 5; Danio rerio; RNA Seq	GSM7156158 r1	GSM7156158	1	RNA extraction was performed using RNAzol® according to the manufacturer's instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP431420		V300083329_L01_5_1.fq.gz V300083329_L01_5_2.fq.gz	fastq fastq	7153463400.0	35767317.0	GSM7156158 r1	0:100 1:100	A:1958525430;C:1615815830;G:1630221563;T:1948754839;N:145738	100	100	1958525430	1615815830	1630221563	1948754839	145738	SRX19900530	SRS17254305	SRA1638521	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	2	0.90204	0.9263	0.09062	0.09528	0.72013	0.71632	0.49222	0.48822	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-04-06	Segmentation	Embryo	Whole Organism	All anatomical structures
74895	74895	SRR24100392	SRX19900529	SRS17254303	SRP431420	PRJNA953151	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during trunk development	GSE229162	Transcriptome Analysis	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during notochord and muscle development. Overall design: Gene expression analysis using RNA seq data from wild type zebrafish embryos and the tpcn2 mutant each with five biological replicates.		pubmed:38028019	Zebrafish embryos Strain: ABTU Stage: 17 18 somite Biol rep 4	GSM7156157	source name:Whole embryo\|tissue:Whole embryo\|strain:ABTU\|genotype:WT\|developmental stage:17 18 somite stage\|geo loc name:missing\|collection date:missing	Zebrafish embryos Strain: ABTU Stage: 17 18 somite Biol rep 4	Performed adapter trimming with cutadapt v3.4 software with parameters: " minimum length=30 a A\{100\} A A\{100\} a CTGTCTCTTATACACATCT A CTGTCTCTTATACACATCT g AGATGTGTATAAGAGACAG G AGATGTGTATAAGAGACAG". Read alignment to mm10 using STAR v2.7 aligner with default settings and extra parameters " outSAMtype BAM SortedByCoordinate quantMode GeneCounts". Gene overlapping read counts and differentially expressed genes were calculated using DEseq2 v1.30.0. Assembly: danRer10 Genome Reference Consortium Zebrafish Build 10 Supplementary files format and content: all.tsv: Tab delimited text file includes raw counts. Supplementary files format and content: Treatment 1 vs Control.diffexp.tsv: Table of differential expression results for per gene calculated with DESeq2.	Whole embryo		RNA extraction was performed using RNAzol® according to the manufacturer’s instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	Embryos were collected from wild type ABTU and mutant TPC2 fish line and kept at 28 °C.	tissue:Whole embryo\|strain:ABTU\|genotype:WT\|developmental stage:17 18 somite stage	GSM7156157	GSM7156157: Zebrafish embryos Strain: ABTU Stage: 17 18 somite Biol rep 4; Danio rerio; RNA Seq	GSM7156157 r1	GSM7156157	1	RNA extraction was performed using RNAzol® according to the manufacturer's instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP431420		V300083329_L01_4_1.fq.gz V300083329_L01_4_2.fq.gz	fastq fastq	6285611800.0	31428059.0	GSM7156157 r1	0:100 1:100	A:1719455856;C:1422165971;G:1433352881;T:1710508916;N:128176	100	100	1719455856	1422165971	1433352881	1710508916	128176	SRX19900529	SRS17254303	SRA1638521	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	2	0.9091	0.92922	0.10155	0.10643	0.71774	0.71514	0.42654	0.42739	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-04-06	Segmentation	Embryo	Whole Organism	All anatomical structures
74896	74896	SRR24100393	SRX19900528	SRS17254302	SRP431420	PRJNA953151	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during trunk development	GSE229162	Transcriptome Analysis	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during notochord and muscle development. Overall design: Gene expression analysis using RNA seq data from wild type zebrafish embryos and the tpcn2 mutant each with five biological replicates.		pubmed:38028019	Zebrafish embryos Strain: ABTU Stage: 17 18 somite Biol rep 3	GSM7156156	source name:Whole embryo\|tissue:Whole embryo\|strain:ABTU\|genotype:WT\|developmental stage:17 18 somite stage\|geo loc name:missing\|collection date:missing	Zebrafish embryos Strain: ABTU Stage: 17 18 somite Biol rep 3	Performed adapter trimming with cutadapt v3.4 software with parameters: " minimum length=30 a A\{100\} A A\{100\} a CTGTCTCTTATACACATCT A CTGTCTCTTATACACATCT g AGATGTGTATAAGAGACAG G AGATGTGTATAAGAGACAG". Read alignment to mm10 using STAR v2.7 aligner with default settings and extra parameters " outSAMtype BAM SortedByCoordinate quantMode GeneCounts". Gene overlapping read counts and differentially expressed genes were calculated using DEseq2 v1.30.0. Assembly: danRer10 Genome Reference Consortium Zebrafish Build 10 Supplementary files format and content: all.tsv: Tab delimited text file includes raw counts. Supplementary files format and content: Treatment 1 vs Control.diffexp.tsv: Table of differential expression results for per gene calculated with DESeq2.	Whole embryo		RNA extraction was performed using RNAzol® according to the manufacturer’s instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	Embryos were collected from wild type ABTU and mutant TPC2 fish line and kept at 28 °C.	tissue:Whole embryo\|strain:ABTU\|genotype:WT\|developmental stage:17 18 somite stage	GSM7156156	GSM7156156: Zebrafish embryos Strain: ABTU Stage: 17 18 somite Biol rep 3; Danio rerio; RNA Seq	GSM7156156 r1	GSM7156156	1	RNA extraction was performed using RNAzol® according to the manufacturer's instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP431420		V300083329_L01_3_1.fq.gz V300083329_L01_3_2.fq.gz	fastq fastq	6045199800.0	30225999.0	GSM7156156 r1	0:100 1:100	A:1655608468;C:1366259339;G:1377040188;T:1646167197;N:124608	100	100	1655608468	1366259339	1377040188	1646167197	124608	SRX19900528	SRS17254302	SRA1638521	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	2	0.91076	0.92838	0.09791	0.10219	0.71687	0.71575	0.50436	0.50374	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-04-06	Segmentation	Embryo	Whole Organism	All anatomical structures
74897	74897	SRR24100394	SRX19900527	SRS17254301	SRP431420	PRJNA953151	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during trunk development	GSE229162	Transcriptome Analysis	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during notochord and muscle development. Overall design: Gene expression analysis using RNA seq data from wild type zebrafish embryos and the tpcn2 mutant each with five biological replicates.		pubmed:38028019	Zebrafish embryos Strain: ABTU Stage: 17 18 somite Biol rep 2	GSM7156155	source name:Whole embryo\|tissue:Whole embryo\|strain:ABTU\|genotype:WT\|developmental stage:17 18 somite stage\|geo loc name:missing\|collection date:missing	Zebrafish embryos Strain: ABTU Stage: 17 18 somite Biol rep 2	Performed adapter trimming with cutadapt v3.4 software with parameters: " minimum length=30 a A\{100\} A A\{100\} a CTGTCTCTTATACACATCT A CTGTCTCTTATACACATCT g AGATGTGTATAAGAGACAG G AGATGTGTATAAGAGACAG". Read alignment to mm10 using STAR v2.7 aligner with default settings and extra parameters " outSAMtype BAM SortedByCoordinate quantMode GeneCounts". Gene overlapping read counts and differentially expressed genes were calculated using DEseq2 v1.30.0. Assembly: danRer10 Genome Reference Consortium Zebrafish Build 10 Supplementary files format and content: all.tsv: Tab delimited text file includes raw counts. Supplementary files format and content: Treatment 1 vs Control.diffexp.tsv: Table of differential expression results for per gene calculated with DESeq2.	Whole embryo		RNA extraction was performed using RNAzol® according to the manufacturer’s instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	Embryos were collected from wild type ABTU and mutant TPC2 fish line and kept at 28 °C.	tissue:Whole embryo\|strain:ABTU\|genotype:WT\|developmental stage:17 18 somite stage	GSM7156155	GSM7156155: Zebrafish embryos Strain: ABTU Stage: 17 18 somite Biol rep 2; Danio rerio; RNA Seq	GSM7156155 r1	GSM7156155	1	RNA extraction was performed using RNAzol® according to the manufacturer's instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP431420		V300083329_L01_2_1.fq.gz V300083329_L01_2_2.fq.gz	fastq fastq	6793710400.0	33968552.0	GSM7156155 r1	0:100 1:100	A:1865228268;C:1530543853;G:1542022266;T:1855776719;N:139294	100	100	1865228268	1530543853	1542022266	1855776719	139294	SRX19900527	SRS17254301	SRA1638521	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	2	0.8964	0.92159	0.09702	0.10256	0.72064	0.71741	0.50202	0.49335	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-04-06	Segmentation	Embryo	Whole Organism	All anatomical structures
74898	74898	SRR24100395	SRX19900526	SRS17254300	SRP431420	PRJNA953151	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during trunk development	GSE229162	Transcriptome Analysis	To investigate gene expression differences between wild type and tpcn2 mutant zebrafish embryos during notochord and muscle development. Overall design: Gene expression analysis using RNA seq data from wild type zebrafish embryos and the tpcn2 mutant each with five biological replicates.		pubmed:38028019	Zebrafish embryos Strain: ABTU Stage: 17 18 somite Biol rep 1	GSM7156154	source name:Whole embryo\|tissue:Whole embryo\|strain:ABTU\|genotype:WT\|developmental stage:17 18 somite stage\|geo loc name:missing\|collection date:missing	Zebrafish embryos Strain: ABTU Stage: 17 18 somite Biol rep 1	Performed adapter trimming with cutadapt v3.4 software with parameters: " minimum length=30 a A\{100\} A A\{100\} a CTGTCTCTTATACACATCT A CTGTCTCTTATACACATCT g AGATGTGTATAAGAGACAG G AGATGTGTATAAGAGACAG". Read alignment to mm10 using STAR v2.7 aligner with default settings and extra parameters " outSAMtype BAM SortedByCoordinate quantMode GeneCounts". Gene overlapping read counts and differentially expressed genes were calculated using DEseq2 v1.30.0. Assembly: danRer10 Genome Reference Consortium Zebrafish Build 10 Supplementary files format and content: all.tsv: Tab delimited text file includes raw counts. Supplementary files format and content: Treatment 1 vs Control.diffexp.tsv: Table of differential expression results for per gene calculated with DESeq2.	Whole embryo		RNA extraction was performed using RNAzol® according to the manufacturer’s instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	Embryos were collected from wild type ABTU and mutant TPC2 fish line and kept at 28 °C.	tissue:Whole embryo\|strain:ABTU\|genotype:WT\|developmental stage:17 18 somite stage	GSM7156154	GSM7156154: Zebrafish embryos Strain: ABTU Stage: 17 18 somite Biol rep 1; Danio rerio; RNA Seq	GSM7156154 r1	GSM7156154	1	RNA extraction was performed using RNAzol® according to the manufacturer's instructions. Samples were submitted to the Bioscience Central Research Facility for library construction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP431420		V300083329_L01_1_1.fq.gz V300083329_L01_1_2.fq.gz	fastq fastq	5850237800.0	29251189.0	GSM7156154 r1	0:100 1:100	A:1604069499;C:1319153587;G:1332426220;T:1594469616;N:118878	100	100	1604069499	1319153587	1332426220	1594469616	118878	SRX19900526	SRS17254300	SRA1638521	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	Calcium Aequorin Imaging Lab, Division of Life Science, The Hong Kong University of Science and Technology	2	0.91271	0.93165	0.09001	0.09367	0.71997	0.71756	0.43066	0.49623	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2023-04-06	Segmentation	Embryo	Whole Organism	All anatomical structures
76526	76526	SRR25007131	SRX20762489	SRS18050783	SRP445520	PRJNA986875	Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish	GSE235668	Transcriptome Analysis	Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target.		pubmed:38542412	T3 1	GSM7507240	source name:Embryos\|tissue:Embryos\|genotype:WT\|developmental stage:36hpf\|geo loc name:missing\|collection date:missing	T3 1	The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	Embryos		Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:Embryos\|genotype:WT\|developmental stage:36hpf	GSM7507240	GSM7507240: T3 1; Danio rerio; RNA Seq	GSM7507240 r1	GSM7507240	1	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP445520		T3_1.R1.fq.gz T3_1.R2.fq.gz	fastq fastq	15316392300.0	51054641.0	GSM7507240 r1	0:150 1:150	A:3880671888;C:3784758050;G:3856071137;T:3794810224;N:81001	150	150	3880671888	3784758050	3856071137	3794810224	81001	SRX20762489	SRS18050783	SRA1661372	henan normal university	henan normal university	2	0.41572	0.57842	0.09076	0.13329	0.79385	0.76142	0.43528	0.43567	150	150	B	B	mate1-mate2 similar by mapping diff	bgi	bgi	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	China	2023-06-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
76527	76527	SRR25007132	SRX20762488	SRS18050782	SRP445520	PRJNA986875	Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish	GSE235668	Transcriptome Analysis	Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target.		pubmed:38542412	T1 1	GSM7507236	source name:Embryos\|tissue:Embryos\|genotype:WT\|developmental stage:10hpf\|geo loc name:missing\|collection date:missing	T1 1	The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	Embryos		Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:Embryos\|genotype:WT\|developmental stage:10hpf	GSM7507236	GSM7507236: T1 1; Danio rerio; RNA Seq	GSM7507236 r1	GSM7507236	1	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP445520		T1_1.R1.fq.gz T1_1.R2.fq.gz	fastq fastq	13484033700.0	44946779.0	GSM7507236 r1	0:150 1:150	A:3415746428;C:3329088326;G:3392039530;T:3347088129;N:71287	150	150	3415746428	3329088326	3392039530	3347088129	71287	SRX20762488	SRS18050782	SRA1661372	henan normal university	henan normal university	2	0.40423	0.57514	0.07655	0.11873	0.80308	0.77092	0.46754	0.46803	150	150	B	B	mate1-mate2 similar by mapping diff	bgi	bgi	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	China	2023-06-23	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
76528	76528	SRR25007133	SRX20762487	SRS18050781	SRP445520	PRJNA986875	Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish	GSE235668	Transcriptome Analysis	Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target.		pubmed:38542412	T1 2	GSM7507237	source name:Embryos\|tissue:Embryos\|genotype:WT\|developmental stage:10hpf\|geo loc name:missing\|collection date:missing	T1 2	The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	Embryos		Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:Embryos\|genotype:WT\|developmental stage:10hpf	GSM7507237	GSM7507237: T1 2; Danio rerio; RNA Seq	GSM7507237 r1	GSM7507237	1	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP445520		T1_2.R1.fq.gz T1_2.R2.fq.gz	fastq fastq	13733190600.0	45777302.0	GSM7507237 r1	0:150 1:150	A:3445382955;C:3412918499;G:3490188153;T:3384626806;N:74187	150	150	3445382955	3412918499	3490188153	3384626806	74187	SRX20762487	SRS18050781	SRA1661372	henan normal university	henan normal university	2	0.43011	0.59623	0.08158	0.13068	0.80288	0.77544	0.47026	0.47364	150	150	B	B	mate1-mate2 similar by mapping diff	bgi	bgi	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	China	2023-06-23	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
76529	76529	SRR25007134	SRX20762486	SRS18050778	SRP445520	PRJNA986875	Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish	GSE235668	Transcriptome Analysis	Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target.		pubmed:38542412	T2 1	GSM7507238	source name:Embryos\|tissue:Embryos\|genotype:WT\|developmental stage:24hpf\|geo loc name:missing\|collection date:missing	T2 1	The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	Embryos		Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:Embryos\|genotype:WT\|developmental stage:24hpf	GSM7507238	GSM7507238: T2 1; Danio rerio; RNA Seq	GSM7507238 r1	GSM7507238	1	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP445520		T2_1.R2.fq.gz T2_1.R1.fq.gz	fastq fastq	14649880200.0	48832934.0	GSM7507238 r1	0:150 1:150	A:3695224943;C:3636149584;G:3688479871;T:3629948859;N:76943	150	150	3695224943	3636149584	3688479871	3629948859	76943	SRX20762486	SRS18050778	SRA1661372	henan normal university	henan normal university	2	0.43452	0.60496	0.08789	0.13132	0.7862	0.7528	0.44881	0.45341	150	150	B	B	mate1-mate2 similar by mapping diff	bgi	bgi	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	China	2023-06-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
76530	76530	SRR25007135	SRX20762485	SRS18050780	SRP445520	PRJNA986875	Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish	GSE235668	Transcriptome Analysis	Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target.		pubmed:38542412	T2 2	GSM7507239	source name:Embryos\|tissue:Embryos\|genotype:WT\|developmental stage:24hpf\|geo loc name:missing\|collection date:missing	T2 2	The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	Embryos		Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:Embryos\|genotype:WT\|developmental stage:24hpf	GSM7507239	GSM7507239: T2 2; Danio rerio; RNA Seq	GSM7507239 r1	GSM7507239	1	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP445520		T2_2.R1.fq.gz T2_2.R2.fq.gz	fastq fastq	14696199900.0	48987333.0	GSM7507239 r1	0:150 1:150	A:3735683721;C:3615176348;G:3714335362;T:3630926317;N:78152	150	150	3735683721	3615176348	3714335362	3630926317	78152	SRX20762485	SRS18050780	SRA1661372	henan normal university	henan normal university	2	0.42139	0.57658	0.08829	0.1292	0.78831	0.75617	0.44949	0.45776	150	150	B	B	mate1-mate2 similar by mapping diff	bgi	bgi	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	China	2023-06-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
76531	76531	SRR25007136	SRX20762484	SRS18050779	SRP445520	PRJNA986875	Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish	GSE235668	Transcriptome Analysis	Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target.		pubmed:38542412	T3 2	GSM7507241	source name:Embryos\|tissue:Embryos\|genotype:WT\|developmental stage:36hpf\|geo loc name:missing\|collection date:missing	T3 2	The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	Embryos		Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.		tissue:Embryos\|genotype:WT\|developmental stage:36hpf	GSM7507241	GSM7507241: T3 2; Danio rerio; RNA Seq	GSM7507241 r1	GSM7507241	1	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP445520		T3_2.R2.fq.gz T3_2.R1.fq.gz	fastq fastq	15346908000.0	51156360.0	GSM7507241 r1	0:150 1:150	A:3937027213;C:3752697817;G:3796118846;T:3860983131;N:80993	150	150	3937027213	3752697817	3796118846	3860983131	80993	SRX20762484	SRS18050779	SRA1661372	henan normal university	henan normal university	2	0.4823	0.64213	0.10848	0.15245	0.77966	0.74752	0.43616	0.43697	150	150	B	B	biological fallback assumption	bgi	bgi	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	China	2023-06-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
76532	76532	SRR25081951	SRX20835391	SRS18112575	SRP446710	PRJNA987386	Single nucleus chromatin landscapes during zebrafish early embryogenesis	PRJNA987386	Other	Vertebrate embryogenesis is a remarkable process during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis regulatory elements CREs and gene expression within the hierarchy of cell fate decisions. Here we employed single nucleus ATAC seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis including 3.3 hpf 5.25 hpf 6 hpf 10 hpf 12 hpf 18 hpf and 24 hpf obtained 51 620 high quality nuclei and 23 clusters. Furthermore by integrating snATAC seq data with single cell RNA seq data we described the dynamics of chromatin accessibility and gene expression across developmental time points which validates the accuracy of the chromatin landscape data. Together our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis.			6 hpf embryos	scRNA zf6hpf 2	strain:AB/Wild type\|isolate:scRNA zf6hpf 2\|breed:not collected\|cultivar:not collected\|ecotype:not determined\|age:embryo\|dev stage:6 hpf\|collection date:2021 08 08\|geo loc name:China: Wuhan\|sex:not determined\|tissue:embryo\|BioSampleModel:Model organism or animal									scRNA 6 hpf	scRNA 6 hpf rep2 oligo	scRNA 6 hpf rep2 oligo	scRNA seq of 6 hpf embryos		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP446710	CNGB Experiment ID:CNX0591993	DP8450003515BR_L01_5_1.fq.gz DP8450003515BR_L01_5_2.fq.gz	fastq fastq	14588474300.0	291769486.0	DP8450003515BR L01 5 1.fq.gz	0:20 1:30	A:3813233297;C:3660627848;G:3388591530;T:3724524333;N:1497292	20	30	3813233297	3660627848	3388591530	3724524333	1497292	SRX20835391	SRS18112575	SRA1664681	BGI Research, Shenzhen	BGI Research, Shenzhen CNGB Nucleotide Sequence Archive (CNSA) BGI-Shenzhen	2	0.00464	0.0003	0.00396	0.00028	0.9978	0.99995	0.39694	0.5	20	30	T	T	mates < 9% mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-06-30	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
76533	76533	SRR25081952	SRX20835390	SRS18112575	SRP446710	PRJNA987386	Single nucleus chromatin landscapes during zebrafish early embryogenesis	PRJNA987386	Other	Vertebrate embryogenesis is a remarkable process during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis regulatory elements CREs and gene expression within the hierarchy of cell fate decisions. Here we employed single nucleus ATAC seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis including 3.3 hpf 5.25 hpf 6 hpf 10 hpf 12 hpf 18 hpf and 24 hpf obtained 51 620 high quality nuclei and 23 clusters. Furthermore by integrating snATAC seq data with single cell RNA seq data we described the dynamics of chromatin accessibility and gene expression across developmental time points which validates the accuracy of the chromatin landscape data. Together our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis.			6 hpf embryos	scRNA zf6hpf 2	strain:AB/Wild type\|isolate:scRNA zf6hpf 2\|breed:not collected\|cultivar:not collected\|ecotype:not determined\|age:embryo\|dev stage:6 hpf\|collection date:2021 08 08\|geo loc name:China: Wuhan\|sex:not determined\|tissue:embryo\|BioSampleModel:Model organism or animal									scRNA 6 hpf	scRNA 6 hpf rep2 cDNA	scRNA 6 hpf rep2 cDNA	scRNA seq of 6 hpf embryos		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP446710	CNGB Experiment ID:CNX0591991	E100036348_L01_5_1.fq.gz E100036348_L01_5_2.fq.gz	fastq fastq	55097250780.0	423825006.0	E100036348 L01 5 1.fq.gz	0:30 1:100	A:16194629059;C:11467532715;G:12387290556;T:15046756280;N:1042170	30	100	16194629059	11467532715	12387290556	15046756280	1042170	SRX20835390	SRS18112575	SRA1664681	BGI Research, Shenzhen	BGI Research, Shenzhen CNGB Nucleotide Sequence Archive (CNSA) BGI-Shenzhen	2	0.00035	0.58961	0.00033	0.06118	0.99993	0.82564	0.33333	0.62483	30	100	T	B	mate1 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-06-30	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
76534	76534	SRR25081953	SRX20835389	SRS18112574	SRP446710	PRJNA987386	Single nucleus chromatin landscapes during zebrafish early embryogenesis	PRJNA987386	Other	Vertebrate embryogenesis is a remarkable process during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis regulatory elements CREs and gene expression within the hierarchy of cell fate decisions. Here we employed single nucleus ATAC seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis including 3.3 hpf 5.25 hpf 6 hpf 10 hpf 12 hpf 18 hpf and 24 hpf obtained 51 620 high quality nuclei and 23 clusters. Furthermore by integrating snATAC seq data with single cell RNA seq data we described the dynamics of chromatin accessibility and gene expression across developmental time points which validates the accuracy of the chromatin landscape data. Together our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis.			6 hpf embryos	scRNA zf6hpf 1	strain:AB/Wild type\|isolate:scRNA zf6hpf 1\|breed:not collected\|cultivar:not collected\|ecotype:not determined\|age:embryo\|dev stage:6 hpf\|collection date:2021 08 08\|geo loc name:China: Wuhan\|sex:not determined\|tissue:embryo\|BioSampleModel:Model organism or animal									scRNA 6 hpf	scRNA 6 hpf rep1 oligo	scRNA 6 hpf rep1 oligo	scRNA seq of 6 hpf embryos		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP446710	CNGB Experiment ID:CNX0591992	DP8450003515BR_L01_4_2.fq.gz DP8450003515BR_L01_4_1.fq.gz	fastq fastq	11338346750.0	226766935.0	DP8450003515BR L01 4 1.fq.gz	0:20 1:30	A:2978703558;C:2824119061;G:2623216087;T:2911128054;N:1179990	20	30	2978703558	2824119061	2623216087	2911128054	1179990	SRX20835389	SRS18112574	SRA1664681	BGI Research, Shenzhen	BGI Research, Shenzhen CNGB Nucleotide Sequence Archive (CNSA) BGI-Shenzhen	2	0.00475	0.00048	0.0041	0.00042	0.99799	0.99979	0.472	0.4	20	30	T	T	mates < 9% mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-06-30	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
76535	76535	SRR25081954	SRX20835388	SRS18112574	SRP446710	PRJNA987386	Single nucleus chromatin landscapes during zebrafish early embryogenesis	PRJNA987386	Other	Vertebrate embryogenesis is a remarkable process during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis regulatory elements CREs and gene expression within the hierarchy of cell fate decisions. Here we employed single nucleus ATAC seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis including 3.3 hpf 5.25 hpf 6 hpf 10 hpf 12 hpf 18 hpf and 24 hpf obtained 51 620 high quality nuclei and 23 clusters. Furthermore by integrating snATAC seq data with single cell RNA seq data we described the dynamics of chromatin accessibility and gene expression across developmental time points which validates the accuracy of the chromatin landscape data. Together our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis.			6 hpf embryos	scRNA zf6hpf 1	strain:AB/Wild type\|isolate:scRNA zf6hpf 1\|breed:not collected\|cultivar:not collected\|ecotype:not determined\|age:embryo\|dev stage:6 hpf\|collection date:2021 08 08\|geo loc name:China: Wuhan\|sex:not determined\|tissue:embryo\|BioSampleModel:Model organism or animal									scRNA 6 hpf	scRNA 6 hpf rep1 cDNA	scRNA 6 hpf rep1 cDNA	scRNA seq of 6 hpf embryos		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP446710	CNGB Experiment ID:CNX0591990	E100036348_L01_6_1.fq.gz E100036348_L01_6_2.fq.gz	fastq fastq	28127062860.0	216362022.0	E100036348 L01 6 1.fq.gz	0:30 1:100	A:8147068380;C:5889045118;G:6317467122;T:7772966880;N:515360	30	100	8147068380	5889045118	6317467122	7772966880	515360	SRX20835388	SRS18112574	SRA1664681	BGI Research, Shenzhen	BGI Research, Shenzhen CNGB Nucleotide Sequence Archive (CNSA) BGI-Shenzhen	2	0.00014	0.82035	0.00012	0.07422	0.99995	0.81412	1.0	0.68234	30	100	T	B	mate1 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-06-30	Gastrula	Embryo	Embryo Imprecise	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");;