metadata: run_metadata: 61 rows where devstage_curation_coarse = "Multi-stage" and experiment.library

61 rows where devstage_curation_coarse = "Multi-stage" and experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL"

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.r3_length	run.r4_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
29175	29175	SRR27292304	SRX22969963	SRS19936063	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…		pubmed:38922186	Burned Larval Zebrafish 48 hours post burn	GSM7982886	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn\|geo loc name:missing\|collection date:missing	Burned Larval Zebrafish 48 hours post burn	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn	GSM7982886	GSM7982886: Burned Larval Zebrafish 48 hours post burn; Danio rerio; RNA Seq	GSM7982886 r1	GSM7982886	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	Burn-48hpb_S5_L001_R2_001.fastq.gz Burn-48hpb_S5_L001_R1_001.fastq.gz	fastq fastq	20874980529.0	178418637.0	GSM7982886 r1	0:28 1:89	A:5945091269;C:4392590896;G:4497688824;T:6035946283;N:3663257	28	89			5945091269	4392590896	4497688824	6035946283	3663257	SRX22969963	SRS19936063	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.00573	0.91666	0.00222	0.19474	0.9931	0.79306	0.42082	0.53801	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29176	29176	SRR27292305	SRX22969963	SRS19936063	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…		pubmed:38922186	Burned Larval Zebrafish 48 hours post burn	GSM7982886	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn\|geo loc name:missing\|collection date:missing	Burned Larval Zebrafish 48 hours post burn	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn	GSM7982886	GSM7982886: Burned Larval Zebrafish 48 hours post burn; Danio rerio; RNA Seq	GSM7982886 r1	GSM7982886	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	Burn-48hpb_S5_L002_R1_001.fastq.gz Burn-48hpb_S5_L002_R2_001.fastq.gz	fastq fastq	20022973425.0	171136525.0	GSM7982886 r2	0:28 1:89	A:5709681181;C:4208386174;G:4307510275;T:5796282368;N:1113427	28	89			5709681181	4208386174	4307510275	5796282368	1113427	SRX22969963	SRS19936063	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.00547	0.9154	0.00202	0.1955	0.99283	0.79423	0.39307	0.53427	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29177	29177	SRR27292306	SRX22969962	SRS19936064	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…		pubmed:38922186	Burned Larval Zebrafish 24 hours post burn	GSM7982885	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn\|geo loc name:missing\|collection date:missing	Burned Larval Zebrafish 24 hours post burn	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn	GSM7982885	GSM7982885: Burned Larval Zebrafish 24 hours post burn; Danio rerio; RNA Seq	GSM7982885 r1	GSM7982885	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	Burn-24hpb_S2_L001_R1_001.fastq.gz Burn-24hpb_S2_L001_R2_001.fastq.gz	fastq fastq	9782870058.0	83614274.0	GSM7982885 r1	0:28 1:89	A:2744737668;C:2140848416;G:2249400157;T:2645170677;N:2713140	28	89			2744737668	2140848416	2249400157	2645170677	2713140	SRX22969962	SRS19936064	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.00752	0.92059	0.00244	0.16143	0.98944	0.82929	0.44176	0.54525	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29178	29178	SRR27292307	SRX22969962	SRS19936064	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…		pubmed:38922186	Burned Larval Zebrafish 24 hours post burn	GSM7982885	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn\|geo loc name:missing\|collection date:missing	Burned Larval Zebrafish 24 hours post burn	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn	GSM7982885	GSM7982885: Burned Larval Zebrafish 24 hours post burn; Danio rerio; RNA Seq	GSM7982885 r1	GSM7982885	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	Burn-24hpb_S2_L002_R2_001.fastq.gz Burn-24hpb_S2_L002_R1_001.fastq.gz	fastq fastq	9861989202.0	84290506.0	GSM7982885 r2	0:28 1:89	A:2769268861;C:2158644227;G:2263475493;T:2669311436;N:1289185	28	89			2769268861	2158644227	2263475493	2669311436	1289185	SRX22969962	SRS19936064	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.0076	0.9197	0.00232	0.16162	0.98995	0.82852	0.43786	0.55256	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29179	29179	SRR27292308	SRX22969961	SRS19936062	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…		pubmed:38922186	Burned Larval Zebrafish 6 hours post burn	GSM7982884	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn\|geo loc name:missing\|collection date:missing	Burned Larval Zebrafish 6 hours post burn	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn	GSM7982884	GSM7982884: Burned Larval Zebrafish 6 hours post burn; Danio rerio; RNA Seq	GSM7982884 r1	GSM7982884	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	Burn-6hpb_S7_L001_R1_001.fastq.gz Burn-6hpb_S7_L001_R2_001.fastq.gz	fastq fastq	12475938384.0	106631952.0	GSM7982884 r1	0:28 1:89	A:3401989108;C:2878275107;G:3114945415;T:3078525361;N:2203393	28	89			3401989108	2878275107	3114945415	3078525361	2203393	SRX22969961	SRS19936062	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.01053	0.89396	0.00429	0.18315	0.99458	0.85756	0.34876	0.58728	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29180	29180	SRR27292309	SRX22969961	SRS19936062	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…		pubmed:38922186	Burned Larval Zebrafish 6 hours post burn	GSM7982884	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn\|geo loc name:missing\|collection date:missing	Burned Larval Zebrafish 6 hours post burn	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn	GSM7982884	GSM7982884: Burned Larval Zebrafish 6 hours post burn; Danio rerio; RNA Seq	GSM7982884 r1	GSM7982884	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	Burn-6hpb_S7_L002_R1_001.fastq.gz Burn-6hpb_S7_L002_R2_001.fastq.gz	fastq fastq	11874083247.0	101487891.0	GSM7982884 r2	0:28 1:89	A:3243501055;C:2735412615;G:2958387721;T:2936117380;N:664476	28	89			3243501055	2735412615	2958387721	2936117380	664476	SRX22969961	SRS19936062	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.01063	0.89389	0.00439	0.18047	0.99403	0.85878	0.36393	0.54831	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29181	29181	SRR27292310	SRX22969960	SRS19936061	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…		pubmed:38922186	Unwounded Larval Zebrafish 5 dpf	GSM7982883	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded\|geo loc name:missing\|collection date:missing	Unwounded Larval Zebrafish 5 dpf	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded	GSM7982883	GSM7982883: Unwounded Larval Zebrafish 5 dpf Danio rerio; RNA Seq	GSM7982883 r1	GSM7982883	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	WT-5dpf_S6_L001_R2_001.fastq.gz WT-5dpf_S6_L001_R1_001.fastq.gz	fastq fastq	31813158312.0	271907336.0	GSM7982883 r1	0:28 1:89	A:8991313503;C:6911976524;G:7105775004;T:8798521232;N:5572049	28	89			8991313503	6911976524	7105775004	8798521232	5572049	SRX22969960	SRS19936061	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.00661	0.92343	0.00245	0.19293	0.99255	0.81379	0.35935	0.54818	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29182	29182	SRR27292311	SRX22969960	SRS19936061	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…		pubmed:38922186	Unwounded Larval Zebrafish 5 dpf	GSM7982883	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded\|geo loc name:missing\|collection date:missing	Unwounded Larval Zebrafish 5 dpf	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded	GSM7982883	GSM7982883: Unwounded Larval Zebrafish 5 dpf Danio rerio; RNA Seq	GSM7982883 r1	GSM7982883	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	WT-5dpf_S6_L002_R1_001.fastq.gz WT-5dpf_S6_L002_R2_001.fastq.gz	fastq fastq	30524386113.0	260892189.0	GSM7982883 r2	0:28 1:89	A:8637605077;C:6625244702;G:6807369409;T:8452468968;N:1697957	28	89			8637605077	6625244702	6807369409	8452468968	1697957	SRX22969960	SRS19936061	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.00648	0.92418	0.00233	0.19549	0.99241	0.81444	0.37733	0.54674	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29183	29183	SRR27292312	SRX22969959	SRS19936060	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…		pubmed:38922186	Unwounded Larval Zebrafish 4 dpf	GSM7982882	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded\|geo loc name:missing\|collection date:missing	Unwounded Larval Zebrafish 4 dpf	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded	GSM7982882	GSM7982882: Unwounded Larval Zebrafish 4 dpf Danio rerio; RNA Seq	GSM7982882 r1	GSM7982882	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	WT-4dpf_S1_L001_R1_001.fastq.gz WT-4dpf_S1_L001_R2_001.fastq.gz	fastq fastq	12682286721.0	108395613.0	GSM7982882 r1	0:28 1:89	A:3575375325;C:2777398557;G:2900088646;T:3425909511;N:3514682	28	89			3575375325	2777398557	2900088646	3425909511	3514682	SRX22969959	SRS19936060	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.00505	0.92112	0.00185	0.16865	0.99257	0.8258	0.38216	0.5512	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29184	29184	SRR27292313	SRX22969959	SRS19936060	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…		pubmed:38922186	Unwounded Larval Zebrafish 4 dpf	GSM7982882	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded\|geo loc name:missing\|collection date:missing	Unwounded Larval Zebrafish 4 dpf	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded	GSM7982882	GSM7982882: Unwounded Larval Zebrafish 4 dpf Danio rerio; RNA Seq	GSM7982882 r1	GSM7982882	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	WT-4dpf_S1_L002_R2_001.fastq.gz WT-4dpf_S1_L002_R1_001.fastq.gz	fastq fastq	12832453413.0	109679089.0	GSM7982882 r2	0:28 1:89	A:3620789787;C:2810897812;G:2929508681;T:3469577031;N:1680102	28	89			3620789787	2810897812	2929508681	3469577031	1680102	SRX22969959	SRS19936060	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.0052	0.92355	0.00192	0.16775	0.99263	0.8253	0.37089	0.55115	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29185	29185	SRR27292314	SRX22969958	SRS19936059	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…		pubmed:38922186	Unwounded Larval Zebrafish 3 dpf	GSM7982881	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded\|geo loc name:missing\|collection date:missing	Unwounded Larval Zebrafish 3 dpf	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded	GSM7982881	GSM7982881: Unwounded Larval Zebrafish 3 dpf Danio rerio; RNA Seq	GSM7982881 r1	GSM7982881	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	WT-3dpf_S4_L001_R1_001.fastq.gz WT-3dpf_S4_L001_R2_001.fastq.gz	fastq fastq	7586138430.0	64838790.0	GSM7982881 r1	0:28 1:89	A:2101749534;C:1692875352;G:1784872358;T:2005308370;N:1332816	28	89			2101749534	1692875352	1784872358	2005308370	1332816	SRX22969958	SRS19936059	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.00976	0.92096	0.00368	0.18077	0.99356	0.83875	0.3661	0.59073	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29186	29186	SRR27292315	SRX22969958	SRS19936059	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…		pubmed:38922186	Unwounded Larval Zebrafish 3 dpf	GSM7982881	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded\|geo loc name:missing\|collection date:missing	Unwounded Larval Zebrafish 3 dpf	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded	GSM7982881	GSM7982881: Unwounded Larval Zebrafish 3 dpf Danio rerio; RNA Seq	GSM7982881 r1	GSM7982881	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	WT-3dpf_S4_L002_R1_001.fastq.gz WT-3dpf_S4_L002_R2_001.fastq.gz	fastq fastq	7258692168.0	62040104.0	GSM7982881 r2	0:28 1:89	A:2013529524;C:1617959197;G:1704796898;T:1922004726;N:401823	28	89			2013529524	1617959197	1704796898	1922004726	401823	SRX22969958	SRS19936059	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.00949	0.92207	0.00359	0.18081	0.99375	0.83751	0.37347	0.55889	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
30256	30256	SRR27747506	SRX23412819	SRS20268140	SRP486180	PRJNA1069776	Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq	GSE254346	Transcriptome Analysis	The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.			Late born vestibular neurons replicate 2	GSM8038041	tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:Neurons born post 36 hpf green unconverted Kaede\|geo loc name:missing\|collection date:missing	Late born vestibular neurons replicate 2	Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Hindbrain vestibular neurons	Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons.	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1		time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:Neurons born post 36 hpf green unconverted Kaede	GSM8038041	GSM8038041: Late born vestibular neurons replicate 2; Danio rerio; RNA Seq	GSM8038041 r1	GSM8038041	1	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486180	loader:fastq load.py	Green_S19_L001_I1_001.fastq.gz Green_S19_L001_I2_001.fastq.gz Green_S19_L001_R1_001.fastq.gz Green_S19_L001_R2_001.fastq.gz	fastq fastq fastq fastq	4923159660.0	35675070.0	GSM8038041 r1	0:10 1:10 2:28 3:90	A:1637293866;C:391317121;G:716609880;T:465465343;N:70090	10	10	28	90	1637293866	391317121	716609880	465465343	70090	SRX23412819	SRS20268140	SRA1792542	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-26	Multi-stage	Multi-stage	Brain	Nervous System
30257	30257	SRR27747507	SRX23412819	SRS20268140	SRP486180	PRJNA1069776	Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq	GSE254346	Transcriptome Analysis	The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.			Late born vestibular neurons replicate 2	GSM8038041	tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:Neurons born post 36 hpf green unconverted Kaede\|geo loc name:missing\|collection date:missing	Late born vestibular neurons replicate 2	Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Hindbrain vestibular neurons	Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons.	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1		time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:Neurons born post 36 hpf green unconverted Kaede	GSM8038041	GSM8038041: Late born vestibular neurons replicate 2; Danio rerio; RNA Seq	GSM8038041 r1	GSM8038041	1	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486180	loader:fastq load.py	Green_S19_L002_I1_001.fastq.gz Green_S19_L002_I2_001.fastq.gz Green_S19_L002_R1_001.fastq.gz Green_S19_L002_R2_001.fastq.gz	fastq fastq fastq fastq	4858633206.0	35207487.0	GSM8038041 r2	0:10 1:10 2:28 3:90	A:1614338875;C:386568724;G:706765488;T:460927318;N:73425	10	10	28	90	1614338875	386568724	706765488	460927318	73425	SRX23412819	SRS20268140	SRA1792542	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-26	Multi-stage	Multi-stage	Brain	Nervous System
30258	30258	SRR27747508	SRX23412819	SRS20268140	SRP486180	PRJNA1069776	Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq	GSE254346	Transcriptome Analysis	The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.			Late born vestibular neurons replicate 2	GSM8038041	tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:Neurons born post 36 hpf green unconverted Kaede\|geo loc name:missing\|collection date:missing	Late born vestibular neurons replicate 2	Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Hindbrain vestibular neurons	Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons.	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1		time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:Neurons born post 36 hpf green unconverted Kaede	GSM8038041	GSM8038041: Late born vestibular neurons replicate 2; Danio rerio; RNA Seq	GSM8038041 r1	GSM8038041	1	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486180	loader:fastq load.py	Green_S19_L003_I1_001.fastq.gz Green_S19_L003_I2_001.fastq.gz Green_S19_L003_R1_001.fastq.gz Green_S19_L003_R2_001.fastq.gz	fastq fastq fastq fastq	4458723696.0	32309592.0	GSM8038041 r3	0:10 1:10 2:28 3:90	A:1463412697;C:359363166;G:655814899;T:429192204;N:80314	10	10	28	90	1463412697	359363166	655814899	429192204	80314	SRX23412819	SRS20268140	SRA1792542	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-26	Multi-stage	Multi-stage	Brain	Nervous System
30259	30259	SRR27747509	SRX23412819	SRS20268140	SRP486180	PRJNA1069776	Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq	GSE254346	Transcriptome Analysis	The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.			Late born vestibular neurons replicate 2	GSM8038041	tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:Neurons born post 36 hpf green unconverted Kaede\|geo loc name:missing\|collection date:missing	Late born vestibular neurons replicate 2	Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Hindbrain vestibular neurons	Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons.	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1		time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:Neurons born post 36 hpf green unconverted Kaede	GSM8038041	GSM8038041: Late born vestibular neurons replicate 2; Danio rerio; RNA Seq	GSM8038041 r1	GSM8038041	1	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486180	loader:fastq load.py	Green_S19_L004_I1_001.fastq.gz Green_S19_L004_I2_001.fastq.gz Green_S19_L004_R1_001.fastq.gz Green_S19_L004_R2_001.fastq.gz	fastq fastq fastq fastq	4425208602.0	32066729.0	GSM8038041 r4	0:10 1:10 2:28 3:90	A:1452148554;C:355763806;G:651302168;T:426718847;N:72235	10	10	28	90	1452148554	355763806	651302168	426718847	72235	SRX23412819	SRS20268140	SRA1792542	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-26	Multi-stage	Multi-stage	Brain	Nervous System
30260	30260	SRR27747510	SRX23412818	SRS20268139	SRP486180	PRJNA1069776	Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq	GSE254346	Transcriptome Analysis	The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.			Early born vestibular neurons replicate 1	GSM8038040	tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:Neurons born before 36 hpf red photoconverted Kaede\|geo loc name:missing\|collection date:missing	Early born vestibular neurons replicate 1	Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Hindbrain vestibular neurons	Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons.	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1		time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:Neurons born before 36 hpf red photoconverted Kaede	GSM8038040	GSM8038040: Early born vestibular neurons replicate 1; Danio rerio; RNA Seq	GSM8038040 r1	GSM8038040	1	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486180	loader:fastq load.py	Red_S20_L001_I1_001.fastq.gz Red_S20_L001_I2_001.fastq.gz Red_S20_L001_R1_001.fastq.gz Red_S20_L001_R2_001.fastq.gz	fastq fastq fastq fastq	5032560816.0	36467832.0	GSM8038040 r1	0:10 1:10 2:28 3:90	A:1626033872;C:414606578;G:755475703;T:485911557;N:77170	10	10	28	90	1626033872	414606578	755475703	485911557	77170	SRX23412818	SRS20268139	SRA1792542	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-26	Multi-stage	Multi-stage	Brain	Nervous System
30261	30261	SRR27747511	SRX23412818	SRS20268139	SRP486180	PRJNA1069776	Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq	GSE254346	Transcriptome Analysis	The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.			Early born vestibular neurons replicate 1	GSM8038040	tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:Neurons born before 36 hpf red photoconverted Kaede\|geo loc name:missing\|collection date:missing	Early born vestibular neurons replicate 1	Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Hindbrain vestibular neurons	Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons.	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1		time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:Neurons born before 36 hpf red photoconverted Kaede	GSM8038040	GSM8038040: Early born vestibular neurons replicate 1; Danio rerio; RNA Seq	GSM8038040 r1	GSM8038040	1	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486180	loader:fastq load.py	Red_S20_L002_I1_001.fastq.gz Red_S20_L002_I2_001.fastq.gz Red_S20_L002_R1_001.fastq.gz Red_S20_L002_R2_001.fastq.gz	fastq fastq fastq fastq	4998616680.0	36221860.0	GSM8038040 r2	0:10 1:10 2:28 3:90	A:1613203224;C:412246760;G:750087642;T:484348061;N:81713	10	10	28	90	1613203224	412246760	750087642	484348061	81713	SRX23412818	SRS20268139	SRA1792542	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-26	Multi-stage	Multi-stage	Brain	Nervous System
30262	30262	SRR27747512	SRX23412818	SRS20268139	SRP486180	PRJNA1069776	Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq	GSE254346	Transcriptome Analysis	The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.			Early born vestibular neurons replicate 1	GSM8038040	tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:Neurons born before 36 hpf red photoconverted Kaede\|geo loc name:missing\|collection date:missing	Early born vestibular neurons replicate 1	Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Hindbrain vestibular neurons	Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons.	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1		time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:Neurons born before 36 hpf red photoconverted Kaede	GSM8038040	GSM8038040: Early born vestibular neurons replicate 1; Danio rerio; RNA Seq	GSM8038040 r1	GSM8038040	1	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486180	loader:fastq load.py	Red_S20_L003_I1_001.fastq.gz Red_S20_L003_I2_001.fastq.gz Red_S20_L003_R1_001.fastq.gz Red_S20_L003_R2_001.fastq.gz	fastq fastq fastq fastq	4628879490.0	33542605.0	GSM8038040 r3	0:10 1:10 2:28 3:90	A:1475662550;C:386397974;G:701772418;T:454914612;N:86896	10	10	28	90	1475662550	386397974	701772418	454914612	86896	SRX23412818	SRS20268139	SRA1792542	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-26	Multi-stage	Multi-stage	Brain	Nervous System
30263	30263	SRR27747513	SRX23412818	SRS20268139	SRP486180	PRJNA1069776	Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq	GSE254346	Transcriptome Analysis	The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.			Early born vestibular neurons replicate 1	GSM8038040	tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:Neurons born before 36 hpf red photoconverted Kaede\|geo loc name:missing\|collection date:missing	Early born vestibular neurons replicate 1	Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Hindbrain vestibular neurons	Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons.	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1		time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:Neurons born before 36 hpf red photoconverted Kaede	GSM8038040	GSM8038040: Early born vestibular neurons replicate 1; Danio rerio; RNA Seq	GSM8038040 r1	GSM8038040	1	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486180	loader:fastq load.py	Red_S20_L004_I1_001.fastq.gz Red_S20_L004_I2_001.fastq.gz Red_S20_L004_R1_001.fastq.gz Red_S20_L004_R2_001.fastq.gz	fastq fastq fastq fastq	4582808190.0	33208755.0	GSM8038040 r4	0:10 1:10 2:28 3:90	A:1460627048;C:381772307;G:695044521;T:451264941;N:79133	10	10	28	90	1460627048	381772307	695044521	451264941	79133	SRX23412818	SRS20268139	SRA1792542	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-26	Multi-stage	Multi-stage	Brain	Nervous System
30264	30264	SRR27747514	SRX23412817	SRS20268138	SRP486180	PRJNA1069776	Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq	GSE254346	Transcriptome Analysis	The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.			All vestibular neurons replicate 3	GSM8038039	tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a\|geo loc name:missing\|collection date:missing	All vestibular neurons replicate 3	Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Hindbrain vestibular neurons	Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons.	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1		time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a	GSM8038039	GSM8038039: All vestibular neurons replicate 3; Danio rerio; RNA Seq	GSM8038039 r1	GSM8038039	1	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486180	loader:fastq load.py	Zebrafish-Replicate3_S3_L001_I1_001.fastq.gz Zebrafish-Replicate3_S3_L001_I2_001.fastq.gz Zebrafish-Replicate3_S3_L001_R1_001.fastq.gz Zebrafish-Replicate3_S3_L001_R2_001.fastq.gz	fastq fastq fastq fastq	10560652880.0	75975920.0	GSM8038039 r1	0:10 1:10 2:28 3:91	A:2623816838;C:1175510072;G:1638990770;T:1474946754;N:544286	10	10	28	91	2623816838	1175510072	1638990770	1474946754	544286	SRX23412817	SRS20268138	SRA1792542	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-26	Multi-stage	Multi-stage	Brain	Nervous System
30265	30265	SRR27747515	SRX23412817	SRS20268138	SRP486180	PRJNA1069776	Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq	GSE254346	Transcriptome Analysis	The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.			All vestibular neurons replicate 3	GSM8038039	tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a\|geo loc name:missing\|collection date:missing	All vestibular neurons replicate 3	Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Hindbrain vestibular neurons	Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons.	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1		time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a	GSM8038039	GSM8038039: All vestibular neurons replicate 3; Danio rerio; RNA Seq	GSM8038039 r1	GSM8038039	1	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486180	loader:fastq load.py	Zebrafish-Replicate3_S3_L002_I1_001.fastq.gz Zebrafish-Replicate3_S3_L002_I2_001.fastq.gz Zebrafish-Replicate3_S3_L002_R1_001.fastq.gz Zebrafish-Replicate3_S3_L002_R2_001.fastq.gz	fastq fastq fastq fastq	10571317933.0	76052647.0	GSM8038039 r2	0:10 1:10 2:28 3:91	A:2631345994;C:1175630391;G:1641110007;T:1472183634;N:520851	10	10	28	91	2631345994	1175630391	1641110007	1472183634	520851	SRX23412817	SRS20268138	SRA1792542	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-26	Multi-stage	Multi-stage	Brain	Nervous System
30266	30266	SRR27747516	SRX23412817	SRS20268138	SRP486180	PRJNA1069776	Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq	GSE254346	Transcriptome Analysis	The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.			All vestibular neurons replicate 3	GSM8038039	tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a\|geo loc name:missing\|collection date:missing	All vestibular neurons replicate 3	Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Hindbrain vestibular neurons	Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons.	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1		time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a	GSM8038039	GSM8038039: All vestibular neurons replicate 3; Danio rerio; RNA Seq	GSM8038039 r1	GSM8038039	1	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486180	loader:fastq load.py	Zebrafish-Replicate3_S3_L003_I1_001.fastq.gz Zebrafish-Replicate3_S3_L003_I2_001.fastq.gz Zebrafish-Replicate3_S3_L003_R1_001.fastq.gz Zebrafish-Replicate3_S3_L003_R2_001.fastq.gz	fastq fastq fastq fastq	10457106081.0	75230979.0	GSM8038039 r3	0:10 1:10 2:28 3:91	A:2588687752;C:1168371662;G:1623033341;T:1465362298;N:564036	10	10	28	91	2588687752	1168371662	1623033341	1465362298	564036	SRX23412817	SRS20268138	SRA1792542	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-26	Multi-stage	Multi-stage	Brain	Nervous System
30267	30267	SRR27747517	SRX23412817	SRS20268138	SRP486180	PRJNA1069776	Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq	GSE254346	Transcriptome Analysis	The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.			All vestibular neurons replicate 3	GSM8038039	tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a\|geo loc name:missing\|collection date:missing	All vestibular neurons replicate 3	Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Hindbrain vestibular neurons	Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons.	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1		time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a	GSM8038039	GSM8038039: All vestibular neurons replicate 3; Danio rerio; RNA Seq	GSM8038039 r1	GSM8038039	1	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486180	loader:fastq load.py	Zebrafish-Replicate3_S3_L004_I1_001.fastq.gz Zebrafish-Replicate3_S3_L004_I2_001.fastq.gz Zebrafish-Replicate3_S3_L004_R1_001.fastq.gz Zebrafish-Replicate3_S3_L004_R2_001.fastq.gz	fastq fastq fastq fastq	10455949462.0	75222658.0	GSM8038039 r4	0:10 1:10 2:28 3:91	A:2581792541;C:1170458560;G:1624194611;T:1468248274;N:567892	10	10	28	91	2581792541	1170458560	1624194611	1468248274	567892	SRX23412817	SRS20268138	SRA1792542	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-26	Multi-stage	Multi-stage	Brain	Nervous System
30268	30268	SRR27747518	SRX23412816	SRS20268137	SRP486180	PRJNA1069776	Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq	GSE254346	Transcriptome Analysis	The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.			All vestibular neurons replicate 2	GSM8038038	tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a\|geo loc name:missing\|collection date:missing	All vestibular neurons replicate 2	Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Hindbrain vestibular neurons	Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons.	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1		time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a	GSM8038038	GSM8038038: All vestibular neurons replicate 2; Danio rerio; RNA Seq	GSM8038038 r1	GSM8038038	1	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486180	loader:fastq load.py	Zebrafish-Replicate2_S2_L001_I1_001.fastq.gz Zebrafish-Replicate2_S2_L001_I2_001.fastq.gz Zebrafish-Replicate2_S2_L001_R1_001.fastq.gz Zebrafish-Replicate2_S2_L001_R2_001.fastq.gz	fastq fastq fastq fastq	9414131535.0	67727565.0	GSM8038038 r1	0:10 1:10 2:28 3:91	A:2659651693;C:894536960;G:1598721159;T:1009819179;N:479424	10	10	28	91	2659651693	894536960	1598721159	1009819179	479424	SRX23412816	SRS20268137	SRA1792542	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-26	Multi-stage	Multi-stage	Brain	Nervous System
30269	30269	SRR27747519	SRX23412816	SRS20268137	SRP486180	PRJNA1069776	Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq	GSE254346	Transcriptome Analysis	The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.			All vestibular neurons replicate 2	GSM8038038	tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a\|geo loc name:missing\|collection date:missing	All vestibular neurons replicate 2	Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Hindbrain vestibular neurons	Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons.	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1		time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a	GSM8038038	GSM8038038: All vestibular neurons replicate 2; Danio rerio; RNA Seq	GSM8038038 r1	GSM8038038	1	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486180	loader:fastq load.py	Zebrafish-Replicate2_S2_L002_I1_001.fastq.gz Zebrafish-Replicate2_S2_L002_I2_001.fastq.gz Zebrafish-Replicate2_S2_L002_R1_001.fastq.gz Zebrafish-Replicate2_S2_L002_R2_001.fastq.gz	fastq fastq fastq fastq	9495760675.0	68314825.0	GSM8038038 r2	0:10 1:10 2:28 3:91	A:2685940540;C:901627244;G:1612080998;T:1016532106;N:468187	10	10	28	91	2685940540	901627244	1612080998	1016532106	468187	SRX23412816	SRS20268137	SRA1792542	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-26	Multi-stage	Multi-stage	Brain	Nervous System
30270	30270	SRR27747520	SRX23412816	SRS20268137	SRP486180	PRJNA1069776	Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq	GSE254346	Transcriptome Analysis	The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.			All vestibular neurons replicate 2	GSM8038038	tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a\|geo loc name:missing\|collection date:missing	All vestibular neurons replicate 2	Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Hindbrain vestibular neurons	Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons.	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1		time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a	GSM8038038	GSM8038038: All vestibular neurons replicate 2; Danio rerio; RNA Seq	GSM8038038 r1	GSM8038038	1	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486180	loader:fastq load.py	Zebrafish-Replicate2_S2_L003_I1_001.fastq.gz Zebrafish-Replicate2_S2_L003_I2_001.fastq.gz Zebrafish-Replicate2_S2_L003_R1_001.fastq.gz Zebrafish-Replicate2_S2_L003_R2_001.fastq.gz	fastq fastq fastq fastq	9299053574.0	66899666.0	GSM8038038 r3	0:10 1:10 2:28 3:91	A:2619668178;C:887003175;G:1580306677;T:1000391033;N:500543	10	10	28	91	2619668178	887003175	1580306677	1000391033	500543	SRX23412816	SRS20268137	SRA1792542	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-26	Multi-stage	Multi-stage	Brain	Nervous System
30271	30271	SRR27747521	SRX23412816	SRS20268137	SRP486180	PRJNA1069776	Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq	GSE254346	Transcriptome Analysis	The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.			All vestibular neurons replicate 2	GSM8038038	tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a\|geo loc name:missing\|collection date:missing	All vestibular neurons replicate 2	Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Hindbrain vestibular neurons	Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons.	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1		time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a	GSM8038038	GSM8038038: All vestibular neurons replicate 2; Danio rerio; RNA Seq	GSM8038038 r1	GSM8038038	1	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486180	loader:fastq load.py	Zebrafish-Replicate2_S2_L004_I1_001.fastq.gz Zebrafish-Replicate2_S2_L004_I2_001.fastq.gz Zebrafish-Replicate2_S2_L004_R1_001.fastq.gz Zebrafish-Replicate2_S2_L004_R2_001.fastq.gz	fastq fastq fastq fastq	9269439763.0	66686617.0	GSM8038038 r4	0:10 1:10 2:28 3:91	A:2605497678;C:885933483;G:1577360287;T:999190994;N:499705	10	10	28	91	2605497678	885933483	1577360287	999190994	499705	SRX23412816	SRS20268137	SRA1792542	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-26	Multi-stage	Multi-stage	Brain	Nervous System
30272	30272	SRR27747522	SRX23412815	SRS20268136	SRP486180	PRJNA1069776	Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq	GSE254346	Transcriptome Analysis	The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.			All vestibular neurons replicate 1	GSM8038037	tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a\|geo loc name:missing\|collection date:missing	All vestibular neurons replicate 1	Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Hindbrain vestibular neurons	Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons.	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1		time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a	GSM8038037	GSM8038037: All vestibular neurons replicate 1; Danio rerio; RNA Seq	GSM8038037 r1	GSM8038037	1	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486180	loader:fastq load.py	Zebrafish-Replicate1_S1_L001_I1_001.fastq.gz Zebrafish-Replicate1_S1_L001_I2_001.fastq.gz Zebrafish-Replicate1_S1_L001_R1_001.fastq.gz Zebrafish-Replicate1_S1_L001_R2_001.fastq.gz	fastq fastq fastq fastq	11844241708.0	85210372.0	GSM8038037 r1	0:10 1:10 2:28 3:91	A:3114181870;C:1253864519;G:2080987238;T:1304504811;N:605414	10	10	28	91	3114181870	1253864519	2080987238	1304504811	605414	SRX23412815	SRS20268136	SRA1792542	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-26	Multi-stage	Multi-stage	Brain	Nervous System
30273	30273	SRR27747523	SRX23412815	SRS20268136	SRP486180	PRJNA1069776	Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq	GSE254346	Transcriptome Analysis	The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.			All vestibular neurons replicate 1	GSM8038037	tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a\|geo loc name:missing\|collection date:missing	All vestibular neurons replicate 1	Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Hindbrain vestibular neurons	Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons.	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1		time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a	GSM8038037	GSM8038037: All vestibular neurons replicate 1; Danio rerio; RNA Seq	GSM8038037 r1	GSM8038037	1	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486180	loader:fastq load.py	Zebrafish-Replicate1_S1_L002_I1_001.fastq.gz Zebrafish-Replicate1_S1_L002_I2_001.fastq.gz Zebrafish-Replicate1_S1_L002_R1_001.fastq.gz Zebrafish-Replicate1_S1_L002_R2_001.fastq.gz	fastq fastq fastq fastq	11897506230.0	85593570.0	GSM8038037 r2	0:10 1:10 2:28 3:91	A:3132719148;C:1257962906;G:2089627351;T:1308117927;N:587538	10	10	28	91	3132719148	1257962906	2089627351	1308117927	587538	SRX23412815	SRS20268136	SRA1792542	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-26	Multi-stage	Multi-stage	Brain	Nervous System
30274	30274	SRR27747524	SRX23412815	SRS20268136	SRP486180	PRJNA1069776	Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq	GSE254346	Transcriptome Analysis	The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.			All vestibular neurons replicate 1	GSM8038037	tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a\|geo loc name:missing\|collection date:missing	All vestibular neurons replicate 1	Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Hindbrain vestibular neurons	Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons.	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1		time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a	GSM8038037	GSM8038037: All vestibular neurons replicate 1; Danio rerio; RNA Seq	GSM8038037 r1	GSM8038037	1	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486180	loader:fastq load.py	Zebrafish-Replicate1_S1_L003_I1_001.fastq.gz Zebrafish-Replicate1_S1_L003_I2_001.fastq.gz Zebrafish-Replicate1_S1_L003_R1_001.fastq.gz Zebrafish-Replicate1_S1_L003_R2_001.fastq.gz	fastq fastq fastq fastq	11710536913.0	84248467.0	GSM8038037 r3	0:10 1:10 2:28 3:91	A:3071431897;C:1243257065;G:2058561915;T:1292732765;N:626855	10	10	28	91	3071431897	1243257065	2058561915	1292732765	626855	SRX23412815	SRS20268136	SRA1792542	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-26	Multi-stage	Multi-stage	Brain	Nervous System
30275	30275	SRR27747525	SRX23412815	SRS20268136	SRP486180	PRJNA1069776	Molecular characterization of hindbrain vestibular neurons in the larval zebrafish scRNA Seq	GSE254346	Transcriptome Analysis	The molecular logic that specifies and assembles closely related subtypes of neurons into functional sensorimotor circuits remains unclear. The goal of this study was to characterize the molecular profiles of hindbrain vestibular neurons in the larval zebrafish to identify candidate molecular programs that specify their subtype fate topography and circuit assembly. We used single cell RNA sequencing to generate a comprehensive atlas of hindbrain vestibular neurons and fluorecent in situ hybridization to annotate profiled neurons. Our dataset serves as a reference for evaluating developmental changes in molecular profiles following perturbations and identifies new candidate molecular solutions that assemble closely related subtypes into functional circuits. Overall design: Hindbrain vestibular neurons labeled by Tg 6.7Tru.Hcrtr2:GAL4 VP16;TgUAS:E1b Kaede harvested from zebrafish embryos between 72 hpf 74 hpf. Fluorescent neurons were isolated by fluorescence activated cell sorting FACS according to Kaede fluorescence. Three samples contained all hindbrain vestibular neurons sorted. One sample had two conditions: neurons born before or post a previously identified "midpoint" in hindbrain vestibular neuron development 36 hpf labeled using Kaede photoconversions. Neurons were sequenced with 10x Genomics.			All vestibular neurons replicate 1	GSM8038037	tissue:Hindbrain vestibular neurons\|time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a\|geo loc name:missing\|collection date:missing	All vestibular neurons replicate 1	Cell Ranger v7.0.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Hindbrain vestibular neurons	Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early born red converted Kaede from late born green unconverted Kaede neurons.	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1		time:72 hpf 74 hpf type:Hindbrain vestibular neurons\|genotype:Tg 6.7Tru.Hcrtr2:GAL4 VP16; TgUAS:E1b Kaede\|treatment:n/a	GSM8038037	GSM8038037: All vestibular neurons replicate 1; Danio rerio; RNA Seq	GSM8038037 r1	GSM8038037	1	Harvested neurons were sorted to isolate single cells resuspended in L15+2% FBS and kept on ice until cDNA synthesis Performed using manufacturer's instructions; 10x Genomics three prime V3.1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP486180	loader:fastq load.py	Zebrafish-Replicate1_S1_L004_I1_001.fastq.gz Zebrafish-Replicate1_S1_L004_I2_001.fastq.gz Zebrafish-Replicate1_S1_L004_R1_001.fastq.gz Zebrafish-Replicate1_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq	11691727294.0	84113146.0	GSM8038037 r4	0:10 1:10 2:28 3:91	A:3060624267;C:1243160034;G:2057238308;T:1292649886;N:623791	10	10	28	91	3060624267	1243160034	2057238308	1292649886	623791	SRX23412815	SRS20268136	SRA1792542	Neuroscience Institute, New York University Grossman School of Medicine	Neuroscience Institute, New York University Grossman School of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-01-26	Multi-stage	Multi-stage	Brain	Nervous System
30662	30662	SRR28125659	SRX23770350	SRS20595835	SRP492124	PRJNA1081449	Thymic mimetic cells in zebrafish	GSE259418	Transcriptome Analysis	We profiled the zebrafish thymus by single cell RNA sequencing to investigate the heterogeneity of zebrafish thymic epithelial cells and determine whether similar mimetic cell populations to those found in mice and humans might also exist in the zebrafish. Overall design: To assess the heterogeneity of zebrafish thymic epithelial cells a total of 11 zebrafish samples derived from 14 adult and 21 juvenile zebrafish were studied. Specifically we re processed single cell RNA sequencing scRNA seq data from 8 zebrafish thymus samples derived from 4 adult zebrafish and 21 juvenile zebrafish previously described in GSE190794 GSM5732067 GSM5732070 GSM5732077 GSM5732078 GSM5732079 GSM5732080 GSM5732081 GSM5732082 so that reads mapping to intronic regions were included in the analysis to increase sensitivity and be consistent with mouse and human scRNA seq studies for cross species comparison. In addition we generated 3 new scRNA seq datasets derived from a total of 10 adult lck:mCherry;cd79a:eGFP transgenic zebrafish. The thymi from 5 of these adult zebrafish were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII whereas thymi from the other 5 adult zebrafish underwent enzymatic dissociation with Liberase TM prior to quenching filtering and cell sorting. The live non autofluorescent GFP negative mCherry negative cells a population depleted of T and B cells thus providing a relative enrichment of thymic epithelial cells were sorted and collected for 10x scRNA seq. One 10x lane was used for the mechanically dissociated sample untreated and two lanes were used for the liberase treated sample to obtain 2 technical replicates. Re analysed Samples in GSE190794/PRJNA788489 and their processed data file: SampleName Experiment BioSample processed data file GSM5732067 Adult Thymus 3 SRX13397695 SAMN24007722 Fish 22 Thymus .filtered feature bc matrix.h5 GSM5732070 Adult Thymus 4 SRX13397698 SAMN24007725 Fish 24 Thymus .filtered feature bc matrix.h5 GSM5732077 Adult Thymus 1 …			adult thy untreated	GSM8115869	tissue:13 wpf wpf loc name:missing\|collection date:missing	adult thy untreated	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 7.0.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Assembly: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: count matrices from the NovaSeq platforms	13 wpf		Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	tissue:13 wpf	GSM8115869	GSM8115869: adult thy untreated; Danio rerio; RNA Seq	GSM8115869 r1	GSM8115869	1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP492124	loader:fastq load.py	adult_thy_untreated_S5_L001_R2_001.fastq.gz adult_thy_untreated_S5_L001_R1_001.fastq.gz adult_thy_untreated_S5_L001_I1_001.fastq.gz	fastq fastq fastq	61867658967.0	487146921.0	GSM8115869 r1	0:8 1:28 2:91	A:12933400034;C:9373762639;G:10188374364;T:11834295354;N:537420	8	28	91		12933400034	9373762639	10188374364	11834295354	537420	SRX23770350	SRS20595835			Oncology/Hematology, Boston Children's Hospital	1	0.90847		0.19603		0.76895		0.56494		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-02-27	Multi-stage	Multi-stage	Undetermined	Undetermined
30663	30663	SRR28125660	SRX23770349	SRS20595836	SRP492124	PRJNA1081449	Thymic mimetic cells in zebrafish	GSE259418	Transcriptome Analysis	We profiled the zebrafish thymus by single cell RNA sequencing to investigate the heterogeneity of zebrafish thymic epithelial cells and determine whether similar mimetic cell populations to those found in mice and humans might also exist in the zebrafish. Overall design: To assess the heterogeneity of zebrafish thymic epithelial cells a total of 11 zebrafish samples derived from 14 adult and 21 juvenile zebrafish were studied. Specifically we re processed single cell RNA sequencing scRNA seq data from 8 zebrafish thymus samples derived from 4 adult zebrafish and 21 juvenile zebrafish previously described in GSE190794 GSM5732067 GSM5732070 GSM5732077 GSM5732078 GSM5732079 GSM5732080 GSM5732081 GSM5732082 so that reads mapping to intronic regions were included in the analysis to increase sensitivity and be consistent with mouse and human scRNA seq studies for cross species comparison. In addition we generated 3 new scRNA seq datasets derived from a total of 10 adult lck:mCherry;cd79a:eGFP transgenic zebrafish. The thymi from 5 of these adult zebrafish were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII whereas thymi from the other 5 adult zebrafish underwent enzymatic dissociation with Liberase TM prior to quenching filtering and cell sorting. The live non autofluorescent GFP negative mCherry negative cells a population depleted of T and B cells thus providing a relative enrichment of thymic epithelial cells were sorted and collected for 10x scRNA seq. One 10x lane was used for the mechanically dissociated sample untreated and two lanes were used for the liberase treated sample to obtain 2 technical replicates. Re analysed Samples in GSE190794/PRJNA788489 and their processed data file: SampleName Experiment BioSample processed data file GSM5732067 Adult Thymus 3 SRX13397695 SAMN24007722 Fish 22 Thymus .filtered feature bc matrix.h5 GSM5732070 Adult Thymus 4 SRX13397698 SAMN24007725 Fish 24 Thymus .filtered feature bc matrix.h5 GSM5732077 Adult Thymus 1 …			adult thy liberase 2	GSM8115868	tissue:13 wpf wpf loc name:missing\|collection date:missing	adult thy liberase 2	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 7.0.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Assembly: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: count matrices from the NovaSeq platforms	13 wpf		Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	tissue:13 wpf	GSM8115868	GSM8115868: adult thy liberase 2; Danio rerio; RNA Seq	GSM8115868 r1	GSM8115868	1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP492124	loader:fastq load.py	adult_thy_liberase_2_S7_L001_I1_001.fastq.gz adult_thy_liberase_2_S7_L001_R1_001.fastq.gz adult_thy_liberase_2_S7_L001_R2_001.fastq.gz	fastq fastq fastq	64816880653.0	510369139.0	GSM8115868 r1	0:8 1:28 2:91	A:12985717325;C:10400471721;G:10926930853;T:12129907262;N:564488	8	28	91		12985717325	10400471721	10926930853	12129907262	564488	SRX23770349	SRS20595836			Oncology/Hematology, Boston Children's Hospital	1	0.90014		0.13619		0.81103		0.54906		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-02-27	Multi-stage	Multi-stage	Undetermined	Undetermined
30664	30664	SRR28125661	SRX23770348	SRS20595834	SRP492124	PRJNA1081449	Thymic mimetic cells in zebrafish	GSE259418	Transcriptome Analysis	We profiled the zebrafish thymus by single cell RNA sequencing to investigate the heterogeneity of zebrafish thymic epithelial cells and determine whether similar mimetic cell populations to those found in mice and humans might also exist in the zebrafish. Overall design: To assess the heterogeneity of zebrafish thymic epithelial cells a total of 11 zebrafish samples derived from 14 adult and 21 juvenile zebrafish were studied. Specifically we re processed single cell RNA sequencing scRNA seq data from 8 zebrafish thymus samples derived from 4 adult zebrafish and 21 juvenile zebrafish previously described in GSE190794 GSM5732067 GSM5732070 GSM5732077 GSM5732078 GSM5732079 GSM5732080 GSM5732081 GSM5732082 so that reads mapping to intronic regions were included in the analysis to increase sensitivity and be consistent with mouse and human scRNA seq studies for cross species comparison. In addition we generated 3 new scRNA seq datasets derived from a total of 10 adult lck:mCherry;cd79a:eGFP transgenic zebrafish. The thymi from 5 of these adult zebrafish were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII whereas thymi from the other 5 adult zebrafish underwent enzymatic dissociation with Liberase TM prior to quenching filtering and cell sorting. The live non autofluorescent GFP negative mCherry negative cells a population depleted of T and B cells thus providing a relative enrichment of thymic epithelial cells were sorted and collected for 10x scRNA seq. One 10x lane was used for the mechanically dissociated sample untreated and two lanes were used for the liberase treated sample to obtain 2 technical replicates. Re analysed Samples in GSE190794/PRJNA788489 and their processed data file: SampleName Experiment BioSample processed data file GSM5732067 Adult Thymus 3 SRX13397695 SAMN24007722 Fish 22 Thymus .filtered feature bc matrix.h5 GSM5732070 Adult Thymus 4 SRX13397698 SAMN24007725 Fish 24 Thymus .filtered feature bc matrix.h5 GSM5732077 Adult Thymus 1 …			adult thy liberase 1	GSM8115867	tissue:13 wpf wpf loc name:missing\|collection date:missing	adult thy liberase 1	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 7.0.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Assembly: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: count matrices from the NovaSeq platforms	13 wpf		Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	tissue:13 wpf	GSM8115867	GSM8115867: adult thy liberase 1; Danio rerio; RNA Seq	GSM8115867 r1	GSM8115867	1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without xxx or magnesium at room temperature. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of between 4 000 and 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP492124	loader:fastq load.py	adult_thy_liberase_1_S6_L001_I1_001.fastq.gz adult_thy_liberase_1_S6_L001_R1_001.fastq.gz adult_thy_liberase_1_S6_L001_R2_001.fastq.gz	fastq fastq fastq	62862684917.0	494981771.0	GSM8115867 r1	0:8 1:28 2:91	A:12631971877;C:10077821577;G:10579831603;T:11753169367;N:546737	8	28	91		12631971877	10077821577	10579831603	11753169367	546737	SRX23770348	SRS20595834			Oncology/Hematology, Boston Children's Hospital	1	0.89921		0.13602		0.814		0.55224		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-02-27	Multi-stage	Multi-stage	Undetermined	Undetermined
33669	33669	SRR30530658	SRX25954305	SRS22536191	SRP530279	PRJNA1156090	Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos	GSE276251	Transcriptome Analysis	Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs proliferating ECs and a series of upregulated proangiogenic genes. Overall design: Firstly we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.		pubmed:39365738;pubmed:39882604	endothelial cells，high glucose	GSM8494124	tissue:endothelial cells\|cell type:endothelial cells\|geo loc name:missing\|collection date:missing	endothelial cells，high glucose	Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.	endothelial cells	Embryos were treated with 6% glucose from 24 hpf to 72 hpf.	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.	Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.	cell type:endothelial cells	GSM8494124	GSM8494124: endothelial cells，high glucose; Danio rerio; RNA Seq	GSM8494124 r1	GSM8494124	1	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP530279		lr57glu96hpf_R1.fq.gz lr57glu96hpf_R2.fq.gz	fastq fastq	196891371600.0	656304572.0	GSM8494124 r1	0:150 1:150	A:46034913013;C:37262343828;G:60636104680;T:52955473756;N:2536323	150	150			46034913013	37262343828	60636104680	52955473756	2536323	SRX25954305	SRS22536191	SRA1961613	Nantong University	Nantong University												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-09-03	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
33670	33670	SRR30530659	SRX25954304	SRS22536190	SRP530279	PRJNA1156090	Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos	GSE276251	Transcriptome Analysis	Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs proliferating ECs and a series of upregulated proangiogenic genes. Overall design: Firstly we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.		pubmed:39365738;pubmed:39882604	endothelial cells，control	GSM8494123	tissue:endothelial cells\|cell type:endothelial cells\|geo loc name:missing\|collection date:missing	endothelial cells，control	Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.	endothelial cells	Embryos were treated with 6% glucose from 24 hpf to 72 hpf.	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.	Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.	cell type:endothelial cells	GSM8494123	GSM8494123: endothelial cells，control; Danio rerio; RNA Seq	GSM8494123 r1	GSM8494123	1	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP530279		SH190424C_LR5796dpf_1_1_R1.fq.gz SH190424C_LR5796dpf_1_1_R2.fq.gz	fastq fastq	18351420300.0	61171401.0	GSM8494123 r1	0:150 1:150	A:3872504772;C:3434009784;G:6583451920;T:4461384217;N:69607	150	150			3872504772	3434009784	6583451920	4461384217	69607	SRX25954304	SRS22536190	SRA1961613	Nantong University	Nantong University												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-09-03	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
33671	33671	SRR30530660	SRX25954304	SRS22536190	SRP530279	PRJNA1156090	Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos	GSE276251	Transcriptome Analysis	Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs proliferating ECs and a series of upregulated proangiogenic genes. Overall design: Firstly we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.		pubmed:39365738;pubmed:39882604	endothelial cells，control	GSM8494123	tissue:endothelial cells\|cell type:endothelial cells\|geo loc name:missing\|collection date:missing	endothelial cells，control	Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.	endothelial cells	Embryos were treated with 6% glucose from 24 hpf to 72 hpf.	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.	Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.	cell type:endothelial cells	GSM8494123	GSM8494123: endothelial cells，control; Danio rerio; RNA Seq	GSM8494123 r1	GSM8494123	1	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP530279		SH190424C_LR5796dpf_1_2_R1.fq.gz SH190424C_LR5796dpf_1_2_R2.fq.gz	fastq fastq	36386960400.0	121289868.0	GSM8494123 r2	0:150 1:150	A:8890006445;C:6974694151;G:10814990376;T:9707137150;N:132278	150	150			8890006445	6974694151	10814990376	9707137150	132278	SRX25954304	SRS22536190	SRA1961613	Nantong University	Nantong University												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-09-03	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
33672	33672	SRR30530661	SRX25954304	SRS22536190	SRP530279	PRJNA1156090	Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos	GSE276251	Transcriptome Analysis	Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs proliferating ECs and a series of upregulated proangiogenic genes. Overall design: Firstly we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.		pubmed:39365738;pubmed:39882604	endothelial cells，control	GSM8494123	tissue:endothelial cells\|cell type:endothelial cells\|geo loc name:missing\|collection date:missing	endothelial cells，control	Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.	endothelial cells	Embryos were treated with 6% glucose from 24 hpf to 72 hpf.	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.	Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.	cell type:endothelial cells	GSM8494123	GSM8494123: endothelial cells，control; Danio rerio; RNA Seq	GSM8494123 r1	GSM8494123	1	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP530279		SH190424C_LR5796dpf_2_1_R1.fq.gz SH190424C_LR5796dpf_2_1_R2.fq.gz	fastq fastq	44811813000.0	149372710.0	GSM8494123 r3	0:150 1:150	A:10939691275;C:8613307673;G:13332283843;T:11926366839;N:163370	150	150			10939691275	8613307673	13332283843	11926366839	163370	SRX25954304	SRS22536190	SRA1961613	Nantong University	Nantong University												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-09-03	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
33673	33673	SRR30530662	SRX25954304	SRS22536190	SRP530279	PRJNA1156090	Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos	GSE276251	Transcriptome Analysis	Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs proliferating ECs and a series of upregulated proangiogenic genes. Overall design: Firstly we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.		pubmed:39365738;pubmed:39882604	endothelial cells，control	GSM8494123	tissue:endothelial cells\|cell type:endothelial cells\|geo loc name:missing\|collection date:missing	endothelial cells，control	Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.	endothelial cells	Embryos were treated with 6% glucose from 24 hpf to 72 hpf.	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.	Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.	cell type:endothelial cells	GSM8494123	GSM8494123: endothelial cells，control; Danio rerio; RNA Seq	GSM8494123 r1	GSM8494123	1	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP530279		SH190424C_LR5796dpf_2_2_R1.fq.gz SH190424C_LR5796dpf_2_2_R2.fq.gz	fastq fastq	22587582300.0	75291941.0	GSM8494123 r4	0:150 1:150	A:4762937825;C:4235264474;G:8108549401;T:5480746863;N:83737	150	150			4762937825	4235264474	8108549401	5480746863	83737	SRX25954304	SRS22536190	SRA1961613	Nantong University	Nantong University												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-09-03	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
33674	33674	SRR30530663	SRX25954304	SRS22536190	SRP530279	PRJNA1156090	Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos	GSE276251	Transcriptome Analysis	Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs proliferating ECs and a series of upregulated proangiogenic genes. Overall design: Firstly we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.		pubmed:39365738;pubmed:39882604	endothelial cells，control	GSM8494123	tissue:endothelial cells\|cell type:endothelial cells\|geo loc name:missing\|collection date:missing	endothelial cells，control	Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.	endothelial cells	Embryos were treated with 6% glucose from 24 hpf to 72 hpf.	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.	Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.	cell type:endothelial cells	GSM8494123	GSM8494123: endothelial cells，control; Danio rerio; RNA Seq	GSM8494123 r1	GSM8494123	1	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP530279		SH190424C_LR5796dpf_3_1_R1.fq.gz SH190424C_LR5796dpf_3_1_R2.fq.gz	fastq fastq	31458502200.0	104861674.0	GSM8494123 r5	0:150 1:150	A:7597642424;C:6175910515;G:9377029875;T:8307805635;N:113751	150	150			7597642424	6175910515	9377029875	8307805635	113751	SRX25954304	SRS22536190	SRA1961613	Nantong University	Nantong University												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-09-03	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
33675	33675	SRR30530664	SRX25954304	SRS22536190	SRP530279	PRJNA1156090	Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos	GSE276251	Transcriptome Analysis	Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs proliferating ECs and a series of upregulated proangiogenic genes. Overall design: Firstly we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.		pubmed:39365738;pubmed:39882604	endothelial cells，control	GSM8494123	tissue:endothelial cells\|cell type:endothelial cells\|geo loc name:missing\|collection date:missing	endothelial cells，control	Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.	endothelial cells	Embryos were treated with 6% glucose from 24 hpf to 72 hpf.	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.	Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.	cell type:endothelial cells	GSM8494123	GSM8494123: endothelial cells，control; Danio rerio; RNA Seq	GSM8494123 r1	GSM8494123	1	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP530279		SH190424C_LR5796dpf_3_2_R1.fq.gz SH190424C_LR5796dpf_3_2_R2.fq.gz	fastq fastq	15812987400.0	52709958.0	GSM8494123 r6	0:150 1:150	A:3317721700;C:3009997461;G:5662825685;T:3822382737;N:59817	150	150			3317721700	3009997461	5662825685	3822382737	59817	SRX25954304	SRS22536190	SRA1961613	Nantong University	Nantong University												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-09-03	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
33676	33676	SRR30530665	SRX25954304	SRS22536190	SRP530279	PRJNA1156090	Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos	GSE276251	Transcriptome Analysis	Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs proliferating ECs and a series of upregulated proangiogenic genes. Overall design: Firstly we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.		pubmed:39365738;pubmed:39882604	endothelial cells，control	GSM8494123	tissue:endothelial cells\|cell type:endothelial cells\|geo loc name:missing\|collection date:missing	endothelial cells，control	Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.	endothelial cells	Embryos were treated with 6% glucose from 24 hpf to 72 hpf.	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.	Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.	cell type:endothelial cells	GSM8494123	GSM8494123: endothelial cells，control; Danio rerio; RNA Seq	GSM8494123 r1	GSM8494123	1	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP530279		SH190424C_LR5796dpf_4_1_R1.fq.gz SH190424C_LR5796dpf_4_1_R2.fq.gz	fastq fastq	19472976900.0	64909923.0	GSM8494123 r7	0:150 1:150	A:4109297307;C:3636046624;G:6996008921;T:4731548865;N:75183	150	150			4109297307	3636046624	6996008921	4731548865	75183	SRX25954304	SRS22536190	SRA1961613	Nantong University	Nantong University												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-09-03	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
33677	33677	SRR30530666	SRX25954304	SRS22536190	SRP530279	PRJNA1156090	Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos	GSE276251	Transcriptome Analysis	Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs proliferating ECs and a series of upregulated proangiogenic genes. Overall design: Firstly we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.		pubmed:39365738;pubmed:39882604	endothelial cells，control	GSM8494123	tissue:endothelial cells\|cell type:endothelial cells\|geo loc name:missing\|collection date:missing	endothelial cells，control	Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.	endothelial cells	Embryos were treated with 6% glucose from 24 hpf to 72 hpf.	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.	Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.	cell type:endothelial cells	GSM8494123	GSM8494123: endothelial cells，control; Danio rerio; RNA Seq	GSM8494123 r1	GSM8494123	1	Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP530279		SH190424C_LR5796dpf_4_2_R1.fq.gz SH190424C_LR5796dpf_4_2_R2.fq.gz	fastq fastq	39005746200.0	130019154.0	GSM8494123 r8	0:150 1:150	A:9542890616;C:7456459618;G:11598648802;T:10407604379;N:142785	150	150			9542890616	7456459618	11598648802	10407604379	142785	SRX25954304	SRS22536190	SRA1961613	Nantong University	Nantong University												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-09-03	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
34264	34264	SRR31620789	SRX26985240	SRS23451898	SRP549631	PRJNA1194578	Tet proteins regulate differentiation potential across retinal cell types	GSE283588	Transcriptome Analysis	Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis–revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq		pubmed:39713311;pubmed:40140485	36hpf dmut replicate 2	GSM8666793	source name:eye\|tissue:eye\|age:36\|genotype:tet2 / tet3 / \|geo loc name:missing\|collection date:missing	36hpf dmut replicate 2	Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files	eye		Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		tissue:eye\|age:36\|genotype:tet2 / tet3 /	GSM8666793	GSM8666793: 36hpf dmut replicate 2; Danio rerio; RNA Seq	GSM8666793 r1	GSM8666793	1	Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP549631		36-2_DMUT_Library_GRO2554A2_S5_L001_R1_001.fastq.gz 36-2_DMUT_Library_GRO2554A2_S5_L001_R2_001.fastq.gz	fastq fastq	78416374900.0	664545550.0	GSM8666793 r1	0:28 1:90	A:21577013150;C:17939516025;G:19237904562;T:19657905130;N:4036033	28	90			21577013150	17939516025	19237904562	19657905130	4036033	SRX26985240	SRS23451898	SRA2028272	Gross, Ophthalmology, University of Pittsburgh	Gross, Ophthalmology, University of Pittsburgh												T	B	sc-like readlen	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-12-05	Multi-stage	Multi-stage	Eye	Sensory System
34265	34265	SRR31620790	SRX26985239	SRS23451897	SRP549631	PRJNA1194578	Tet proteins regulate differentiation potential across retinal cell types	GSE283588	Transcriptome Analysis	Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis–revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq		pubmed:39713311;pubmed:40140485	36hpf dmut replicate 1	GSM8666792	source name:eye\|tissue:eye\|age:36\|genotype:tet2 / tet3 / \|geo loc name:missing\|collection date:missing	36hpf dmut replicate 1	Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files	eye		Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		tissue:eye\|age:36\|genotype:tet2 / tet3 /	GSM8666792	GSM8666792: 36hpf dmut replicate 1; Danio rerio; RNA Seq	GSM8666792 r1	GSM8666792	1	Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP549631		36_1DMUT_LIBRARY_GRO2455A6_S8_L001_R1_001.fastq.gz 36_1DMUT_LIBRARY_GRO2455A6_S8_L001_R2_001.fastq.gz	fastq fastq	59960371084.0	508138738.0	GSM8666792 r1	0:28 1:90	A:16529389286;C:13737763948;G:14793638663;T:14896546895;N:3032292	28	90			16529389286	13737763948	14793638663	14896546895	3032292	SRX26985239	SRS23451897	SRA2028272	Gross, Ophthalmology, University of Pittsburgh	Gross, Ophthalmology, University of Pittsburgh												T	B	sc-like readlen	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-12-05	Multi-stage	Multi-stage	Eye	Sensory System
34266	34266	SRR31620791	SRX26985238	SRS23451896	SRP549631	PRJNA1194578	Tet proteins regulate differentiation potential across retinal cell types	GSE283588	Transcriptome Analysis	Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis–revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq		pubmed:39713311;pubmed:40140485	36hpf sibCTL replicate 2	GSM8666791	source name:eye\|tissue:eye\|age:36\|genotype:sibCTL\|geo loc name:missing\|collection date:missing	36hpf sibCTL replicate 2	Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files	eye		Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		tissue:eye\|age:36\|genotype:sibCTL	GSM8666791	GSM8666791: 36hpf sibCTL replicate 2; Danio rerio; RNA Seq	GSM8666791 r1	GSM8666791	1	Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP549631		36-2_CTL_Library_GRO2554A1_S1_L001_R1_001.fastq.gz 36-2_CTL_Library_GRO2554A1_S1_L001_R2_001.fastq.gz	fastq fastq	75169575046.0	637030297.0	GSM8666791 r1	0:28 1:90	A:20921408123;C:16872043260;G:18114737773;T:19257530991;N:3854899	28	90			20921408123	16872043260	18114737773	19257530991	3854899	SRX26985238	SRS23451896	SRA2028272	Gross, Ophthalmology, University of Pittsburgh	Gross, Ophthalmology, University of Pittsburgh												T	B	sc-like readlen	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-12-05	Multi-stage	Multi-stage	Eye	Sensory System
34267	34267	SRR31620792	SRX26985237	SRS23451894	SRP549631	PRJNA1194578	Tet proteins regulate differentiation potential across retinal cell types	GSE283588	Transcriptome Analysis	Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis–revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq		pubmed:39713311;pubmed:40140485	36hpf sibCTL replicate 1	GSM8666790	source name:eye\|tissue:eye\|age:36\|genotype:sibCTL\|geo loc name:missing\|collection date:missing	36hpf sibCTL replicate 1	Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files	eye		Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		tissue:eye\|age:36\|genotype:sibCTL	GSM8666790	GSM8666790: 36hpf sibCTL replicate 1; Danio rerio; RNA Seq	GSM8666790 r1	GSM8666790	1	Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP549631		36_1CTL_LIBRARY_GRO2455A5_S4_L001_R1_001.fastq.gz 36_1CTL_LIBRARY_GRO2455A5_S4_L001_R2_001.fastq.gz	fastq fastq	70127226422.0	594298529.0	GSM8666790 r1	0:28 1:90	A:19313304121;C:16059894416;G:17310188720;T:17440239265;N:3599900	28	90			19313304121	16059894416	17310188720	17440239265	3599900	SRX26985237	SRS23451894	SRA2028272	Gross, Ophthalmology, University of Pittsburgh	Gross, Ophthalmology, University of Pittsburgh												T	B	sc-like readlen	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-12-05	Multi-stage	Multi-stage	Eye	Sensory System
34268	34268	SRR31620793	SRX26985236	SRS23451895	SRP549631	PRJNA1194578	Tet proteins regulate differentiation potential across retinal cell types	GSE283588	Transcriptome Analysis	Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis–revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq		pubmed:39713311;pubmed:40140485	48hpf dmut replicate 2	GSM8666789	source name:eye\|tissue:eye\|age:48\|genotype:tet2 / tet3 / \|geo loc name:missing\|collection date:missing	48hpf dmut replicate 2	Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files	eye		Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		tissue:eye\|age:48\|genotype:tet2 / tet3 /	GSM8666789	GSM8666789: 48hpf dmut replicate 2; Danio rerio; RNA Seq	GSM8666789 r1	GSM8666789	1	Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP549631		D48_2_GRO1775A18_S13_L001_R1_001.fastq.gz D48_2_GRO1775A18_S13_L001_R2_001.fastq.gz	fastq fastq	49713593756.0	421301642.0	GSM8666789 r1	0:28 1:90	A:13764945916;C:11293471135;G:11713999638;T:12938678190;N:2498877	28	90			13764945916	11293471135	11713999638	12938678190	2498877	SRX26985236	SRS23451895	SRA2028272	Gross, Ophthalmology, University of Pittsburgh	Gross, Ophthalmology, University of Pittsburgh												T	B	sc-like readlen	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-12-05	Multi-stage	Multi-stage	Eye	Sensory System
34269	34269	SRR31620794	SRX26985235	SRS23451893	SRP549631	PRJNA1194578	Tet proteins regulate differentiation potential across retinal cell types	GSE283588	Transcriptome Analysis	Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis–revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq		pubmed:39713311;pubmed:40140485	48hpf dmut replicate 1	GSM8666788	source name:eye\|tissue:eye\|age:48\|genotype:tet2 / tet3 / \|geo loc name:missing\|collection date:missing	48hpf dmut replicate 1	Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files	eye		Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		tissue:eye\|age:48\|genotype:tet2 / tet3 /	GSM8666788	GSM8666788: 48hpf dmut replicate 1; Danio rerio; RNA Seq	GSM8666788 r1	GSM8666788	1	Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP549631		D48_1_GRO1775A16_S6_L001_R1_001.fastq.gz D48_1_GRO1775A16_S6_L001_R2_001.fastq.gz	fastq fastq	61017340862.0	517096109.0	GSM8666788 r1	0:28 1:90	A:16897864299;C:13758942283;G:14653497314;T:15703925956;N:3111010	28	90			16897864299	13758942283	14653497314	15703925956	3111010	SRX26985235	SRS23451893	SRA2028272	Gross, Ophthalmology, University of Pittsburgh	Gross, Ophthalmology, University of Pittsburgh												T	B	sc-like readlen	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-12-05	Multi-stage	Multi-stage	Eye	Sensory System
34270	34270	SRR31620795	SRX26985234	SRS23451891	SRP549631	PRJNA1194578	Tet proteins regulate differentiation potential across retinal cell types	GSE283588	Transcriptome Analysis	Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis–revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq		pubmed:39713311;pubmed:40140485	48hpf sibCTL replicate 2	GSM8666787	source name:eye\|tissue:eye\|age:48\|genotype:sibCTL\|geo loc name:missing\|collection date:missing	48hpf sibCTL replicate 2	Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files	eye		Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		tissue:eye\|age:48\|genotype:sibCTL	GSM8666787	GSM8666787: 48hpf sibCTL replicate 2; Danio rerio; RNA Seq	GSM8666787 r1	GSM8666787	1	Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP549631		C48_2_GRO1775A17_S10_L001_R1_001.fastq.gz C48_2_GRO1775A17_S10_L001_R2_001.fastq.gz	fastq fastq	41617041928.0	352686796.0	GSM8666787 r1	0:28 1:90	A:11784184401;C:9157967637;G:9647105654;T:11025644618;N:2139618	28	90			11784184401	9157967637	9647105654	11025644618	2139618	SRX26985234	SRS23451891	SRA2028272	Gross, Ophthalmology, University of Pittsburgh	Gross, Ophthalmology, University of Pittsburgh												T	B	sc-like readlen	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-12-05	Multi-stage	Multi-stage	Eye	Sensory System
34271	34271	SRR31620796	SRX26985233	SRS23451892	SRP549631	PRJNA1194578	Tet proteins regulate differentiation potential across retinal cell types	GSE283588	Transcriptome Analysis	Tet enzymes are epigenetic modifiers that impact gene expression via 5mC to 5hmC oxidation; 5hmC generation is known to induce chromatin remodeling and promote transcriptional accessibility and therefore gene expression. Previous work demonstrated the requirement for Tet and 5hmC in early retinogenesis–revealing that Tet nulltet2 / ;tet3 / zebrafish exhibit extensive retinal defects. Here we leveraged scRNAseq technologies to better understand cell type specific deficits and molecular signatures underlying the tet2 / ;tet3 / phenotype across differentiation stages. Our results revealed phenotypes in developing tet2 / ;tet3 / retinae including delayed specification of several retinal cell types reduced maturity across late stage tet2 / ;tet3 / cones expansions of immature subpopulations of both horizontal and bipolar cells and altered biases of bipolar cell subtype fates at late differentiation stages. Together these data support Tet proteins as regulators of cell specification lineage fate commitment and terminal differentiation. This study enables a better understanding of how Tet proteins impact the differentiation of many unique yet interacting cell types in a cellularly complex neuronal tissue. Overall design: Embryonic and larval eye cells were collected from 36 48 72 and 120 hpf zebrafish retinae from sibling control sibCTL and tet2 / tet3 / retinae. Dissociated cells were analyzed via scRNAseq		pubmed:39713311;pubmed:40140485	48hpf sibCTL replicate 1	GSM8666786	source name:eye\|tissue:eye\|age:48\|genotype:sibCTL\|geo loc name:missing\|collection date:missing	48hpf sibCTL replicate 1	Generation of base count matrices were generated using cellRangerversion 6.1.2. Low quality cells were removed and ambient RNA correction was performed. post ambient RNA correction normalized logcounts were calcluated Assembly: Danio rerio.GRCz11.106 Supplementary files format and content: matrix files	eye		Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.		tissue:eye\|age:48\|genotype:sibCTL	GSM8666786	GSM8666786: 48hpf sibCTL replicate 1; Danio rerio; RNA Seq	GSM8666786 r1	GSM8666786	1	Whole sibCTL and tet2 / tet3 / eyes were extracted from zebrafish embryos and larvae and were dissociated using either papain or trypsin with genotype and timepoint specific protocols utilized Library was generated using manaufacturer's instructions scRNAseq v2 three prime Paired End. For each experiment in 2 separate wells sibCTL and tet2 / tet3 / dissociated cells were resuspended in 10x mastermix and loaded with gel beads and partitioning oil to generate GEMS. Each GEM contained sufficient priming material to enable cDNA amplification of poly adenylated mRNA molecules with cell specific10x barcode and transcript specificUMI tags. Pooled cDNA was then cleaned up with silane beads and PCR amplified. post PCR amplification cDNAs were size selected using SPRIselect reagent. During library construction P5 and P7 ends were added for sequencing.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP549631		C48_1_GRO1775A15_S2_L001_R1_001.fastq.gz C48_1_GRO1775A15_S2_L001_R2_001.fastq.gz	fastq fastq	54112599182.0	458581349.0	GSM8666786 r1	0:28 1:90	A:15198773029;C:11981463118;G:12618365415;T:14311218195;N:2779425	28	90			15198773029	11981463118	12618365415	14311218195	2779425	SRX26985233	SRS23451892	SRA2028272	Gross, Ophthalmology, University of Pittsburgh	Gross, Ophthalmology, University of Pittsburgh												T	B	sc-like readlen	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-12-05	Multi-stage	Multi-stage	Eye	Sensory System
35500	35500	SRR32834046	SRX28117231	SRS24473011	SRP572644	PRJNA1241156	Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish	GSE292726	Transcriptome Analysis	Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.			mCherry cells early HSPCs 2 dpf	GSM8864259	tissue:Hematopoietic & Immune Cells\|cell type:Hematopoietic & Immune Cells\|geo loc name:missing\|collection date:missing	mCherry cells early HSPCs 2 dpf	For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix	Hematopoietic & Immune Cells	The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	Larvae were maintained in standard conditions at 28C	cell type:Hematopoietic & Immune Cells	GSM8864259	GSM8864259: mCherry cells early HSPCs 2 dpf; Danio rerio; RNA Seq	GSM8864259 r1	GSM8864259	1	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP572644	loader:fastq load.py\|options: readTypes=TBTT read1PairFiles=earlyHSPC 2dpf S5 L003 R1 001.fastq.gz read2PairFiles=earlyHSPC 2dpf S5 L003 R2 001.fastq.gz read3PairFiles=earlyHSPC 2dpf S5 L003 I1 001.fastq.gz read4PairFiles=earlyHSPC 2dpf S5 L003 I2 001.fastq.gz	earlyHSPC_2dpf_S5_L003_I1_001.fastq.gz earlyHSPC_2dpf_S5_L003_I2_001.fastq.gz earlyHSPC_2dpf_S5_L003_R1_001.fastq.gz earlyHSPC_2dpf_S5_L003_R2_001.fastq.gz	fastq fastq fastq fastq	80730897280.0	252284054.0	GSM8864259 r1	0:150 1:150 2:10 3:10	A:10564796609;C:7860706889;G:9394625294;T:8808848403;N:1213630905	150	150	10	10	10564796609	7860706889	9394625294	8808848403	1213630905	SRX28117231	SRS24473011	SRA2098862	Albert Einstein College of Medicine	Albert Einstein College of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-03-24	Multi-stage	Multi-stage	Blood	Hematopoietic System
72819	72819	SRR23190058	SRX19140398	SRS16550346	SRP418629	PRJNA926357	Single cell transcriptional profiles of endothelial cells sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq]	GSE223461	Transcriptome Analysis	To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.	parent bioproject:PRJNA926354	pubmed:39395410	EC MTZ scRNAseq	GSM6956592	source name:Heart\|tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:MTZ	EC MTZ scRNAseq	The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample	Heart	Fish were treated with DMSO or 5 mM MTZ dissolved in fish water for 12 h in the dark. post exposure to chemicals the water was changed to remove the chemicals and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:MTZ	GSM6956592	GSM6956592: EC MTZ scRNAseq; Danio rerio; RNA Seq	GSM6956592 r1	GSM6956592	1	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418629	loader:fastq load.py\|options: readTypes=BBTT read1PairFiles=M S1 L001 R1 001.fastq.gz read2PairFiles=M S1 L001 R2 001.fastq.gz read3PairFiles=M S1 L001 I1 001.fastq.gz read4PairFiles=M S1 L001 I2 001.fastq.gz	M_S1_L001_I1_001.fastq.gz M_S1_L001_I2_001.fastq.gz M_S1_L001_R1_001.fastq.gz M_S1_L001_R2_001.fastq.gz	fastq fastq fastq fastq	10297935498.0	74622721.0	GSM6956592 r1	0:28 1:90 2:10 3:10	A:2422395373;C:2014936837;G:2115011813;T:2251686635;N:1450420	28	90	10	10	2422395373	2014936837	2115011813	2251686635	1450420	SRX19140398	SRS16550346	SRA1578143	Department of Pharmacology, Yamagata University	Department of Pharmacology, Yamagata University	2	0.01687	0.92938	0.00583	0.17709	0.98549	0.82603	0.28254	0.55599	28	90	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Japan	2023-01-22	Multi-stage	Multi-stage	Heart	Cardiovascular System
72820	72820	SRR23190059	SRX19140398	SRS16550346	SRP418629	PRJNA926357	Single cell transcriptional profiles of endothelial cells sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq]	GSE223461	Transcriptome Analysis	To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.	parent bioproject:PRJNA926354	pubmed:39395410	EC MTZ scRNAseq	GSM6956592	source name:Heart\|tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:MTZ	EC MTZ scRNAseq	The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample	Heart	Fish were treated with DMSO or 5 mM MTZ dissolved in fish water for 12 h in the dark. post exposure to chemicals the water was changed to remove the chemicals and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:MTZ	GSM6956592	GSM6956592: EC MTZ scRNAseq; Danio rerio; RNA Seq	GSM6956592 r1	GSM6956592	1	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418629	loader:fastq load.py\|options: readTypes=BBTT read1PairFiles=M S1 L002 R1 001.fastq.gz read2PairFiles=M S1 L002 R2 001.fastq.gz read3PairFiles=M S1 L002 I1 001.fastq.gz read4PairFiles=M S1 L002 I2 001.fastq.gz	M_S1_L002_I1_001.fastq.gz M_S1_L002_I2_001.fastq.gz M_S1_L002_R1_001.fastq.gz M_S1_L002_R2_001.fastq.gz	fastq fastq fastq fastq	10255307022.0	74313819.0	GSM6956592 r2	0:28 1:90 2:10 3:10	A:2413672015;C:2007739816;G:2105898639;T:2240007297;N:1712875	28	90	10	10	2413672015	2007739816	2105898639	2240007297	1712875	SRX19140398	SRS16550346	SRA1578143	Department of Pharmacology, Yamagata University	Department of Pharmacology, Yamagata University	2	0.01711	0.93111	0.00583	0.17637	0.98514	0.82639	0.27373	0.56532	28	90	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Japan	2023-01-22	Multi-stage	Multi-stage	Heart	Cardiovascular System
72821	72821	SRR23190060	SRX19140398	SRS16550346	SRP418629	PRJNA926357	Single cell transcriptional profiles of endothelial cells sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq]	GSE223461	Transcriptome Analysis	To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.	parent bioproject:PRJNA926354	pubmed:39395410	EC MTZ scRNAseq	GSM6956592	source name:Heart\|tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:MTZ	EC MTZ scRNAseq	The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample	Heart	Fish were treated with DMSO or 5 mM MTZ dissolved in fish water for 12 h in the dark. post exposure to chemicals the water was changed to remove the chemicals and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:MTZ	GSM6956592	GSM6956592: EC MTZ scRNAseq; Danio rerio; RNA Seq	GSM6956592 r1	GSM6956592	1	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418629	loader:fastq load.py\|options: readTypes=BBTT read1PairFiles=M S1 L003 R1 001.fastq.gz read2PairFiles=M S1 L003 R2 001.fastq.gz read3PairFiles=M S1 L003 I1 001.fastq.gz read4PairFiles=M S1 L003 I2 001.fastq.gz	M_S1_L003_I1_001.fastq.gz M_S1_L003_I2_001.fastq.gz M_S1_L003_R1_001.fastq.gz M_S1_L003_R2_001.fastq.gz	fastq fastq fastq fastq	10416242898.0	75480021.0	GSM6956592 r3	0:28 1:90 2:10 3:10	A:2449287942;C:2038757909;G:2142133631;T:2275795705;N:667291	28	90	10	10	2449287942	2038757909	2142133631	2275795705	667291	SRX19140398	SRS16550346	SRA1578143	Department of Pharmacology, Yamagata University	Department of Pharmacology, Yamagata University	2	0.01658	0.92887	0.00568	0.17653	0.98593	0.82795	0.28335	0.55226	28	90	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Japan	2023-01-22	Multi-stage	Multi-stage	Heart	Cardiovascular System
72822	72822	SRR23190061	SRX19140398	SRS16550346	SRP418629	PRJNA926357	Single cell transcriptional profiles of endothelial cells sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq]	GSE223461	Transcriptome Analysis	To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.	parent bioproject:PRJNA926354	pubmed:39395410	EC MTZ scRNAseq	GSM6956592	source name:Heart\|tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:MTZ	EC MTZ scRNAseq	The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample	Heart	Fish were treated with DMSO or 5 mM MTZ dissolved in fish water for 12 h in the dark. post exposure to chemicals the water was changed to remove the chemicals and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:MTZ	GSM6956592	GSM6956592: EC MTZ scRNAseq; Danio rerio; RNA Seq	GSM6956592 r1	GSM6956592	1	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418629	loader:fastq load.py\|options: readTypes=BBTT read1PairFiles=M S1 L004 R1 001.fastq.gz read2PairFiles=M S1 L004 R2 001.fastq.gz read3PairFiles=M S1 L004 I1 001.fastq.gz read4PairFiles=M S1 L004 I2 001.fastq.gz	M_S1_L004_I1_001.fastq.gz M_S1_L004_I2_001.fastq.gz M_S1_L004_R1_001.fastq.gz M_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq	10441110360.0	75660220.0	GSM6956592 r4	0:28 1:90 2:10 3:10	A:2455796397;C:2044932269;G:2145932306;T:2280585820;N:659168	28	90	10	10	2455796397	2044932269	2145932306	2280585820	659168	SRX19140398	SRS16550346	SRA1578143	Department of Pharmacology, Yamagata University	Department of Pharmacology, Yamagata University	2	0.01734	0.92942	0.00594	0.17578	0.98502	0.82605	0.27199	0.55089	28	90	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Japan	2023-01-22	Multi-stage	Multi-stage	Heart	Cardiovascular System
72823	72823	SRR23190062	SRX19140397	SRS16550345	SRP418629	PRJNA926357	Single cell transcriptional profiles of endothelial cells sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq]	GSE223461	Transcriptome Analysis	To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.	parent bioproject:PRJNA926354	pubmed:39395410	EC DMSO scRNAseq	GSM6956591	source name:Heart\|tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:DMSO	EC DMSO scRNAseq	The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample	Heart	Fish were treated with DMSO or 5 mM MTZ dissolved in fish water for 12 h in the dark. post exposure to chemicals the water was changed to remove the chemicals and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:DMSO	GSM6956591	GSM6956591: EC DMSO scRNAseq; Danio rerio; RNA Seq	GSM6956591 r1	GSM6956591	1	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418629	loader:fastq load.py\|options: readTypes=BBTT read1PairFiles=D S1 L001 R1 001.fastq.gz read2PairFiles=D S1 L001 R2 001.fastq.gz read3PairFiles=D S1 L001 I1 001.fastq.gz read4PairFiles=D S1 L001 I2 001.fastq.gz	D_S1_L001_I1_001.fastq.gz D_S1_L001_I2_001.fastq.gz D_S1_L001_R1_001.fastq.gz D_S1_L001_R2_001.fastq.gz	fastq fastq fastq fastq	10595595012.0	76779674.0	GSM6956591 r1	0:28 1:90 2:10 3:10	A:2544857509;C:2041473878;G:2166945643;T:2305102603;N:1621899	28	90	10	10	2544857509	2041473878	2166945643	2305102603	1621899	SRX19140397	SRS16550345	SRA1578143	Department of Pharmacology, Yamagata University	Department of Pharmacology, Yamagata University	2	0.01657	0.92608	0.00601	0.18008	0.98602	0.82844	0.27705	0.55772	28	90	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Japan	2023-01-22	Multi-stage	Multi-stage	Heart	Cardiovascular System
72824	72824	SRR23190063	SRX19140397	SRS16550345	SRP418629	PRJNA926357	Single cell transcriptional profiles of endothelial cells sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq]	GSE223461	Transcriptome Analysis	To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.	parent bioproject:PRJNA926354	pubmed:39395410	EC DMSO scRNAseq	GSM6956591	source name:Heart\|tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:DMSO	EC DMSO scRNAseq	The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample	Heart	Fish were treated with DMSO or 5 mM MTZ dissolved in fish water for 12 h in the dark. post exposure to chemicals the water was changed to remove the chemicals and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:DMSO	GSM6956591	GSM6956591: EC DMSO scRNAseq; Danio rerio; RNA Seq	GSM6956591 r1	GSM6956591	1	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418629	loader:fastq load.py\|options: readTypes=BBTT read1PairFiles=D S1 L002 R1 001.fastq.gz read2PairFiles=D S1 L002 R2 001.fastq.gz read3PairFiles=D S1 L002 I1 001.fastq.gz read4PairFiles=D S1 L002 I2 001.fastq.gz	D_S1_L002_I1_001.fastq.gz D_S1_L002_I2_001.fastq.gz D_S1_L002_R1_001.fastq.gz D_S1_L002_R2_001.fastq.gz	fastq fastq fastq fastq	10505133804.0	76124158.0	GSM6956591 r2	0:28 1:90 2:10 3:10	A:2524419025;C:2024371965;G:2148601948;T:2283479741;N:1777965	28	90	10	10	2524419025	2024371965	2148601948	2283479741	1777965	SRX19140397	SRS16550345	SRA1578143	Department of Pharmacology, Yamagata University	Department of Pharmacology, Yamagata University	2	0.01639	0.92559	0.00547	0.17815	0.98524	0.83004	0.2875	0.56427	28	90	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Japan	2023-01-22	Multi-stage	Multi-stage	Heart	Cardiovascular System
72825	72825	SRR23190064	SRX19140397	SRS16550345	SRP418629	PRJNA926357	Single cell transcriptional profiles of endothelial cells sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq]	GSE223461	Transcriptome Analysis	To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.	parent bioproject:PRJNA926354	pubmed:39395410	EC DMSO scRNAseq	GSM6956591	source name:Heart\|tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:DMSO	EC DMSO scRNAseq	The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample	Heart	Fish were treated with DMSO or 5 mM MTZ dissolved in fish water for 12 h in the dark. post exposure to chemicals the water was changed to remove the chemicals and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:DMSO	GSM6956591	GSM6956591: EC DMSO scRNAseq; Danio rerio; RNA Seq	GSM6956591 r1	GSM6956591	1	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418629	loader:fastq load.py\|options: readTypes=BBTT read1PairFiles=D S1 L003 R1 001.fastq.gz read2PairFiles=D S1 L003 R2 001.fastq.gz read3PairFiles=D S1 L003 I1 001.fastq.gz read4PairFiles=D S1 L003 I2 001.fastq.gz	D_S1_L003_I1_001.fastq.gz D_S1_L003_I2_001.fastq.gz D_S1_L003_R1_001.fastq.gz D_S1_L003_R2_001.fastq.gz	fastq fastq fastq fastq	10715702622.0	77650019.0	GSM6956591 r3	0:28 1:90 2:10 3:10	A:2573807593;C:2065042721;G:2193827962;T:2329228642;N:795324	28	90	10	10	2573807593	2065042721	2193827962	2329228642	795324	SRX19140397	SRS16550345	SRA1578143	Department of Pharmacology, Yamagata University	Department of Pharmacology, Yamagata University	2	0.0164	0.92651	0.00558	0.17924	0.98559	0.82816	0.27685	0.56637	28	90	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Japan	2023-01-22	Multi-stage	Multi-stage	Heart	Cardiovascular System
72826	72826	SRR23190065	SRX19140397	SRS16550345	SRP418629	PRJNA926357	Single cell transcriptional profiles of endothelial cells sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq]	GSE223461	Transcriptome Analysis	To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.	parent bioproject:PRJNA926354	pubmed:39395410	EC DMSO scRNAseq	GSM6956591	source name:Heart\|tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:DMSO	EC DMSO scRNAseq	The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample	Heart	Fish were treated with DMSO or 5 mM MTZ dissolved in fish water for 12 h in the dark. post exposure to chemicals the water was changed to remove the chemicals and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:DMSO	GSM6956591	GSM6956591: EC DMSO scRNAseq; Danio rerio; RNA Seq	GSM6956591 r1	GSM6956591	1	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418629	loader:fastq load.py\|options: readTypes=BBTT read1PairFiles=D S1 L004 R1 001.fastq.gz read2PairFiles=D S1 L004 R2 001.fastq.gz read3PairFiles=D S1 L004 I1 001.fastq.gz read4PairFiles=D S1 L004 I2 001.fastq.gz	D_S1_L004_I1_001.fastq.gz D_S1_L004_I2_001.fastq.gz D_S1_L004_R1_001.fastq.gz D_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq	10731126882.0	77761789.0	GSM6956591 r4	0:28 1:90 2:10 3:10	A:2577638514;C:2068754148;G:2196571470;T:2332228096;N:698874	28	90	10	10	2577638514	2068754148	2196571470	2332228096	698874	SRX19140397	SRS16550345	SRA1578143	Department of Pharmacology, Yamagata University	Department of Pharmacology, Yamagata University	2	0.01687	0.9273	0.00577	0.18031	0.98476	0.82954	0.28103	0.55337	28	90	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Japan	2023-01-22	Multi-stage	Multi-stage	Heart	Cardiovascular System

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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");;