run_metadata
94 rows where devstage_curation_coarse = "Multi-stage" and technology = "10x"
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| Link | rowid ▼ | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | 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 | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
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| 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 | ||||||||||||||||||||
| 52209 | 52209 | SRR8992787 | SRX5771765 | SRS4705624 | SRP194294 | PRJNA540521 | Fate plasticity and reprogramming in genetically distinct populations of Danio leucophores | GSE130526 | Other | Understanding genetic and cellular bases of adult form remains a fundamental goal at the intersection of developmental and evolutionary biology. The skin pigment cells of vertebrates derived from embryonic neural crest are a useful system for elucidating mechanisms of fate specification pattern formation and how particular phenotypes impact organismal behavior and ecology. In a survey of Danio fishes including zebrafish Danio rerio we identified two populations of white pigment cells—leucophores—one of which arises by transdifferentiation of adult melanophores and another that develops from a yellow/orange xanthophore like progenitor. Single cell transcriptomic mutational chemical and ultrastructural analyses of zebrafish leucophores revealed cell type specific chemical compositions organelle configurations and genetic requirements. At the organismal level we identified distinct physiological responses of leucophores during environmental background matching and we show that leucophore complement influences behavior. Together our studies revealed new independently arisen pigment cell types and mechanisms of fate acquisition in zebrafish and illustrate how concerted analyses across hierarchical levels can provide insights into phenotypes and their evolution. Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform using zebrafish fin pigment cells FACs sorted for mCherry. For additional details see associated publication | pubmed:31138706 | Zebrafish fin pigment cells | GSM3741778 | tissue:Dorsal and anal fins|cell type:pigment cells|treatment:Untreated | Zebrafish fin pigment cells | Expression matrix files were generated using cellranger 10X genomics version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Genome build: GRCz11/danRer11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files. | Dorsal and anal fins | Fins were amputated from fish expressing both pnp4a:palmmCherry and tyrp1b:palmmCherry. To approximately normalize capture of relevant cell types by quantity and improve the likelihood of recovering cells at intermediate states of differentiation we extracted distal dorsal fin regions 10 mm standard length SL; n=20 and proximal interstripe anal fin regions 14 mm SL; n=10. Tissue was enzymatically dissociated with Liberase 0.25 mg/mL in dPBS at 25°C for 15 min followed by manual trituration with a flame polished glass pipette for 5 min. Cell suspensions were then filtered through a 70 μm Nylon cell strainer to obtain a single cell suspension. Liberated cells were re suspended in 1% BSA / 5% FBS in dPBS and DAPI 0.1 μg/mL 15 min before FACS purification. All plastic and glass surfaces of cell contact were coated with 1% BSA in dPBS before to use. Prior to sorting for fluorescence levels single cells were isolated by sequentially gating cells according to their SSC A vs. FSC A FSC H vs FSC W and SSC H vs SSC W profiles according to standard flow cytometry practices. Cells with high levels of DAPI staining were excluded as dead or damaged. Cells from wild type zebrafish were used as negative control to determine gates for detection of mCherry and GFP fluorescence and then cells from transgenic fish were purified according to these gates. All samples were kept on ice except during Liberase incubation and then sorted chilled. | 10X genomics V1 protocol following manufacturer recommendations. | Fish were maintained at 28.5C with 10 h : 14 h light:dark conditions. Larvae were reared with marine rotifers supplemented with Artemac Aquafauna followed by Artemia and flake food. Adults were maintained on Artemia and flake food. Fish stocks of Danio rerio: WTABb a derivative of inbred ABwp Tgtyrp1b:palm mCherrywp.rt11 Tgpnp4a:palmmCherrywp.rt10 | cell type:pigment cells|treatment:Untreated | GSM3741778 | GSM3741778: Zebrafish fin pigment cells; Danio rerio; RNA Seq | GSM3741778 | 1 | 10X genomics V1 protocol following manufacturer recommendations. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP194294 | leucophore_S9_L003_R2_001.fastq.gz leucophore_S9_L004_R1_001.fastq.gz | fastq fastq | 424061944.0 | 10241510.0 | GSM3741778 r1 | 0:26 1:57 | A:119042142;C:89897538;G:98172861;T:116716009;N:233394 | 26 | 57 | 119042142 | 89897538 | 98172861 | 116716009 | 233394 | SRX5771765 | SRS4705624 | SRA881136 | GEO | Parichy Lab, Biology, University of Washington | 1 | 0.33934 | 0.07693 | 0.8742 | 0.51425 | 57 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2019-04-30 | Multi-stage | Multi-stage | Fin | Surface Structure | |||||||||||||||||
| 52250 | 52250 | SRR9050625 | SRX5827016 | SRS4754830 | SRP198298 | PRJNA542704 | Thyroid hormone regulates distinct paths to maturation in pigment cell lineages | GSE131136 | Transcriptome Analysis | Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone. | pubmed:31140974;pubmed:33933422 | Neural crest derived cells from hypothyroid juvenile zebrafish trunks biological replicate 1 | GSM3764572 | tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:2135 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 11 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid | Neural crest derived cells from hypothyroid juvenile zebrafish trunks biological replicate 1 | Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files. | sox10:Cre+ cells from post embryonic zebrafish trunk tissue | Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations. | 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. | Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms. | cell type:2135 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 11 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid | GSM3764572 | GSM3764572: Neural crest derived cells from hypothyroid juvenile zebrafish trunks biological replicate 1; Danio rerio; RNA Seq | GSM3764572 | 1 | 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP198298 | dangling references:treat as unmapped | hypo7_possorted_genome_bam.bam | 10X Genomics bam file | 5078170983.0 | 89090719.0 | GSM3764572 r1 | 0:57 | A:1526791201;C:989860604;G:1192544480;T:1366270035;N:2704663 | 57 | 1526791201 | 989860604 | 1192544480 | 1366270035 | 2704663 | SRX5827016 | SRS4754830 | SRA886020 | GEO | Biology, University of Virginia | 1 | 0.92899 | 0.25348 | 0.83571 | 0.48794 | 57 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2019-05-13 | Multi-stage | Multi-stage | Trunk | Surface Structure | |||||||||||||||||
| 52256 | 52256 | SRR9050619 | SRX5827010 | SRS4754824 | SRP198298 | PRJNA542704 | Thyroid hormone regulates distinct paths to maturation in pigment cell lineages | GSE131136 | Transcriptome Analysis | Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone. | pubmed:31140974;pubmed:33933422 | Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 1 | GSM3764566 | tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:2168 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Zebrafish were stage 11 SSL stage juvenile.|treatment:Euthyroid | Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 1 | Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files. | sox10:Cre+ cells from post embryonic zebrafish trunk tissue | Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations. | 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. | Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms. | cell type:2168 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Zebrafish were stage 11 SSL stage juvenile.|treatment:Euthyroid | GSM3764566 | GSM3764566: Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 1; Danio rerio; RNA Seq | GSM3764566 | 1 | 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP198298 | dangling references:treat as unmapped | eu6_possorted_genome_bam.bam | 10X Genomics bam file | 5005233954.0 | 87811122.0 | GSM3764566 r1 | 0:57 | A:1531421605;C:966957285;G:1151579626;T:1352667292;N:2608146 | 57 | 1531421605 | 966957285 | 1151579626 | 1352667292 | 2608146 | SRX5827010 | SRS4754824 | SRA886020 | GEO | Biology, University of Virginia | 1 | 0.92288 | 0.25231 | 0.83479 | 0.5014 | 57 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2019-05-13 | Multi-stage | Multi-stage | Trunk | Surface Structure | |||||||||||||||||
| 55196 | 55196 | SRR10153191 | SRX6878621 | SRS5414403 | SRP222786 | PRJNA573063 | Single cell transcriptomic analysis of two models of zebrafish beta catenin driven HCC | GSE137784 | Transcriptome Analysis | Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of three 6mpf liver samples from three different transgenic lines with/without xxx hydroxytamoxifen TAM treatment. | parent bioproject:PRJNA573068 | pubmed:31575545 | NoHCC [Single cell] | GSM4087821 | tissue:Liver|transgenic line:Tgfabp10a flox beta catenin|age:6 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf HCC | NoHCC [Single cell] | 10x Genomics’ Cell Ranger software v2.2.0 executed primary data analysis for each sample. Pipeline 'cellranger mkfastq' generated R1 26 bp and R2 100 bp FASTQ files. Custom transgenic genomic reference was built with ‘cellranger mkref’ but shared the common Danio rerio genome reference build GRCz11 with annotations from Ensembl release 94. The Ensembl gene annotations were filtered with ‘cellranger mkgtf’ for gene biotypes matching ‘protein coding’ ‘lincRNA’ and ‘antisense’ tags. All samples had additional transgenic sequence/annotations added. Each sample was processed with ‘cellranger count’ pipeline with their respective transgenic genome build with parameter ‘ expect cells=3000’ In attempt to recover those perhaps lower quality GEM partitions the raw gene barcode matrices from ‘cellranger count’ located in ‘outs/raw gene bc matrices’ was processed with the EmptyDrops algorithm R package DropletUtils v1.2.2 to discriminate cells from background GEM partitions at a false discovery rate FDR of 1% Lun ATL et al. 2019. GEM partitions with 500 UMI counts or less were considered to be devoid of viable cells while those with at least 10 000 UMI counts were automatically considered to be cells. Cell based QC metrics were calculated with R package scater v1.10.1 using the calculateQCMetrics function McCarthy DJ et al. 2017. Principal component analysis PCA on the cell based QC metrics combined with a multivariate outlier method flagged cells with outlying values in QC metrics as suspect P. Filzmoser et al. 2008. Cells with extremely low UMI counts extremely low gene counts or extremely high percentage of expression attributed to mitochondrial genes were also flagged as low quality. Extremeness in any of these three measures was determined by 3 median absolute deviations from the median with the scater::isOutlier function applied to each sample individually. Additionally cells were required to have greater than 800 UMIs and less than 20% of total expression attributed to mitochondrial transcripts. Those cells… | Liver | Larvae for Samples 2 and 3 were treated with 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf | Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank’s Buffered Saline Solution HBSS without xxx red with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter and the filtrate was centrifuged at 1200 RPM 4C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin. The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific. The Chromium Single Cell Gene Expression Solution with 3’ chemistry version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction. Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs the micro droplets. Within individual GEMs cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53°C for 45 min followed by 85°C for 5 min. Subsequent A tailing end repair adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three prime RNA Se… | Fish were raised following IACUC approved protocols in insititutional zebrafish facility. | transgenic line:Tgfabp10a flox beta catenin|age:6 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf HCC | GSM4087821 | GSM4087821: NoHCC [Single cell]; Danio rerio; RNA Seq | GSM4087821 | 1 | Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank's Buffered Saline Solution HBSS without xxx red with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter and the filtrate was centrifuged at 1200 RPM 4C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin. The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific. The Chromium Single Cell Gene Expression Solution with three prime chemistry version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction. Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs the micro droplets. Within individual GEMs cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53°C for 45 min followed by 85°C for 5 min. Subsequent A tailing end repair adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three pri… | GEO Accession:GSM4087821 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP222786 | 15547X4_S11_L007_R2_001.fastq.gz 15547X4_S11_L007_R1_001.fastq.gz | fastq fastq | 16861988178.0 | 133825303.0 | GSM4087821 r1 | 0:26 1:100 | A:4788108995;C:3905645218;G:3694064311;T:4468647482;N:5522172 | 26 | 100 | 4788108995 | 3905645218 | 3694064311 | 4468647482 | 5522172 | SRX6878621 | SRS5414403 | SRA965504 | GEO | Pathology, University of California, San Francisco | 2 | 0.00236 | 0.93017 | 0.0008 | 0.04645 | 0.99626 | 0.89043 | 0.52233 | 0.64352 | 26 | 100 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2019-09-20 | Multi-stage | Multi-stage | Liver | Liver and Biliary System | |||||||||
| 55197 | 55197 | SRR10153190 | SRX6878620 | SRS5414402 | SRP222786 | PRJNA573063 | Single cell transcriptomic analysis of two models of zebrafish beta catenin driven HCC | GSE137784 | Transcriptome Analysis | Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of three 6mpf liver samples from three different transgenic lines with/without xxx hydroxytamoxifen TAM treatment. | parent bioproject:PRJNA573068 | pubmed:31575545 | HCCCreLox [Single cell] | GSM4087820 | tissue:Liver|transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:6 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf | HCCCreLox [Single cell] | 10x Genomics’ Cell Ranger software v2.2.0 executed primary data analysis for each sample. Pipeline 'cellranger mkfastq' generated R1 26 bp and R2 100 bp FASTQ files. Custom transgenic genomic reference was built with ‘cellranger mkref’ but shared the common Danio rerio genome reference build GRCz11 with annotations from Ensembl release 94. The Ensembl gene annotations were filtered with ‘cellranger mkgtf’ for gene biotypes matching ‘protein coding’ ‘lincRNA’ and ‘antisense’ tags. All samples had additional transgenic sequence/annotations added. Each sample was processed with ‘cellranger count’ pipeline with their respective transgenic genome build with parameter ‘ expect cells=3000’ In attempt to recover those perhaps lower quality GEM partitions the raw gene barcode matrices from ‘cellranger count’ located in ‘outs/raw gene bc matrices’ was processed with the EmptyDrops algorithm R package DropletUtils v1.2.2 to discriminate cells from background GEM partitions at a false discovery rate FDR of 1% Lun ATL et al. 2019. GEM partitions with 500 UMI counts or less were considered to be devoid of viable cells while those with at least 10 000 UMI counts were automatically considered to be cells. Cell based QC metrics were calculated with R package scater v1.10.1 using the calculateQCMetrics function McCarthy DJ et al. 2017. Principal component analysis PCA on the cell based QC metrics combined with a multivariate outlier method flagged cells with outlying values in QC metrics as suspect P. Filzmoser et al. 2008. Cells with extremely low UMI counts extremely low gene counts or extremely high percentage of expression attributed to mitochondrial genes were also flagged as low quality. Extremeness in any of these three measures was determined by 3 median absolute deviations from the median with the scater::isOutlier function applied to each sample individually. Additionally cells were required to have greater than 800 UMIs and less than 20% of total expression attributed to mitochondrial transcripts. Those cells… | Liver | Larvae for Samples 2 and 3 were treated with 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf | Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank’s Buffered Saline Solution HBSS without xxx red with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter and the filtrate was centrifuged at 1200 RPM 4C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin. The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific. The Chromium Single Cell Gene Expression Solution with 3’ chemistry version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction. Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs the micro droplets. Within individual GEMs cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53°C for 45 min followed by 85°C for 5 min. Subsequent A tailing end repair adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three prime RNA Se… | Fish were raised following IACUC approved protocols in insititutional zebrafish facility. | transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:6 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf | GSM4087820 | GSM4087820: HCCCreLox [Single cell]; Danio rerio; RNA Seq | GSM4087820 | 1 | Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank's Buffered Saline Solution HBSS without xxx red with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter and the filtrate was centrifuged at 1200 RPM 4C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin. The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific. The Chromium Single Cell Gene Expression Solution with three prime chemistry version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction. Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs the micro droplets. Within individual GEMs cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53°C for 45 min followed by 85°C for 5 min. Subsequent A tailing end repair adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three pri… | GEO Accession:GSM4087820 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP222786 | 15547X2_S9_L006_R1_001.fastq.gz 15547X2_S9_L006_R2_001.fastq.gz | fastq fastq | 16758654318.0 | 133005193.0 | GSM4087820 r1 | 0:26 1:100 | A:4758015356;C:3904784528;G:3787834220;T:4302283542;N:5736672 | 26 | 100 | 4758015356 | 3904784528 | 3787834220 | 4302283542 | 5736672 | SRX6878620 | SRS5414402 | SRA965504 | GEO | Pathology, University of California, San Francisco | 2 | 0.00291 | 0.94432 | 0.00084 | 0.04281 | 0.99539 | 0.88203 | 0.48041 | 0.60684 | 26 | 100 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2019-09-20 | Multi-stage | Multi-stage | Liver | Liver and Biliary System | |||||||||
| 59859 | 59859 | SRR12054798 | SRX8583217 | SRS6874834 | SRP268010 | PRJNA640615 | Molecular classification of zebrafish retinal ganglion cells links genes to behavior | GSE152842 | Transcriptome Analysis | Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. | pubmed:33357413 | Adult Zebrafish 15 | GSM4627227 | source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina | Adult Zebrafish 15 | Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using “cellranger count” with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples | Zebrafish retina 4 mpf 6 mpf | All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed. | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3’ v2 platform 10X Genomics Pleasanton CA | Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES. | tissue:retina | GSM4627227 | GSM4627227: Adult Zebrafish 15; Danio rerio; RNA Seq | GSM4627227 | 1 | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA | GEO Accession:GSM4627227 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP268010 | assembly:GRCz10|intentional duplicate | ZebrafishRGC15.bam | 10X Genomics bam file | 17489597440.0 | 178465280.0 | GSM4627227 r1 | 0:98 | A:5144837324;C:3453657332;G:3688751956;T:5199397147;N:2953681 | 98 | 5144837324 | 3453657332 | 3688751956 | 5199397147 | 2953681 | SRX8583217 | SRS6874834 | SRA1089100 | GEO | Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley | 1 | 0.88384 | 0.24019 | 0.78979 | 0.51275 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2020-06-19 | Multi-stage | Multi-stage | Eye | Sensory System | ||||||||||||||||
| 59860 | 59860 | SRR12054797 | SRX8583216 | SRS6874833 | SRP268010 | PRJNA640615 | Molecular classification of zebrafish retinal ganglion cells links genes to behavior | GSE152842 | Transcriptome Analysis | Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. | pubmed:33357413 | Adult Zebrafish 14 | GSM4627226 | source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina | Adult Zebrafish 14 | Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using “cellranger count” with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples | Zebrafish retina 4 mpf 6 mpf | All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed. | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3’ v2 platform 10X Genomics Pleasanton CA | Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES. | tissue:retina | GSM4627226 | GSM4627226: Adult Zebrafish 14; Danio rerio; RNA Seq | GSM4627226 | 1 | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA | GEO Accession:GSM4627226 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP268010 | assembly:GRCz10|intentional duplicate | ZebrafishRGC14.bam | 10X Genomics bam file | 16163588938.0 | 164934581.0 | GSM4627226 r1 | 0:98 | A:4767424342;C:3189871576;G:3410422503;T:4793151919;N:2718598 | 98 | 4767424342 | 3189871576 | 3410422503 | 4793151919 | 2718598 | SRX8583216 | SRS6874833 | SRA1089100 | GEO | Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley | 1 | 0.88242 | 0.24257 | 0.78892 | 0.49263 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2020-06-19 | Multi-stage | Multi-stage | Eye | Sensory System | ||||||||||||||||
| 59861 | 59861 | SRR12054796 | SRX8583215 | SRS6874832 | SRP268010 | PRJNA640615 | Molecular classification of zebrafish retinal ganglion cells links genes to behavior | GSE152842 | Transcriptome Analysis | Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. | pubmed:33357413 | Adult Zebrafish 13 | GSM4627225 | source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina | Adult Zebrafish 13 | Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using “cellranger count” with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples | Zebrafish retina 4 mpf 6 mpf | All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed. | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3’ v2 platform 10X Genomics Pleasanton CA | Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES. | tissue:retina | GSM4627225 | GSM4627225: Adult Zebrafish 13; Danio rerio; RNA Seq | GSM4627225 | 1 | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA | GEO Accession:GSM4627225 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP268010 | assembly:GRCz10|intentional duplicate | ZebrafishRGC13.bam | 10X Genomics bam file | 14166392450.0 | 144555025.0 | GSM4627225 r1 | 0:98 | A:4156001799;C:2794969042;G:2979050667;T:4233954883;N:2416059 | 98 | 4156001799 | 2794969042 | 2979050667 | 4233954883 | 2416059 | SRX8583215 | SRS6874832 | SRA1089100 | GEO | Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley | 1 | 0.88338 | 0.24795 | 0.7893 | 0.49627 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2020-06-19 | Multi-stage | Multi-stage | Eye | Sensory System | ||||||||||||||||
| 59862 | 59862 | SRR12054795 | SRX8583214 | SRS6874831 | SRP268010 | PRJNA640615 | Molecular classification of zebrafish retinal ganglion cells links genes to behavior | GSE152842 | Transcriptome Analysis | Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. | pubmed:33357413 | Adult Zebrafish 12 | GSM4627224 | source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina | Adult Zebrafish 12 | Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using “cellranger count” with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples | Zebrafish retina 4 mpf 6 mpf | All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed. | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3’ v2 platform 10X Genomics Pleasanton CA | Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES. | tissue:retina | GSM4627224 | GSM4627224: Adult Zebrafish 12; Danio rerio; RNA Seq | GSM4627224 | 1 | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA | GEO Accession:GSM4627224 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP268010 | assembly:GRCz10|intentional duplicate | ZebrafishRGC12.bam | 10X Genomics bam file | 15484230986.0 | 158002357.0 | GSM4627224 r1 | 0:98 | A:4556531984;C:3035955488;G:3233886544;T:4655230637;N:2626333 | 98 | 4556531984 | 3035955488 | 3233886544 | 4655230637 | 2626333 | SRX8583214 | SRS6874831 | SRA1089100 | GEO | Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley | 1 | 0.88248 | 0.25141 | 0.78782 | 0.49785 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2020-06-19 | Multi-stage | Multi-stage | Eye | Sensory System | ||||||||||||||||
| 59863 | 59863 | SRR12054794 | SRX8583213 | SRS6874830 | SRP268010 | PRJNA640615 | Molecular classification of zebrafish retinal ganglion cells links genes to behavior | GSE152842 | Transcriptome Analysis | Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. | pubmed:33357413 | Adult Zebrafish 11 | GSM4627223 | source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina | Adult Zebrafish 11 | Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using “cellranger count” with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples | Zebrafish retina 4 mpf 6 mpf | All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed. | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3’ v2 platform 10X Genomics Pleasanton CA | Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES. | tissue:retina | GSM4627223 | GSM4627223: Adult Zebrafish 11; Danio rerio; RNA Seq | GSM4627223 | 1 | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA | GEO Accession:GSM4627223 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP268010 | assembly:GRCz10|intentional duplicate | ZebrafishRGC11.bam | 10X Genomics bam file | 18012879710.0 | 183804895.0 | GSM4627223 r1 | 0:98 | A:5278772392;C:3561457870;G:3799039640;T:5370568922;N:3040886 | 98 | 5278772392 | 3561457870 | 3799039640 | 5370568922 | 3040886 | SRX8583213 | SRS6874830 | SRA1089100 | GEO | Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley | 1 | 0.88456 | 0.25211 | 0.7894 | 0.50115 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2020-06-19 | Multi-stage | Multi-stage | Eye | Sensory System | ||||||||||||||||
| 59864 | 59864 | SRR12054791 | SRX8583210 | SRS6874827 | SRP268010 | PRJNA640615 | Molecular classification of zebrafish retinal ganglion cells links genes to behavior | GSE152842 | Transcriptome Analysis | Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. | pubmed:33357413 | Adult Zebrafish 8 | GSM4627220 | source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina | Adult Zebrafish 8 | Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using “cellranger count” with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples | Zebrafish retina 4 mpf 6 mpf | All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed. | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3’ v2 platform 10X Genomics Pleasanton CA | Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES. | tissue:retina | GSM4627220 | GSM4627220: Adult Zebrafish 8; Danio rerio; RNA Seq | GSM4627220 | 1 | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA | GEO Accession:GSM4627220 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP268010 | assembly:GRCz10|intentional duplicate | ZebrafishRGC8.bam | 10X Genomics bam file | 14551197976.0 | 148481612.0 | GSM4627220 r1 | 0:98 | A:4325239722;C:2863430626;G:2994943270;T:4365215038;N:2369320 | 98 | 4325239722 | 2863430626 | 2994943270 | 4365215038 | 2369320 | SRX8583210 | SRS6874827 | SRA1089100 | GEO | Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley | 1 | 0.87211 | 0.29067 | 0.79431 | 0.49957 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2020-06-19 | Multi-stage | Multi-stage | Eye | Sensory System | ||||||||||||||||
| 59865 | 59865 | SRR12054790 | SRX8583209 | SRS6874826 | SRP268010 | PRJNA640615 | Molecular classification of zebrafish retinal ganglion cells links genes to behavior | GSE152842 | Transcriptome Analysis | Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. | pubmed:33357413 | Adult Zebrafish 7 | GSM4627219 | source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina | Adult Zebrafish 7 | Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using “cellranger count” with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples | Zebrafish retina 4 mpf 6 mpf | All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed. | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3’ v2 platform 10X Genomics Pleasanton CA | Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES. | tissue:retina | GSM4627219 | GSM4627219: Adult Zebrafish 7; Danio rerio; RNA Seq | GSM4627219 | 1 | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA | GEO Accession:GSM4627219 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP268010 | assembly:GRCz10|intentional duplicate | ZebrafishRGC7.bam | 10X Genomics bam file | 12894390180.0 | 131575410.0 | GSM4627219 r1 | 0:98 | A:3809964234;C:2548974567;G:2667179504;T:3866166531;N:2105344 | 98 | 3809964234 | 2548974567 | 2667179504 | 3866166531 | 2105344 | SRX8583209 | SRS6874826 | SRA1089100 | GEO | Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley | 1 | 0.87565 | 0.28214 | 0.78918 | 0.51085 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2020-06-19 | Multi-stage | Multi-stage | Eye | Sensory System | ||||||||||||||||
| 59866 | 59866 | SRR12054789 | SRX8583208 | SRS6874825 | SRP268010 | PRJNA640615 | Molecular classification of zebrafish retinal ganglion cells links genes to behavior | GSE152842 | Transcriptome Analysis | Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. | pubmed:33357413 | Adult Zebrafish 6 | GSM4627218 | source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina | Adult Zebrafish 6 | Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using “cellranger count” with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples | Zebrafish retina 4 mpf 6 mpf | All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed. | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3’ v2 platform 10X Genomics Pleasanton CA | Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES. | tissue:retina | GSM4627218 | GSM4627218: Adult Zebrafish 6; Danio rerio; RNA Seq | GSM4627218 | 1 | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA | GEO Accession:GSM4627218 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP268010 | assembly:GRCz10|intentional duplicate | ZebrafishRGC6.bam | 10X Genomics bam file | 11333584262.0 | 115648819.0 | GSM4627218 r1 | 0:98 | A:3357618948;C:2223130462;G:2352697999;T:3398318533;N:1818320 | 98 | 3357618948 | 2223130462 | 2352697999 | 3398318533 | 1818320 | SRX8583208 | SRS6874825 | SRA1089100 | GEO | Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley | 1 | 0.87718 | 0.26282 | 0.7838 | 0.50701 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2020-06-19 | Multi-stage | Multi-stage | Eye | Sensory System | ||||||||||||||||
| 59867 | 59867 | SRR12054786 | SRX8583205 | SRS6874822 | SRP268010 | PRJNA640615 | Molecular classification of zebrafish retinal ganglion cells links genes to behavior | GSE152842 | Transcriptome Analysis | Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. | pubmed:33357413 | Adult Zebrafish 3 | GSM4627215 | source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina | Adult Zebrafish 3 | Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using “cellranger count” with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples | Zebrafish retina 4 mpf 6 mpf | All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed. | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3’ v2 platform 10X Genomics Pleasanton CA | Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES. | tissue:retina | GSM4627215 | GSM4627215: Adult Zebrafish 3; Danio rerio; RNA Seq | GSM4627215 | 1 | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA | GEO Accession:GSM4627215 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP268010 | assembly:GRCz10|intentional duplicate | ZebrafishRGC3.bam | 10X Genomics bam file | 22433937540.0 | 228917730.0 | GSM4627215 r1 | 0:98 | A:6661186629;C:4423555909;G:4672058698;T:6668698022;N:8438282 | 98 | 6661186629 | 4423555909 | 4672058698 | 6668698022 | 8438282 | SRX8583205 | SRS6874822 | SRA1089100 | GEO | Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley | 1 | 0.88295 | 0.30604 | 0.79228 | 0.53139 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2020-06-19 | Multi-stage | Multi-stage | Eye | Sensory System | ||||||||||||||||
| 59868 | 59868 | SRR12054785 | SRX8583204 | SRS6874821 | SRP268010 | PRJNA640615 | Molecular classification of zebrafish retinal ganglion cells links genes to behavior | GSE152842 | Transcriptome Analysis | Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. | pubmed:33357413 | Adult Zebrafish 2 | GSM4627214 | source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina | Adult Zebrafish 2 | Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using “cellranger count” with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples | Zebrafish retina 4 mpf 6 mpf | All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed. | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3’ v2 platform 10X Genomics Pleasanton CA | Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES. | tissue:retina | GSM4627214 | GSM4627214: Adult Zebrafish 2; Danio rerio; RNA Seq | GSM4627214 | 1 | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA | GEO Accession:GSM4627214 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP268010 | assembly:GRCz10|intentional duplicate | ZebrafishRGC2.bam | 10X Genomics bam file | 25334714412.0 | 258517494.0 | GSM4627214 r1 | 0:98 | A:7365387325;C:5107021128;G:5455973330;T:7396374911;N:9957718 | 98 | 7365387325 | 5107021128 | 5455973330 | 7396374911 | 9957718 | SRX8583204 | SRS6874821 | SRA1089100 | GEO | Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley | 1 | 0.90152 | 0.22907 | 0.78776 | 0.50123 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2020-06-19 | Multi-stage | Multi-stage | Eye | Sensory System | ||||||||||||||||
| 59869 | 59869 | SRR12054784 | SRX8583203 | SRS6874820 | SRP268010 | PRJNA640615 | Molecular classification of zebrafish retinal ganglion cells links genes to behavior | GSE152842 | Transcriptome Analysis | Retinal ganglion cells RGCs form an array of feature detectors which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single cell transcriptomics we systematically classified RGCs in adult and larval zebrafish thereby identifying marker genes for >30 stable and several transient cell types cell type specific markers and their maturational changes. We used this catalog to engineer transgenic driverreporter lines enabling experimental genetic access to specific RGC types. Strikingly expression of a few transcription factors often predicts dendrite morphological features in particular and axonal projections to specific tectal layers and extratectal targets. Moreover iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally chemogenetic ablation of eomesa+ RGCs which comprise three melanopsin expressing types with a specific projections to thalamus pretectum and one deep tectal layerpattern selectively impaired a visual behavior phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset 200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. | pubmed:33357413 | Adult Zebrafish 1 | GSM4627213 | source name:Zebrafish retina 4 mpf 6 mpf|tissue:retina | Adult Zebrafish 1 | Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0 10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10 release 82 using “cellranger count” with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10 release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples | Zebrafish retina 4 mpf 6 mpf | All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed. | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3’ v2 platform 10X Genomics Pleasanton CA | Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s solution 17 mM NaCl 2 mM KCl 0.12 mM MgSO4 1.8 mM CaNO32 1.5 mM HEPES. | tissue:retina | GSM4627213 | GSM4627213: Adult Zebrafish 1; Danio rerio; RNA Seq | GSM4627213 | 1 | Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics Pleasanton CA | GEO Accession:GSM4627213 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP268010 | assembly:GRCz10|intentional duplicate | ZebrafishRGC1.bam | 10X Genomics bam file | 25693480848.0 | 262178376.0 | GSM4627213 r1 | 0:98 | A:7491507845;C:5131022895;G:5429848529;T:7631356264;N:9745315 | 98 | 7491507845 | 5131022895 | 5429848529 | 7631356264 | 9745315 | SRX8583203 | SRS6874820 | SRA1089100 | GEO | Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley | 1 | 0.90363 | 0.22835 | 0.78632 | 0.48812 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2020-06-19 | Multi-stage | Multi-stage | Eye | Sensory System | ||||||||||||||||
| 66207 | 66207 | SRR16097999 | SRX12384068 | SRS10354360 | SRP339110 | PRJNA767032 | Amino acid primed mTOR activity is essential for heart regeneration [scRNA seq] | GSE184914 | Transcriptome Analysis | Heart disease is the leading cause of death as there is no current method to repair damaged myocardium due to the limited proliferative capacity of adult cardiomyocytes. Curiously mouse neonates and zebrafish larvae or adult are able to regenerate their hearts via cardiomyocyte de differentiation and proliferation. However a molecular mechanism of why these cardiomyocytes can re enter cell cycle is poorly understood. Here we identify a unique metabolic state that primes adult zebrafish and neonatal mouse ventricular cardiomyocytes to proliferate. Zebrafish and neonatal mouse hearts display elevated glutamine levels predisposing them to amino acid driven activation of TOR. We show that this TOR activation is required for zebrafish cardiomyocyte regeneration in vivo. post injury we observe pS6 in both the epicardium and ventricular cardiomyocytes suggesting these are amino acid primed cells necessary for regeneration. Through single cell and system wide RNA sequencing LQC proteomics and microscopy we identify dramatic metabolic and mitochondrial changes during the first week of regeneration. These data suggest that regeneration of zebrafish myocardium is driven by metabolic remodeling and reveals a unique metabolic regulator TOR primed state in which zebrafish and mammalian cardiomyocytes are regeneration competent. Overall design: We performed single cell RNA seq of zebrafish heart pre injury and 3 7 xxx post injury | parent bioproject:PRJNA778001 | pubmed:34988408 | zebrafish day 7 | GSM5600324 | source name:Zebrafish heart|tissue:heart|strain:AB|time:xxx post injury | zebrafish day 7 | Raw reads were processed using the CellRanger software from 10X genomics using recommended default settings. Monocle version 3 alpha was used for single cell RNA seq data analysis and visualization. We kept cells with at least 200 expressed genes and 1000 Unique Molecular Identifiers UMIs and less than 40% reads mapped to mitochondrial transcripts. Genome build: GRCz10 Supplementary files format and content: tab delimited file of normalized gene level read counts for each cell | Zebrafish heart | All chemical ventricular cardiomyocyte VCM ablation were conducted on adult Zebrafish 5 mpf 12 mpf. For chemical mediated VCM ablation fish were treated with 5 mM Metronidiazole MTZ; Sigma containing 0.1% dimethyl sulfoxide DMSO or vehicle control 0.1% DMSO for 48 hours protected from light and refreshed every 24 hours. For Wnt and DKK heat shock heterozygous animals 7.5 mM MTZ was used. Following chemical treatment fish were placed back in original aquaria and hearts were collected at 0 prior to MTZ 3 7 12 and 30 xxx post injury dpi. Larval hearts 72 hpf were isolated and pooled as previously described [68 69]. 6 hearts 3 males and 3 females were isolated from Adult UI 3 dpi and 7 dpi zebrafish. Each group had 2 sets of samples of 3 hearts each for the digestion process. Each set of 3 hearts were single celled as previously described [79]. All cells per group were then pooled and sent for sequencing. | Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total 2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart 141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis reverse transcription cDNA amplification and library preparation with indexing per the manufacturer’s protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc. San Diego CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics. | Wild type AB; Zebrafish International Resource Center Eugene OR USA hsWnt8:GFP [Tghsp70l:Wnt8a GFPw34] and hsDKK1:GFP [Tghsp70l:DKK1b GFPw32] [19] and vmhc:mCherry NTR [Tgvmhc:mCherry Eco.NfsB] [5] were used and maintained using standard procedures [67] in accordance with the Institutional Animal Care and Use Committee approved protocols IACUC 2057 01 & 4364 02. Reverse osmosis system water is used and the water chemistry was adjusted to a temperature of 27.5°C pH of 7.5 conductivity of 800 µS hardness of 140 ppm alkalinity of 35 ppm dissolved oxygen content of 7.8 mg/L and a total gas pressure of 101%. The average nitrate level is 55 ppm the average nitrite level is 0.05 ppm and the average ammonium level is 0.01 ppm. Larval feed starting at 5 dpf dpf is a rotifer polyculture supplemented with the Zeigler larval diet at 12 dpf live artemia is added to the diet and at 60 dpf 90 dpf the fish are started on the Zeigler adult diet supplemented with live artemia once per day. The health status of the colony showed low presence of pseudoloma neurophilia and an extremely low presence of mycobacterium spp. with no major clinical or subclinical findings of significance. | tissue:heart|strain:AB|time:xxx post injury | GSM5600324 | GSM5600324: zebrafish day 7; Danio rerio; RNA Seq | GSM5600324 r1 | GSM5600324 | 1 | Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total 2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart 141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis reverse transcription cDNA amplification and library preparation with indexing per the manufacturer's protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc. San Diego CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP339110 | assembly:GRCz10|intentional duplicate | zf_7db_possorted_genome_bam.bam | 10X Genomics bam file | 38062513314.0 | 388392993.0 | GSM5600324 r1 | 0:98 | A:11679656809;C:7784611418;G:8037807349;T:10544896124;N:15541614 | 98 | 11679656809 | 7784611418 | 8037807349 | 10544896124 | 15541614 | SRX12384068 | SRS10354360 | SRA1301815 | Institute for Stem Cell and Regenerative Medicine | Institute for Stem Cell and Regenerative Medicine | 1 | 0.93286 | 0.08896 | 0.87237 | 0.56993 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-09-28 | Multi-stage | Multi-stage | Heart | Cardiovascular System | |||||||||||||||
| 66208 | 66208 | SRR16098000 | SRX12384067 | SRS10354361 | SRP339110 | PRJNA767032 | Amino acid primed mTOR activity is essential for heart regeneration [scRNA seq] | GSE184914 | Transcriptome Analysis | Heart disease is the leading cause of death as there is no current method to repair damaged myocardium due to the limited proliferative capacity of adult cardiomyocytes. Curiously mouse neonates and zebrafish larvae or adult are able to regenerate their hearts via cardiomyocyte de differentiation and proliferation. However a molecular mechanism of why these cardiomyocytes can re enter cell cycle is poorly understood. Here we identify a unique metabolic state that primes adult zebrafish and neonatal mouse ventricular cardiomyocytes to proliferate. Zebrafish and neonatal mouse hearts display elevated glutamine levels predisposing them to amino acid driven activation of TOR. We show that this TOR activation is required for zebrafish cardiomyocyte regeneration in vivo. post injury we observe pS6 in both the epicardium and ventricular cardiomyocytes suggesting these are amino acid primed cells necessary for regeneration. Through single cell and system wide RNA sequencing LQC proteomics and microscopy we identify dramatic metabolic and mitochondrial changes during the first week of regeneration. These data suggest that regeneration of zebrafish myocardium is driven by metabolic remodeling and reveals a unique metabolic regulator TOR primed state in which zebrafish and mammalian cardiomyocytes are regeneration competent. Overall design: We performed single cell RNA seq of zebrafish heart pre injury and 3 7 xxx post injury | parent bioproject:PRJNA778001 | pubmed:34988408 | zebrafish day 3 | GSM5600323 | source name:Zebrafish heart|tissue:heart|strain:AB|time:xxx post injury | zebrafish day 3 | Raw reads were processed using the CellRanger software from 10X genomics using recommended default settings. Monocle version 3 alpha was used for single cell RNA seq data analysis and visualization. We kept cells with at least 200 expressed genes and 1000 Unique Molecular Identifiers UMIs and less than 40% reads mapped to mitochondrial transcripts. Genome build: GRCz10 Supplementary files format and content: tab delimited file of normalized gene level read counts for each cell | Zebrafish heart | All chemical ventricular cardiomyocyte VCM ablation were conducted on adult Zebrafish 5 mpf 12 mpf. For chemical mediated VCM ablation fish were treated with 5 mM Metronidiazole MTZ; Sigma containing 0.1% dimethyl sulfoxide DMSO or vehicle control 0.1% DMSO for 48 hours protected from light and refreshed every 24 hours. For Wnt and DKK heat shock heterozygous animals 7.5 mM MTZ was used. Following chemical treatment fish were placed back in original aquaria and hearts were collected at 0 prior to MTZ 3 7 12 and 30 xxx post injury dpi. Larval hearts 72 hpf were isolated and pooled as previously described [68 69]. 6 hearts 3 males and 3 females were isolated from Adult UI 3 dpi and 7 dpi zebrafish. Each group had 2 sets of samples of 3 hearts each for the digestion process. Each set of 3 hearts were single celled as previously described [79]. All cells per group were then pooled and sent for sequencing. | Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total 2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart 141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis reverse transcription cDNA amplification and library preparation with indexing per the manufacturer’s protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc. San Diego CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics. | Wild type AB; Zebrafish International Resource Center Eugene OR USA hsWnt8:GFP [Tghsp70l:Wnt8a GFPw34] and hsDKK1:GFP [Tghsp70l:DKK1b GFPw32] [19] and vmhc:mCherry NTR [Tgvmhc:mCherry Eco.NfsB] [5] were used and maintained using standard procedures [67] in accordance with the Institutional Animal Care and Use Committee approved protocols IACUC 2057 01 & 4364 02. Reverse osmosis system water is used and the water chemistry was adjusted to a temperature of 27.5°C pH of 7.5 conductivity of 800 µS hardness of 140 ppm alkalinity of 35 ppm dissolved oxygen content of 7.8 mg/L and a total gas pressure of 101%. The average nitrate level is 55 ppm the average nitrite level is 0.05 ppm and the average ammonium level is 0.01 ppm. Larval feed starting at 5 dpf dpf is a rotifer polyculture supplemented with the Zeigler larval diet at 12 dpf live artemia is added to the diet and at 60 dpf 90 dpf the fish are started on the Zeigler adult diet supplemented with live artemia once per day. The health status of the colony showed low presence of pseudoloma neurophilia and an extremely low presence of mycobacterium spp. with no major clinical or subclinical findings of significance. | tissue:heart|strain:AB|time:xxx post injury | GSM5600323 | GSM5600323: zebrafish day 3; Danio rerio; RNA Seq | GSM5600323 r1 | GSM5600323 | 1 | Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total 2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart 141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis reverse transcription cDNA amplification and library preparation with indexing per the manufacturer's protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc. San Diego CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP339110 | assembly:GRCz10|intentional duplicate | zf_3db_possorted_genome_bam.bam | 10X Genomics bam file | 35567557578.0 | 362934261.0 | GSM5600323 r1 | 0:98 | A:11273935957;C:7072680901;G:7397087735;T:9812130858;N:11722127 | 98 | 11273935957 | 7072680901 | 7397087735 | 9812130858 | 11722127 | SRX12384067 | SRS10354361 | SRA1301815 | Institute for Stem Cell and Regenerative Medicine | Institute for Stem Cell and Regenerative Medicine | 1 | 0.91795 | 0.07118 | 0.87418 | 0.58423 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-09-28 | Multi-stage | Multi-stage | Heart | Cardiovascular System | |||||||||||||||
| 66209 | 66209 | SRR16098001 | SRX12384066 | SRS10354359 | SRP339110 | PRJNA767032 | Amino acid primed mTOR activity is essential for heart regeneration [scRNA seq] | GSE184914 | Transcriptome Analysis | Heart disease is the leading cause of death as there is no current method to repair damaged myocardium due to the limited proliferative capacity of adult cardiomyocytes. Curiously mouse neonates and zebrafish larvae or adult are able to regenerate their hearts via cardiomyocyte de differentiation and proliferation. However a molecular mechanism of why these cardiomyocytes can re enter cell cycle is poorly understood. Here we identify a unique metabolic state that primes adult zebrafish and neonatal mouse ventricular cardiomyocytes to proliferate. Zebrafish and neonatal mouse hearts display elevated glutamine levels predisposing them to amino acid driven activation of TOR. We show that this TOR activation is required for zebrafish cardiomyocyte regeneration in vivo. post injury we observe pS6 in both the epicardium and ventricular cardiomyocytes suggesting these are amino acid primed cells necessary for regeneration. Through single cell and system wide RNA sequencing LQC proteomics and microscopy we identify dramatic metabolic and mitochondrial changes during the first week of regeneration. These data suggest that regeneration of zebrafish myocardium is driven by metabolic remodeling and reveals a unique metabolic regulator TOR primed state in which zebrafish and mammalian cardiomyocytes are regeneration competent. Overall design: We performed single cell RNA seq of zebrafish heart pre injury and 3 7 xxx post injury | parent bioproject:PRJNA778001 | pubmed:34988408 | zebrafish day x | GSM5600322 | source name:Zebrafish heart|tissue:heart|strain:AB|time:0d | zebrafish day x | Raw reads were processed using the CellRanger software from 10X genomics using recommended default settings. Monocle version 3 alpha was used for single cell RNA seq data analysis and visualization. We kept cells with at least 200 expressed genes and 1000 Unique Molecular Identifiers UMIs and less than 40% reads mapped to mitochondrial transcripts. Genome build: GRCz10 Supplementary files format and content: tab delimited file of normalized gene level read counts for each cell | Zebrafish heart | All chemical ventricular cardiomyocyte VCM ablation were conducted on adult Zebrafish 5 mpf 12 mpf. For chemical mediated VCM ablation fish were treated with 5 mM Metronidiazole MTZ; Sigma containing 0.1% dimethyl sulfoxide DMSO or vehicle control 0.1% DMSO for 48 hours protected from light and refreshed every 24 hours. For Wnt and DKK heat shock heterozygous animals 7.5 mM MTZ was used. Following chemical treatment fish were placed back in original aquaria and hearts were collected at 0 prior to MTZ 3 7 12 and 30 xxx post injury dpi. Larval hearts 72 hpf were isolated and pooled as previously described [68 69]. 6 hearts 3 males and 3 females were isolated from Adult UI 3 dpi and 7 dpi zebrafish. Each group had 2 sets of samples of 3 hearts each for the digestion process. Each set of 3 hearts were single celled as previously described [79]. All cells per group were then pooled and sent for sequencing. | Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total 2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart 141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis reverse transcription cDNA amplification and library preparation with indexing per the manufacturer’s protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc. San Diego CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics. | Wild type AB; Zebrafish International Resource Center Eugene OR USA hsWnt8:GFP [Tghsp70l:Wnt8a GFPw34] and hsDKK1:GFP [Tghsp70l:DKK1b GFPw32] [19] and vmhc:mCherry NTR [Tgvmhc:mCherry Eco.NfsB] [5] were used and maintained using standard procedures [67] in accordance with the Institutional Animal Care and Use Committee approved protocols IACUC 2057 01 & 4364 02. Reverse osmosis system water is used and the water chemistry was adjusted to a temperature of 27.5°C pH of 7.5 conductivity of 800 µS hardness of 140 ppm alkalinity of 35 ppm dissolved oxygen content of 7.8 mg/L and a total gas pressure of 101%. The average nitrate level is 55 ppm the average nitrite level is 0.05 ppm and the average ammonium level is 0.01 ppm. Larval feed starting at 5 dpf dpf is a rotifer polyculture supplemented with the Zeigler larval diet at 12 dpf live artemia is added to the diet and at 60 dpf 90 dpf the fish are started on the Zeigler adult diet supplemented with live artemia once per day. The health status of the colony showed low presence of pseudoloma neurophilia and an extremely low presence of mycobacterium spp. with no major clinical or subclinical findings of significance. | tissue:heart|strain:AB|time:0d | GSM5600322 | GSM5600322: zebrafish day x; Danio rerio; RNA Seq | GSM5600322 r1 | GSM5600322 | 1 | Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total 2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart 141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis reverse transcription cDNA amplification and library preparation with indexing per the manufacturer's protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc. San Diego CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP339110 | assembly:GRCz10|intentional duplicate | zf_0db_possorted_genome_bam.bam | 10X Genomics bam file | 37627884490.0 | 383958005.0 | GSM5600322 r1 | 0:98 | A:12219568490;C:7567146496;G:7074688134;T:10754586205;N:11895165 | 98 | 12219568490 | 7567146496 | 7074688134 | 10754586205 | 11895165 | SRX12384066 | SRS10354359 | SRA1301815 | Institute for Stem Cell and Regenerative Medicine | Institute for Stem Cell and Regenerative Medicine | 1 | 0.90337 | 0.0832 | 0.88562 | 0.62367 | 98 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-09-28 | Multi-stage | Multi-stage | Heart | Cardiovascular System | |||||||||||||||
| 67584 | 67584 | SRR17218121 | SRX13397710 | SRS11300870 | SRP350544 | PRJNA788489 | Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish | GSE190794 | Transcriptome Analysis | The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane… | pubmed:35938989 | Juvenile Thymus 4 | GSM5732082 | tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+|dissection temperature:room temperature | Juvenile Thymus 4 | The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms | sorted live thymus cells | Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. 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. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 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 in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq | 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. | cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+|dissection temperature:room temperature | GSM5732082 | GSM5732082: Juvenile Thymus 4; Danio rerio; RNA Seq | GSM5732082 | 1 | Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. 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. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 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 in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq | GEO Accession:GSM5732082 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP350544 | loader:fastq load.py | 4wpfThymus_6_S4_L001_I1_001.fastq.gz 4wpfThymus_6_S4_L001_R1_001.fastq.gz 4wpfThymus_6_S4_L001_R2_001.fastq.gz | fastq fastq fastq | 14767492309.0 | 116279467.0 | GSM5732082 r1 | 0:8 1:28 2:91 | A:3176407665;C:2147673056;G:2551453338;T:2705740495;N:156943 | 8 | 28 | 91 | 3176407665 | 2147673056 | 2551453338 | 2705740495 | 156943 | SRX13397710 | SRS11300870 | SRA1342645 | GEO | Oncology/Hematology, Boston Children's Hospital | 1 | 0.87149 | 0.22037 | 0.84049 | 0.53423 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-12-13 | Multi-stage | Multi-stage | Thymus | Hematopoietic System | |||||||||||||||
| 67585 | 67585 | SRR17218122 | SRX13397710 | SRS11300870 | SRP350544 | PRJNA788489 | Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish | GSE190794 | Transcriptome Analysis | The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane… | pubmed:35938989 | Juvenile Thymus 4 | GSM5732082 | tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+|dissection temperature:room temperature | Juvenile Thymus 4 | The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms | sorted live thymus cells | Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. 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. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 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 in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq | 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. | cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+|dissection temperature:room temperature | GSM5732082 | GSM5732082: Juvenile Thymus 4; Danio rerio; RNA Seq | GSM5732082 | 1 | Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. 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. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 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 in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq | GEO Accession:GSM5732082 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP350544 | loader:fastq load.py | 4wpfThymus_6_S4_L002_I1_001.fastq.gz 4wpfThymus_6_S4_L002_R1_001.fastq.gz 4wpfThymus_6_S4_L002_R2_001.fastq.gz | fastq fastq fastq | 14660763541.0 | 115439083.0 | GSM5732082 r2 | 0:8 1:28 2:91 | A:3154820274;C:2128697452;G:2532561232;T:2688755742;N:121853 | 8 | 28 | 91 | 3154820274 | 2128697452 | 2532561232 | 2688755742 | 121853 | SRX13397710 | SRS11300870 | SRA1342645 | GEO | Oncology/Hematology, Boston Children's Hospital | 1 | 0.87166 | 0.22046 | 0.8407 | 0.5334 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-12-13 | Multi-stage | Multi-stage | Thymus | Hematopoietic System | |||||||||||||||
| 67586 | 67586 | SRR17218119 | SRX13397709 | SRS11300871 | SRP350544 | PRJNA788489 | Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish | GSE190794 | Transcriptome Analysis | The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane… | pubmed:35938989 | Juvenile Thymus 3 | GSM5732081 | tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+|dissection temperature:room temperature | Juvenile Thymus 3 | The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms | sorted live thymus cells | Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. 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. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 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 in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq | 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. | cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+|dissection temperature:room temperature | GSM5732081 | GSM5732081: Juvenile Thymus 3; Danio rerio; RNA Seq | GSM5732081 | 1 | Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. 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. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 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 in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq | GEO Accession:GSM5732081 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP350544 | loader:fastq load.py | 4wpfThymus_5_S3_L001_I1_001.fastq.gz 4wpfThymus_5_S3_L001_R1_001.fastq.gz 4wpfThymus_5_S3_L001_R2_001.fastq.gz | fastq fastq fastq | 14488701909.0 | 114084267.0 | GSM5732081 r1 | 0:8 1:28 2:91 | A:3107408243;C:2119850736;G:2503503910;T:2650750983;N:154425 | 8 | 28 | 91 | 3107408243 | 2119850736 | 2503503910 | 2650750983 | 154425 | SRX13397709 | SRS11300871 | SRA1342645 | GEO | Oncology/Hematology, Boston Children's Hospital | 1 | 0.85944 | 0.20997 | 0.84064 | 0.53634 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-12-13 | Multi-stage | Multi-stage | Thymus | Hematopoietic System | |||||||||||||||
| 67587 | 67587 | SRR17218120 | SRX13397709 | SRS11300871 | SRP350544 | PRJNA788489 | Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish | GSE190794 | Transcriptome Analysis | The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane… | pubmed:35938989 | Juvenile Thymus 3 | GSM5732081 | tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+|dissection temperature:room temperature | Juvenile Thymus 3 | The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms | sorted live thymus cells | Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. 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. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 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 in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq | 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. | cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+|dissection temperature:room temperature | GSM5732081 | GSM5732081: Juvenile Thymus 3; Danio rerio; RNA Seq | GSM5732081 | 1 | Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. 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. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 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 in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq | GEO Accession:GSM5732081 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP350544 | loader:fastq load.py | 4wpfThymus_5_S3_L002_I1_001.fastq.gz 4wpfThymus_5_S3_L002_R1_001.fastq.gz 4wpfThymus_5_S3_L002_R2_001.fastq.gz | fastq fastq fastq | 14352524508.0 | 113012004.0 | GSM5732081 r2 | 0:8 1:28 2:91 | A:3079316058;C:2096769810;G:2479668921;T:2628218918;N:118657 | 8 | 28 | 91 | 3079316058 | 2096769810 | 2479668921 | 2628218918 | 118657 | SRX13397709 | SRS11300871 | SRA1342645 | GEO | Oncology/Hematology, Boston Children's Hospital | 1 | 0.85981 | 0.21085 | 0.8393 | 0.52667 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-12-13 | Multi-stage | Multi-stage | Thymus | Hematopoietic System | |||||||||||||||
| 67588 | 67588 | SRR17218117 | SRX13397708 | SRS11300869 | SRP350544 | PRJNA788489 | Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish | GSE190794 | Transcriptome Analysis | The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane… | pubmed:35938989 | Juvenile Thymus 2 | GSM5732080 | tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+|dissection temperature:room temperature | Juvenile Thymus 2 | The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms | sorted live thymus cells | Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. 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. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 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 in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq | 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. | cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+|dissection temperature:room temperature | GSM5732080 | GSM5732080: Juvenile Thymus 2; Danio rerio; RNA Seq | GSM5732080 | 1 | Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. 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. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 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 in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq | GEO Accession:GSM5732080 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP350544 | loader:fastq load.py | 4wpfThymus_3_S2_L001_I1_001.fastq.gz 4wpfThymus_3_S2_L001_R1_001.fastq.gz 4wpfThymus_3_S2_L001_R2_001.fastq.gz | fastq fastq fastq | 17459416821.0 | 137475723.0 | GSM5732080 r1 | 0:8 1:28 2:91 | A:3740652508;C:2562291967;G:3023715848;T:3183446304;N:184166 | 8 | 28 | 91 | 3740652508 | 2562291967 | 3023715848 | 3183446304 | 184166 | SRX13397708 | SRS11300869 | SRA1342645 | GEO | Oncology/Hematology, Boston Children's Hospital | 1 | 0.84416 | 0.21191 | 0.83897 | 0.53108 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-12-13 | Multi-stage | Multi-stage | Thymus | Hematopoietic System | |||||||||||||||
| 67589 | 67589 | SRR17218118 | SRX13397708 | SRS11300869 | SRP350544 | PRJNA788489 | Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish | GSE190794 | Transcriptome Analysis | The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane… | pubmed:35938989 | Juvenile Thymus 2 | GSM5732080 | tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+|dissection temperature:room temperature | Juvenile Thymus 2 | The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms | sorted live thymus cells | Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. 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. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 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 in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq | 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. | cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+|dissection temperature:room temperature | GSM5732080 | GSM5732080: Juvenile Thymus 2; Danio rerio; RNA Seq | GSM5732080 | 1 | Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. 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. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 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 in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq | GEO Accession:GSM5732080 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP350544 | loader:fastq load.py | 4wpfThymus_3_S2_L002_I1_001.fastq.gz 4wpfThymus_3_S2_L002_R1_001.fastq.gz 4wpfThymus_3_S2_L002_R2_001.fastq.gz | fastq fastq fastq | 17241251014.0 | 135757882.0 | GSM5732080 r2 | 0:8 1:28 2:91 | A:3695117374;C:2526230853;G:2985988000;T:3146489343;N:141692 | 8 | 28 | 91 | 3695117374 | 2526230853 | 2985988000 | 3146489343 | 141692 | SRX13397708 | SRS11300869 | SRA1342645 | GEO | Oncology/Hematology, Boston Children's Hospital | 1 | 0.84569 | 0.21301 | 0.83899 | 0.53404 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-12-13 | Multi-stage | Multi-stage | Thymus | Hematopoietic System | |||||||||||||||
| 67590 | 67590 | SRR17218115 | SRX13397707 | SRS11300868 | SRP350544 | PRJNA788489 | Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish | GSE190794 | Transcriptome Analysis | The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane… | pubmed:35938989 | Juvenile Thymus 1 | GSM5732079 | tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+|dissection temperature:room temperature | Juvenile Thymus 1 | The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms | sorted live thymus cells | Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. 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. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 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 in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq | 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. | cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+|dissection temperature:room temperature | GSM5732079 | GSM5732079: Juvenile Thymus 1; Danio rerio; RNA Seq | GSM5732079 | 1 | Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. 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. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 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 in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq | GEO Accession:GSM5732079 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP350544 | loader:fastq load.py | 4wpfThymus_1_S1_L001_I1_001.fastq.gz 4wpfThymus_1_S1_L001_R1_001.fastq.gz 4wpfThymus_1_S1_L001_R2_001.fastq.gz | fastq fastq fastq | 16221392627.0 | 127727501.0 | GSM5732079 r1 | 0:8 1:28 2:91 | A:3503038095;C:2359078159;G:2792714907;T:2968200161;N:171269 | 8 | 28 | 91 | 3503038095 | 2359078159 | 2792714907 | 2968200161 | 171269 | SRX13397707 | SRS11300868 | SRA1342645 | GEO | Oncology/Hematology, Boston Children's Hospital | 1 | 0.84501 | 0.21705 | 0.8379 | 0.53566 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-12-13 | Multi-stage | Multi-stage | Thymus | Hematopoietic System | |||||||||||||||
| 67591 | 67591 | SRR17218116 | SRX13397707 | SRS11300868 | SRP350544 | PRJNA788489 | Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish | GSE190794 | Transcriptome Analysis | The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane… | pubmed:35938989 | Juvenile Thymus 1 | GSM5732079 | tissue:sorted live thymus cells|cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+|dissection temperature:room temperature | Juvenile Thymus 1 | The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms | sorted live thymus cells | Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. 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. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 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 in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq | 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. | cell type:sorted live thymus cells|strain:Tglck:eGFP|developmental stage:Juvenile|age:4 wpf bleed:no|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+|dissection temperature:room temperature | GSM5732079 | GSM5732079: Juvenile Thymus 1; Danio rerio; RNA Seq | GSM5732079 | 1 | Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. 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. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 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 in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq | GEO Accession:GSM5732079 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP350544 | loader:fastq load.py | 4wpfThymus_1_S1_L002_I1_001.fastq.gz 4wpfThymus_1_S1_L002_R1_001.fastq.gz 4wpfThymus_1_S1_L002_R2_001.fastq.gz | fastq fastq fastq | 16074886951.0 | 126573913.0 | GSM5732079 r2 | 0:8 1:28 2:91 | A:3472769520;C:2334135014;G:2767323491;T:2943866297;N:131761 | 8 | 28 | 91 | 3472769520 | 2334135014 | 2767323491 | 2943866297 | 131761 | SRX13397707 | SRS11300868 | SRA1342645 | GEO | Oncology/Hematology, Boston Children's Hospital | 1 | 0.84624 | 0.21812 | 0.83918 | 0.52823 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-12-13 | Multi-stage | Multi-stage | Thymus | 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 | |||||||
| 75581 | 75581 | SRR24658739 | SRX20438405 | SRS17745022 | SRP438621 | PRJNA974396 | Single cell gene expression profiling of prenoplastic cells and myeloid cells during tumour initiation wihin a larval zebrafish model of skin oncogenis driven by inducible HRASG12V | GSE232900 | Transcriptome Analysis | Tumour initiation begins with a single oncogenic mutation within a single cell leading to hyperproliferation and clonal expansion. These mutant preneoplastic cells may undergo various fates such as: death dormancy benign growth or malignant growth. Whilst further genetic mutations have been linked to progression of preneoplastic cells even genetically identical preneoplastic cells may undergo different fates. To better understand the phenotypic heterogeneity between genetically identical preneoplastic cells during tumour initiation we have performed single cell RNA sequencing on preneoplastic cells derived from an inducible larval zebrafish model of skin cancer. Furthermore inflammation has been identified as a potent driving force in oncogenesis. Macrophages have especially been shown to promote cancer cell growth and progression whilst neutrophils have the potential to perform either pro or anti tumour functions. To study the first responses of myeloid cells following initial oncogenic transformation we also profiled sorted myeloid cells at the single cell level. Overall design: Preneoplastic cells and myeloid cells were sorted by FACS from transgenic zebrafish larvae in which the human oncogene HRASG12V is expressed specifically within epidermal keratinocytes following induction with 4OH Tamoxifen. Induction was carried out at 3dpf. To determine how these preneoplastic cells develop over time within their first day of oncogenic transformation we profiled cells at both 8 and 24 hours post induction. As a control we also sorted keratinocytes and myeloid cells from time matched larvae which do not express HRASG12V. Preneoplastic cells and keratinocytes were identified by mCherry fluorescence whilst myeloid cells were identified by EGFP fluorescence from the following larvae: Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry HRASG12V;mpeg1.1:EGFP and Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry CAAX;mpeg1.1:EGFP. | pubmed:38272902 | HRAS 24hpi biological replicate 2 | GSM7389057 | source name:whole larvae|tissue:whole larvae|cell types:keratinocytes and myeloid cells|strain:Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry HRASG12V; mpeg1.1:EGFP|treatment:4 OH Tamoxifen|geo loc name:missing|collection date:missing | HRAS 24hpi biological replicate 2 | First each sample was processed individually. The CellRanger pipeline was used to carry out demultiplexing UMI processing cell barcode processing genome alignment gene counting and identification of empty drops. Removal of ambient RNA was carried out using SoupX. Low quality cells were then removed on the basis of low total counts low number of detected genes and high percentage of mitochondrial transcripts. Low coverage genes were removed if they were not detected in at least 2 cells. Normalisation was carried out using SCTransform. Principle components and Uniform Manifold Projections UMAP were calculated. A priori markers of keratinocytes macrophage and neutrophils were inspected visually on UMAPs to aid subsequent clustering. Graph based Louvain clustering was performed and the number of k nearest neighbours varied to capture suitable population as indicated by the expression of a priori markers. Doublets were identified and removed using Scrublet and Doublet Decon. Finally all samples were aggregated and the data was re normalised and re clustered using the same methods as above. Differential expression analysis between each cluster and the rest of the sample was performed to identify cluster enriched genes Welch’s T test FDR <0.05 FC > 1.5. The identity of each cluster was confirmed by comparing the cluster enriched genes with the literature and publicly available datasets. Assembly: Danio rerio.GRCz11.101 Supplementary files format and content: Comma separated values files and matrix files | whole larvae | Whole larvae were dissociated by collagenase and rapid pipetting. Dissociation Solution consisted of HBSS no mag no cal plus phenol red HEPES 15mM D Glucose 25mM 2% Sterile Goat Serum Collagenase IV 2.5mg/ml. Groups of 50 larvae were submerged in 2ml of Dissociation Solution prewarmed to 28 degrees and transferred to a 12 well plate. Each well was incubated at 28 degrees with shaking for 5 minutes followed by 1 minute of rapid pipetting through a P1000 filter tip. Incubation and pipetting were repeated a further two times until a single cell suspension was obtained. For each sample 5 wells were pooled into a single falcon tube then washed and resuspended in 500ul of Dissociation Solution sans collagenase. Samples were filtered and stained with DAPI shortly prior to sorting using a FACS Fusion Becton Dickson. Keratinocytes/preneoplastic cells and myeloid cells were sorted into a single tube for each sample on the basis of mcherry and EGFP expression respectively. Freshly collected cells were washed once in HBSS at 4 degrees. Cells were counted and checked for viability with a cytometer and approx. 7000 cells were loaded to the 10X chromium chip. Library preparation was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly cells were resuspended in master mix and loaded onto the 10X chip alongside partitioning oil and beads to form GEMs gel beads in emulsion. A poly A capture method was used to reverse transcribe each transcript within each GEM whilst adding a Unique Molecular Identifier UMI cell barcode and Illumina R1 primer sequence. The resulting cDNA was captured on Silane DynaBeads and washed prior to amplification by PCR. To prepare the libraries further rounds of PCR were carried out in which the Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added. | tissue:whole larvae|cell types:keratinocytes and myeloid cells|strain:Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry HRASG12V;mpeg1.1:EGFP|treatment:4 OH Tamoxifen | GSM7389057 | GSM7389057: HRAS 24hpi biological replicate 2; Danio rerio; RNA Seq | GSM7389057 r1 | GSM7389057 | 1 | Whole larvae were dissociated by collagenase and rapid pipetting. Dissociation Solution consisted of HBSS no mag no cal plus phenol red HEPES 15mM D Glucose 25mM 2% Sterile Goat Serum Collagenase IV 2.5mg/ml. Groups of 50 larvae were submerged in 2ml of Dissociation Solution prewarmed to 28 degrees and transferred to a 12 well plate. Each well was incubated at 28 degrees with shaking for 5 minutes followed by 1 minute of rapid pipetting through a P1000 filter tip. Incubation and pipetting were repeated a further two times until a single cell suspension was obtained. For each sample 5 wells were pooled into a single falcon tube then washed and resuspended in 500ul of Dissociation Solution sans collagenase. Samples were filtered and stained with DAPI shortly prior to sorting using a FACS Fusion Becton Dickson. Keratinocytes/preneoplastic cells and myeloid cells were sorted into a single tube for each sample on the basis of mcherry and EGFP expression respectively. Freshly collected cells were washed once in HBSS at 4 degrees. Cells were counted and checked for viability with a cytometer and approx. 7000 cells were loaded to the 10X chromium chip. Library preparation was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly cells were resuspended in master mix and loaded onto the 10X chip alongside partitioning oil and beads to form GEMs gel beads in emulsion. A poly A capture method was used to reverse transcribe each transcript within each GEM whilst adding a Unique Molecular Identifier UMI cell barcode and Illumina R1 primer sequence. The resulting cDNA was captured on Silane DynaBeads and washed prior to amplification by PCR. To prepare the libraries further rounds of PCR were carried out in which the Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP438621 | loader:fastq load.py | H24b_S3_L001_R1_001.fastq.gz H24b_S3_L001_R2_001.fastq.gz | fastq fastq | 54025485801.0 | 453995679.0 | GSM7389057 r1 | 0:28 1:91 | A:15094230852;C:12129058397;G:12342885455;T:14457944312;N:1366785 | 28 | 91 | 15094230852 | 12129058397 | 12342885455 | 14457944312 | 1366785 | SRX20438405 | SRS17745022 | SRA1641488 | University of Edinburgh | University of Edinburgh | 2 | 0.01283 | 0.93826 | 0.00296 | 0.13471 | 0.97893 | 0.78044 | 0.43872 | 0.5309 | 28 | 91 | T | B | sc-like readlen | illumina | novaseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2023-05-19 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||
| 75582 | 75582 | SRR24658740 | SRX20438404 | SRS17745021 | SRP438621 | PRJNA974396 | Single cell gene expression profiling of prenoplastic cells and myeloid cells during tumour initiation wihin a larval zebrafish model of skin oncogenis driven by inducible HRASG12V | GSE232900 | Transcriptome Analysis | Tumour initiation begins with a single oncogenic mutation within a single cell leading to hyperproliferation and clonal expansion. These mutant preneoplastic cells may undergo various fates such as: death dormancy benign growth or malignant growth. Whilst further genetic mutations have been linked to progression of preneoplastic cells even genetically identical preneoplastic cells may undergo different fates. To better understand the phenotypic heterogeneity between genetically identical preneoplastic cells during tumour initiation we have performed single cell RNA sequencing on preneoplastic cells derived from an inducible larval zebrafish model of skin cancer. Furthermore inflammation has been identified as a potent driving force in oncogenesis. Macrophages have especially been shown to promote cancer cell growth and progression whilst neutrophils have the potential to perform either pro or anti tumour functions. To study the first responses of myeloid cells following initial oncogenic transformation we also profiled sorted myeloid cells at the single cell level. Overall design: Preneoplastic cells and myeloid cells were sorted by FACS from transgenic zebrafish larvae in which the human oncogene HRASG12V is expressed specifically within epidermal keratinocytes following induction with 4OH Tamoxifen. Induction was carried out at 3dpf. To determine how these preneoplastic cells develop over time within their first day of oncogenic transformation we profiled cells at both 8 and 24 hours post induction. As a control we also sorted keratinocytes and myeloid cells from time matched larvae which do not express HRASG12V. Preneoplastic cells and keratinocytes were identified by mCherry fluorescence whilst myeloid cells were identified by EGFP fluorescence from the following larvae: Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry HRASG12V;mpeg1.1:EGFP and Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry CAAX;mpeg1.1:EGFP. | pubmed:38272902 | HRAS 24hpi biological replicate 1 | GSM7389056 | source name:whole larvae|tissue:whole larvae|cell types:keratinocytes and myeloid cells|strain:Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry HRASG12V; mpeg1.1:EGFP|treatment:4 OH Tamoxifen|geo loc name:missing|collection date:missing | HRAS 24hpi biological replicate 1 | First each sample was processed individually. The CellRanger pipeline was used to carry out demultiplexing UMI processing cell barcode processing genome alignment gene counting and identification of empty drops. Removal of ambient RNA was carried out using SoupX. Low quality cells were then removed on the basis of low total counts low number of detected genes and high percentage of mitochondrial transcripts. Low coverage genes were removed if they were not detected in at least 2 cells. Normalisation was carried out using SCTransform. Principle components and Uniform Manifold Projections UMAP were calculated. A priori markers of keratinocytes macrophage and neutrophils were inspected visually on UMAPs to aid subsequent clustering. Graph based Louvain clustering was performed and the number of k nearest neighbours varied to capture suitable population as indicated by the expression of a priori markers. Doublets were identified and removed using Scrublet and Doublet Decon. Finally all samples were aggregated and the data was re normalised and re clustered using the same methods as above. Differential expression analysis between each cluster and the rest of the sample was performed to identify cluster enriched genes Welch’s T test FDR <0.05 FC > 1.5. The identity of each cluster was confirmed by comparing the cluster enriched genes with the literature and publicly available datasets. Assembly: Danio rerio.GRCz11.101 Supplementary files format and content: Comma separated values files and matrix files | whole larvae | Whole larvae were dissociated by collagenase and rapid pipetting. Dissociation Solution consisted of HBSS no mag no cal plus phenol red HEPES 15mM D Glucose 25mM 2% Sterile Goat Serum Collagenase IV 2.5mg/ml. Groups of 50 larvae were submerged in 2ml of Dissociation Solution prewarmed to 28 degrees and transferred to a 12 well plate. Each well was incubated at 28 degrees with shaking for 5 minutes followed by 1 minute of rapid pipetting through a P1000 filter tip. Incubation and pipetting were repeated a further two times until a single cell suspension was obtained. For each sample 5 wells were pooled into a single falcon tube then washed and resuspended in 500ul of Dissociation Solution sans collagenase. Samples were filtered and stained with DAPI shortly prior to sorting using a FACS Fusion Becton Dickson. Keratinocytes/preneoplastic cells and myeloid cells were sorted into a single tube for each sample on the basis of mcherry and EGFP expression respectively. Freshly collected cells were washed once in HBSS at 4 degrees. Cells were counted and checked for viability with a cytometer and approx. 7000 cells were loaded to the 10X chromium chip. Library preparation was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly cells were resuspended in master mix and loaded onto the 10X chip alongside partitioning oil and beads to form GEMs gel beads in emulsion. A poly A capture method was used to reverse transcribe each transcript within each GEM whilst adding a Unique Molecular Identifier UMI cell barcode and Illumina R1 primer sequence. The resulting cDNA was captured on Silane DynaBeads and washed prior to amplification by PCR. To prepare the libraries further rounds of PCR were carried out in which the Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added. | tissue:whole larvae|cell types:keratinocytes and myeloid cells|strain:Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry HRASG12V;mpeg1.1:EGFP|treatment:4 OH Tamoxifen | GSM7389056 | GSM7389056: HRAS 24hpi biological replicate 1; Danio rerio; RNA Seq | GSM7389056 r1 | GSM7389056 | 1 | Whole larvae were dissociated by collagenase and rapid pipetting. Dissociation Solution consisted of HBSS no mag no cal plus phenol red HEPES 15mM D Glucose 25mM 2% Sterile Goat Serum Collagenase IV 2.5mg/ml. Groups of 50 larvae were submerged in 2ml of Dissociation Solution prewarmed to 28 degrees and transferred to a 12 well plate. Each well was incubated at 28 degrees with shaking for 5 minutes followed by 1 minute of rapid pipetting through a P1000 filter tip. Incubation and pipetting were repeated a further two times until a single cell suspension was obtained. For each sample 5 wells were pooled into a single falcon tube then washed and resuspended in 500ul of Dissociation Solution sans collagenase. Samples were filtered and stained with DAPI shortly prior to sorting using a FACS Fusion Becton Dickson. Keratinocytes/preneoplastic cells and myeloid cells were sorted into a single tube for each sample on the basis of mcherry and EGFP expression respectively. Freshly collected cells were washed once in HBSS at 4 degrees. Cells were counted and checked for viability with a cytometer and approx. 7000 cells were loaded to the 10X chromium chip. Library preparation was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly cells were resuspended in master mix and loaded onto the 10X chip alongside partitioning oil and beads to form GEMs gel beads in emulsion. A poly A capture method was used to reverse transcribe each transcript within each GEM whilst adding a Unique Molecular Identifier UMI cell barcode and Illumina R1 primer sequence. The resulting cDNA was captured on Silane DynaBeads and washed prior to amplification by PCR. To prepare the libraries further rounds of PCR were carried out in which the Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP438621 | H24a_S2_L001_R1_001.fastq.gz H24a_S2_L001_R2_001.fastq.gz | fastq fastq | 18107807907.0 | 152166453.0 | GSM7389056 r1 | 0:28 1:91 | A:5035796418;C:3961860116;G:4103474182;T:5006217899;N:459292 | 28 | 91 | 5035796418 | 3961860116 | 4103474182 | 5006217899 | 459292 | SRX20438404 | SRS17745021 | SRA1641488 | University of Edinburgh | University of Edinburgh | 2 | 0.00467 | 0.94028 | 0.00136 | 0.1411 | 0.9893 | 0.78141 | 0.40506 | 0.5178 | 28 | 91 | T | B | sc-like readlen | illumina | novaseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2023-05-19 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||
| 75583 | 75583 | SRR24658741 | SRX20438403 | SRS17745025 | SRP438621 | PRJNA974396 | Single cell gene expression profiling of prenoplastic cells and myeloid cells during tumour initiation wihin a larval zebrafish model of skin oncogenis driven by inducible HRASG12V | GSE232900 | Transcriptome Analysis | Tumour initiation begins with a single oncogenic mutation within a single cell leading to hyperproliferation and clonal expansion. These mutant preneoplastic cells may undergo various fates such as: death dormancy benign growth or malignant growth. Whilst further genetic mutations have been linked to progression of preneoplastic cells even genetically identical preneoplastic cells may undergo different fates. To better understand the phenotypic heterogeneity between genetically identical preneoplastic cells during tumour initiation we have performed single cell RNA sequencing on preneoplastic cells derived from an inducible larval zebrafish model of skin cancer. Furthermore inflammation has been identified as a potent driving force in oncogenesis. Macrophages have especially been shown to promote cancer cell growth and progression whilst neutrophils have the potential to perform either pro or anti tumour functions. To study the first responses of myeloid cells following initial oncogenic transformation we also profiled sorted myeloid cells at the single cell level. Overall design: Preneoplastic cells and myeloid cells were sorted by FACS from transgenic zebrafish larvae in which the human oncogene HRASG12V is expressed specifically within epidermal keratinocytes following induction with 4OH Tamoxifen. Induction was carried out at 3dpf. To determine how these preneoplastic cells develop over time within their first day of oncogenic transformation we profiled cells at both 8 and 24 hours post induction. As a control we also sorted keratinocytes and myeloid cells from time matched larvae which do not express HRASG12V. Preneoplastic cells and keratinocytes were identified by mCherry fluorescence whilst myeloid cells were identified by EGFP fluorescence from the following larvae: Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry HRASG12V;mpeg1.1:EGFP and Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry CAAX;mpeg1.1:EGFP. | pubmed:38272902 | HRAS 8hpi | GSM7389054 | source name:whole larvae|tissue:whole larvae|cell types:keratinocytes and myeloid cells|strain:Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry HRASG12V; mpeg1.1:EGFP|treatment:4 OH Tamoxifen|geo loc name:missing|collection date:missing | HRAS 8hpi | First each sample was processed individually. The CellRanger pipeline was used to carry out demultiplexing UMI processing cell barcode processing genome alignment gene counting and identification of empty drops. Removal of ambient RNA was carried out using SoupX. Low quality cells were then removed on the basis of low total counts low number of detected genes and high percentage of mitochondrial transcripts. Low coverage genes were removed if they were not detected in at least 2 cells. Normalisation was carried out using SCTransform. Principle components and Uniform Manifold Projections UMAP were calculated. A priori markers of keratinocytes macrophage and neutrophils were inspected visually on UMAPs to aid subsequent clustering. Graph based Louvain clustering was performed and the number of k nearest neighbours varied to capture suitable population as indicated by the expression of a priori markers. Doublets were identified and removed using Scrublet and Doublet Decon. Finally all samples were aggregated and the data was re normalised and re clustered using the same methods as above. Differential expression analysis between each cluster and the rest of the sample was performed to identify cluster enriched genes Welch’s T test FDR <0.05 FC > 1.5. The identity of each cluster was confirmed by comparing the cluster enriched genes with the literature and publicly available datasets. Assembly: Danio rerio.GRCz11.101 Supplementary files format and content: Comma separated values files and matrix files | whole larvae | Whole larvae were dissociated by collagenase and rapid pipetting. Dissociation Solution consisted of HBSS no mag no cal plus phenol red HEPES 15mM D Glucose 25mM 2% Sterile Goat Serum Collagenase IV 2.5mg/ml. Groups of 50 larvae were submerged in 2ml of Dissociation Solution prewarmed to 28 degrees and transferred to a 12 well plate. Each well was incubated at 28 degrees with shaking for 5 minutes followed by 1 minute of rapid pipetting through a P1000 filter tip. Incubation and pipetting were repeated a further two times until a single cell suspension was obtained. For each sample 5 wells were pooled into a single falcon tube then washed and resuspended in 500ul of Dissociation Solution sans collagenase. Samples were filtered and stained with DAPI shortly prior to sorting using a FACS Fusion Becton Dickson. Keratinocytes/preneoplastic cells and myeloid cells were sorted into a single tube for each sample on the basis of mcherry and EGFP expression respectively. Freshly collected cells were washed once in HBSS at 4 degrees. Cells were counted and checked for viability with a cytometer and approx. 7000 cells were loaded to the 10X chromium chip. Library preparation was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly cells were resuspended in master mix and loaded onto the 10X chip alongside partitioning oil and beads to form GEMs gel beads in emulsion. A poly A capture method was used to reverse transcribe each transcript within each GEM whilst adding a Unique Molecular Identifier UMI cell barcode and Illumina R1 primer sequence. The resulting cDNA was captured on Silane DynaBeads and washed prior to amplification by PCR. To prepare the libraries further rounds of PCR were carried out in which the Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added. | tissue:whole larvae|cell types:keratinocytes and myeloid cells|strain:Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry HRASG12V;mpeg1.1:EGFP|treatment:4 OH Tamoxifen | GSM7389054 | GSM7389054: HRAS 8hpi; Danio rerio; RNA Seq | GSM7389054 r1 | GSM7389054 | 1 | Whole larvae were dissociated by collagenase and rapid pipetting. Dissociation Solution consisted of HBSS no mag no cal plus phenol red HEPES 15mM D Glucose 25mM 2% Sterile Goat Serum Collagenase IV 2.5mg/ml. Groups of 50 larvae were submerged in 2ml of Dissociation Solution prewarmed to 28 degrees and transferred to a 12 well plate. Each well was incubated at 28 degrees with shaking for 5 minutes followed by 1 minute of rapid pipetting through a P1000 filter tip. Incubation and pipetting were repeated a further two times until a single cell suspension was obtained. For each sample 5 wells were pooled into a single falcon tube then washed and resuspended in 500ul of Dissociation Solution sans collagenase. Samples were filtered and stained with DAPI shortly prior to sorting using a FACS Fusion Becton Dickson. Keratinocytes/preneoplastic cells and myeloid cells were sorted into a single tube for each sample on the basis of mcherry and EGFP expression respectively. Freshly collected cells were washed once in HBSS at 4 degrees. Cells were counted and checked for viability with a cytometer and approx. 7000 cells were loaded to the 10X chromium chip. Library preparation was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly cells were resuspended in master mix and loaded onto the 10X chip alongside partitioning oil and beads to form GEMs gel beads in emulsion. A poly A capture method was used to reverse transcribe each transcript within each GEM whilst adding a Unique Molecular Identifier UMI cell barcode and Illumina R1 primer sequence. The resulting cDNA was captured on Silane DynaBeads and washed prior to amplification by PCR. To prepare the libraries further rounds of PCR were carried out in which the Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP438621 | H8_S1_L001_R1_001.fastq.gz H8_S1_L001_R2_001.fastq.gz | fastq fastq | 13911277548.0 | 116901492.0 | GSM7389054 r1 | 0:28 1:91 | A:3894814708;C:3146160732;G:3170201864;T:3699746876;N:353368 | 28 | 91 | 3894814708 | 3146160732 | 3170201864 | 3699746876 | 353368 | SRX20438403 | SRS17745025 | SRA1641488 | University of Edinburgh | University of Edinburgh | 2 | 0.02025 | 0.93987 | 0.00402 | 0.11509 | 0.96546 | 0.78792 | 0.38628 | 0.52045 | 28 | 91 | T | B | sc-like readlen | illumina | novaseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2023-05-19 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||
| 75584 | 75584 | SRR24658742 | SRX20438402 | SRS17745018 | SRP438621 | PRJNA974396 | Single cell gene expression profiling of prenoplastic cells and myeloid cells during tumour initiation wihin a larval zebrafish model of skin oncogenis driven by inducible HRASG12V | GSE232900 | Transcriptome Analysis | Tumour initiation begins with a single oncogenic mutation within a single cell leading to hyperproliferation and clonal expansion. These mutant preneoplastic cells may undergo various fates such as: death dormancy benign growth or malignant growth. Whilst further genetic mutations have been linked to progression of preneoplastic cells even genetically identical preneoplastic cells may undergo different fates. To better understand the phenotypic heterogeneity between genetically identical preneoplastic cells during tumour initiation we have performed single cell RNA sequencing on preneoplastic cells derived from an inducible larval zebrafish model of skin cancer. Furthermore inflammation has been identified as a potent driving force in oncogenesis. Macrophages have especially been shown to promote cancer cell growth and progression whilst neutrophils have the potential to perform either pro or anti tumour functions. To study the first responses of myeloid cells following initial oncogenic transformation we also profiled sorted myeloid cells at the single cell level. Overall design: Preneoplastic cells and myeloid cells were sorted by FACS from transgenic zebrafish larvae in which the human oncogene HRASG12V is expressed specifically within epidermal keratinocytes following induction with 4OH Tamoxifen. Induction was carried out at 3dpf. To determine how these preneoplastic cells develop over time within their first day of oncogenic transformation we profiled cells at both 8 and 24 hours post induction. As a control we also sorted keratinocytes and myeloid cells from time matched larvae which do not express HRASG12V. Preneoplastic cells and keratinocytes were identified by mCherry fluorescence whilst myeloid cells were identified by EGFP fluorescence from the following larvae: Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry HRASG12V;mpeg1.1:EGFP and Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry CAAX;mpeg1.1:EGFP. | pubmed:38272902 | CAAX control 24hpi biological replicate 2 | GSM7389053 | source name:whole larvae|tissue:whole larvae|cell types:keratinocytes and myeloid cells|strain:Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry CAAX; mpeg1.1:EGFP|treatment:4 OH Tamoxifen|geo loc name:missing|collection date:missing | CAAX control 24hpi biological replicate 2 | First each sample was processed individually. The CellRanger pipeline was used to carry out demultiplexing UMI processing cell barcode processing genome alignment gene counting and identification of empty drops. Removal of ambient RNA was carried out using SoupX. Low quality cells were then removed on the basis of low total counts low number of detected genes and high percentage of mitochondrial transcripts. Low coverage genes were removed if they were not detected in at least 2 cells. Normalisation was carried out using SCTransform. Principle components and Uniform Manifold Projections UMAP were calculated. A priori markers of keratinocytes macrophage and neutrophils were inspected visually on UMAPs to aid subsequent clustering. Graph based Louvain clustering was performed and the number of k nearest neighbours varied to capture suitable population as indicated by the expression of a priori markers. Doublets were identified and removed using Scrublet and Doublet Decon. Finally all samples were aggregated and the data was re normalised and re clustered using the same methods as above. Differential expression analysis between each cluster and the rest of the sample was performed to identify cluster enriched genes Welch’s T test FDR <0.05 FC > 1.5. The identity of each cluster was confirmed by comparing the cluster enriched genes with the literature and publicly available datasets. Assembly: Danio rerio.GRCz11.101 Supplementary files format and content: Comma separated values files and matrix files | whole larvae | Whole larvae were dissociated by collagenase and rapid pipetting. Dissociation Solution consisted of HBSS no mag no cal plus phenol red HEPES 15mM D Glucose 25mM 2% Sterile Goat Serum Collagenase IV 2.5mg/ml. Groups of 50 larvae were submerged in 2ml of Dissociation Solution prewarmed to 28 degrees and transferred to a 12 well plate. Each well was incubated at 28 degrees with shaking for 5 minutes followed by 1 minute of rapid pipetting through a P1000 filter tip. Incubation and pipetting were repeated a further two times until a single cell suspension was obtained. For each sample 5 wells were pooled into a single falcon tube then washed and resuspended in 500ul of Dissociation Solution sans collagenase. Samples were filtered and stained with DAPI shortly prior to sorting using a FACS Fusion Becton Dickson. Keratinocytes/preneoplastic cells and myeloid cells were sorted into a single tube for each sample on the basis of mcherry and EGFP expression respectively. Freshly collected cells were washed once in HBSS at 4 degrees. Cells were counted and checked for viability with a cytometer and approx. 7000 cells were loaded to the 10X chromium chip. Library preparation was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly cells were resuspended in master mix and loaded onto the 10X chip alongside partitioning oil and beads to form GEMs gel beads in emulsion. A poly A capture method was used to reverse transcribe each transcript within each GEM whilst adding a Unique Molecular Identifier UMI cell barcode and Illumina R1 primer sequence. The resulting cDNA was captured on Silane DynaBeads and washed prior to amplification by PCR. To prepare the libraries further rounds of PCR were carried out in which the Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added. | tissue:whole larvae|cell types:keratinocytes and myeloid cells|strain:Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry CAAX;mpeg1.1:EGFP|treatment:4 OH Tamoxifen | GSM7389053 | GSM7389053: CAAX control 24hpi biological replicate 2; Danio rerio; RNA Seq | GSM7389053 r1 | GSM7389053 | 1 | Whole larvae were dissociated by collagenase and rapid pipetting. Dissociation Solution consisted of HBSS no mag no cal plus phenol red HEPES 15mM D Glucose 25mM 2% Sterile Goat Serum Collagenase IV 2.5mg/ml. Groups of 50 larvae were submerged in 2ml of Dissociation Solution prewarmed to 28 degrees and transferred to a 12 well plate. Each well was incubated at 28 degrees with shaking for 5 minutes followed by 1 minute of rapid pipetting through a P1000 filter tip. Incubation and pipetting were repeated a further two times until a single cell suspension was obtained. For each sample 5 wells were pooled into a single falcon tube then washed and resuspended in 500ul of Dissociation Solution sans collagenase. Samples were filtered and stained with DAPI shortly prior to sorting using a FACS Fusion Becton Dickson. Keratinocytes/preneoplastic cells and myeloid cells were sorted into a single tube for each sample on the basis of mcherry and EGFP expression respectively. Freshly collected cells were washed once in HBSS at 4 degrees. Cells were counted and checked for viability with a cytometer and approx. 7000 cells were loaded to the 10X chromium chip. Library preparation was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly cells were resuspended in master mix and loaded onto the 10X chip alongside partitioning oil and beads to form GEMs gel beads in emulsion. A poly A capture method was used to reverse transcribe each transcript within each GEM whilst adding a Unique Molecular Identifier UMI cell barcode and Illumina R1 primer sequence. The resulting cDNA was captured on Silane DynaBeads and washed prior to amplification by PCR. To prepare the libraries further rounds of PCR were carried out in which the Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP438621 | loader:fastq load.py | C24b_S8_L001_R1_001.fastq.gz C24b_S8_L001_R2_001.fastq.gz | fastq fastq | 50832860148.0 | 427166892.0 | GSM7389053 r1 | 0:28 1:91 | A:14417344610;C:11253484004;G:11479088004;T:13681660951;N:1282579 | 28 | 91 | 14417344610 | 11253484004 | 11479088004 | 13681660951 | 1282579 | SRX20438402 | SRS17745018 | SRA1641488 | University of Edinburgh | University of Edinburgh | 2 | 0.008 | 0.93154 | 0.00198 | 0.13785 | 0.98557 | 0.78599 | 0.43972 | 0.53172 | 28 | 91 | T | B | sc-like readlen | illumina | novaseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2023-05-19 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | |||||||||||
| 75585 | 75585 | SRR24658743 | SRX20438401 | SRS17745019 | SRP438621 | PRJNA974396 | Single cell gene expression profiling of prenoplastic cells and myeloid cells during tumour initiation wihin a larval zebrafish model of skin oncogenis driven by inducible HRASG12V | GSE232900 | Transcriptome Analysis | Tumour initiation begins with a single oncogenic mutation within a single cell leading to hyperproliferation and clonal expansion. These mutant preneoplastic cells may undergo various fates such as: death dormancy benign growth or malignant growth. Whilst further genetic mutations have been linked to progression of preneoplastic cells even genetically identical preneoplastic cells may undergo different fates. To better understand the phenotypic heterogeneity between genetically identical preneoplastic cells during tumour initiation we have performed single cell RNA sequencing on preneoplastic cells derived from an inducible larval zebrafish model of skin cancer. Furthermore inflammation has been identified as a potent driving force in oncogenesis. Macrophages have especially been shown to promote cancer cell growth and progression whilst neutrophils have the potential to perform either pro or anti tumour functions. To study the first responses of myeloid cells following initial oncogenic transformation we also profiled sorted myeloid cells at the single cell level. Overall design: Preneoplastic cells and myeloid cells were sorted by FACS from transgenic zebrafish larvae in which the human oncogene HRASG12V is expressed specifically within epidermal keratinocytes following induction with 4OH Tamoxifen. Induction was carried out at 3dpf. To determine how these preneoplastic cells develop over time within their first day of oncogenic transformation we profiled cells at both 8 and 24 hours post induction. As a control we also sorted keratinocytes and myeloid cells from time matched larvae which do not express HRASG12V. Preneoplastic cells and keratinocytes were identified by mCherry fluorescence whilst myeloid cells were identified by EGFP fluorescence from the following larvae: Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry HRASG12V;mpeg1.1:EGFP and Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry CAAX;mpeg1.1:EGFP. | pubmed:38272902 | CAAX control 24hpi biological replicate 1 | GSM7389052 | source name:whole larvae|tissue:whole larvae|cell types:keratinocytes and myeloid cells|strain:Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry CAAX; mpeg1.1:EGFP|treatment:4 OH Tamoxifen|geo loc name:missing|collection date:missing | CAAX control 24hpi biological replicate 1 | First each sample was processed individually. The CellRanger pipeline was used to carry out demultiplexing UMI processing cell barcode processing genome alignment gene counting and identification of empty drops. Removal of ambient RNA was carried out using SoupX. Low quality cells were then removed on the basis of low total counts low number of detected genes and high percentage of mitochondrial transcripts. Low coverage genes were removed if they were not detected in at least 2 cells. Normalisation was carried out using SCTransform. Principle components and Uniform Manifold Projections UMAP were calculated. A priori markers of keratinocytes macrophage and neutrophils were inspected visually on UMAPs to aid subsequent clustering. Graph based Louvain clustering was performed and the number of k nearest neighbours varied to capture suitable population as indicated by the expression of a priori markers. Doublets were identified and removed using Scrublet and Doublet Decon. Finally all samples were aggregated and the data was re normalised and re clustered using the same methods as above. Differential expression analysis between each cluster and the rest of the sample was performed to identify cluster enriched genes Welch’s T test FDR <0.05 FC > 1.5. The identity of each cluster was confirmed by comparing the cluster enriched genes with the literature and publicly available datasets. Assembly: Danio rerio.GRCz11.101 Supplementary files format and content: Comma separated values files and matrix files | whole larvae | Whole larvae were dissociated by collagenase and rapid pipetting. Dissociation Solution consisted of HBSS no mag no cal plus phenol red HEPES 15mM D Glucose 25mM 2% Sterile Goat Serum Collagenase IV 2.5mg/ml. Groups of 50 larvae were submerged in 2ml of Dissociation Solution prewarmed to 28 degrees and transferred to a 12 well plate. Each well was incubated at 28 degrees with shaking for 5 minutes followed by 1 minute of rapid pipetting through a P1000 filter tip. Incubation and pipetting were repeated a further two times until a single cell suspension was obtained. For each sample 5 wells were pooled into a single falcon tube then washed and resuspended in 500ul of Dissociation Solution sans collagenase. Samples were filtered and stained with DAPI shortly prior to sorting using a FACS Fusion Becton Dickson. Keratinocytes/preneoplastic cells and myeloid cells were sorted into a single tube for each sample on the basis of mcherry and EGFP expression respectively. Freshly collected cells were washed once in HBSS at 4 degrees. Cells were counted and checked for viability with a cytometer and approx. 7000 cells were loaded to the 10X chromium chip. Library preparation was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly cells were resuspended in master mix and loaded onto the 10X chip alongside partitioning oil and beads to form GEMs gel beads in emulsion. A poly A capture method was used to reverse transcribe each transcript within each GEM whilst adding a Unique Molecular Identifier UMI cell barcode and Illumina R1 primer sequence. The resulting cDNA was captured on Silane DynaBeads and washed prior to amplification by PCR. To prepare the libraries further rounds of PCR were carried out in which the Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added. | tissue:whole larvae|cell types:keratinocytes and myeloid cells|strain:Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry CAAX;mpeg1.1:EGFP|treatment:4 OH Tamoxifen | GSM7389052 | GSM7389052: CAAX control 24hpi biological replicate 1; Danio rerio; RNA Seq | GSM7389052 r1 | GSM7389052 | 1 | Whole larvae were dissociated by collagenase and rapid pipetting. Dissociation Solution consisted of HBSS no mag no cal plus phenol red HEPES 15mM D Glucose 25mM 2% Sterile Goat Serum Collagenase IV 2.5mg/ml. Groups of 50 larvae were submerged in 2ml of Dissociation Solution prewarmed to 28 degrees and transferred to a 12 well plate. Each well was incubated at 28 degrees with shaking for 5 minutes followed by 1 minute of rapid pipetting through a P1000 filter tip. Incubation and pipetting were repeated a further two times until a single cell suspension was obtained. For each sample 5 wells were pooled into a single falcon tube then washed and resuspended in 500ul of Dissociation Solution sans collagenase. Samples were filtered and stained with DAPI shortly prior to sorting using a FACS Fusion Becton Dickson. Keratinocytes/preneoplastic cells and myeloid cells were sorted into a single tube for each sample on the basis of mcherry and EGFP expression respectively. Freshly collected cells were washed once in HBSS at 4 degrees. Cells were counted and checked for viability with a cytometer and approx. 7000 cells were loaded to the 10X chromium chip. Library preparation was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly cells were resuspended in master mix and loaded onto the 10X chip alongside partitioning oil and beads to form GEMs gel beads in emulsion. A poly A capture method was used to reverse transcribe each transcript within each GEM whilst adding a Unique Molecular Identifier UMI cell barcode and Illumina R1 primer sequence. The resulting cDNA was captured on Silane DynaBeads and washed prior to amplification by PCR. To prepare the libraries further rounds of PCR were carried out in which the Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP438621 | C24a_S7_L001_R1_001.fastq.gz C24a_S7_L001_R2_001.fastq.gz | fastq fastq | 16830453339.0 | 141432381.0 | GSM7389052 r1 | 0:28 1:91 | A:4705072415;C:3671527815;G:3780778905;T:4672644538;N:429666 | 28 | 91 | 4705072415 | 3671527815 | 3780778905 | 4672644538 | 429666 | SRX20438401 | SRS17745019 | SRA1641488 | University of Edinburgh | University of Edinburgh | 2 | 0.00383 | 0.93899 | 0.00124 | 0.14413 | 0.99204 | 0.78388 | 0.43002 | 0.50704 | 28 | 91 | T | B | sc-like readlen | illumina | novaseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2023-05-19 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures | ||||||||||||
| 75586 | 75586 | SRR24658744 | SRX20438400 | SRS17745024 | SRP438621 | PRJNA974396 | Single cell gene expression profiling of prenoplastic cells and myeloid cells during tumour initiation wihin a larval zebrafish model of skin oncogenis driven by inducible HRASG12V | GSE232900 | Transcriptome Analysis | Tumour initiation begins with a single oncogenic mutation within a single cell leading to hyperproliferation and clonal expansion. These mutant preneoplastic cells may undergo various fates such as: death dormancy benign growth or malignant growth. Whilst further genetic mutations have been linked to progression of preneoplastic cells even genetically identical preneoplastic cells may undergo different fates. To better understand the phenotypic heterogeneity between genetically identical preneoplastic cells during tumour initiation we have performed single cell RNA sequencing on preneoplastic cells derived from an inducible larval zebrafish model of skin cancer. Furthermore inflammation has been identified as a potent driving force in oncogenesis. Macrophages have especially been shown to promote cancer cell growth and progression whilst neutrophils have the potential to perform either pro or anti tumour functions. To study the first responses of myeloid cells following initial oncogenic transformation we also profiled sorted myeloid cells at the single cell level. Overall design: Preneoplastic cells and myeloid cells were sorted by FACS from transgenic zebrafish larvae in which the human oncogene HRASG12V is expressed specifically within epidermal keratinocytes following induction with 4OH Tamoxifen. Induction was carried out at 3dpf. To determine how these preneoplastic cells develop over time within their first day of oncogenic transformation we profiled cells at both 8 and 24 hours post induction. As a control we also sorted keratinocytes and myeloid cells from time matched larvae which do not express HRASG12V. Preneoplastic cells and keratinocytes were identified by mCherry fluorescence whilst myeloid cells were identified by EGFP fluorescence from the following larvae: Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry HRASG12V;mpeg1.1:EGFP and Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry CAAX;mpeg1.1:EGFP. | pubmed:38272902 | CAAX control 8hpi | GSM7389050 | source name:whole larvae|tissue:whole larvae|cell types:keratinocytes and myeloid cells|strain:Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry CAAX; mpeg1.1:EGFP|treatment:4 OH Tamoxifen|geo loc name:missing|collection date:missing | CAAX control 8hpi | First each sample was processed individually. The CellRanger pipeline was used to carry out demultiplexing UMI processing cell barcode processing genome alignment gene counting and identification of empty drops. Removal of ambient RNA was carried out using SoupX. Low quality cells were then removed on the basis of low total counts low number of detected genes and high percentage of mitochondrial transcripts. Low coverage genes were removed if they were not detected in at least 2 cells. Normalisation was carried out using SCTransform. Principle components and Uniform Manifold Projections UMAP were calculated. A priori markers of keratinocytes macrophage and neutrophils were inspected visually on UMAPs to aid subsequent clustering. Graph based Louvain clustering was performed and the number of k nearest neighbours varied to capture suitable population as indicated by the expression of a priori markers. Doublets were identified and removed using Scrublet and Doublet Decon. Finally all samples were aggregated and the data was re normalised and re clustered using the same methods as above. Differential expression analysis between each cluster and the rest of the sample was performed to identify cluster enriched genes Welch’s T test FDR <0.05 FC > 1.5. The identity of each cluster was confirmed by comparing the cluster enriched genes with the literature and publicly available datasets. Assembly: Danio rerio.GRCz11.101 Supplementary files format and content: Comma separated values files and matrix files | whole larvae | Whole larvae were dissociated by collagenase and rapid pipetting. Dissociation Solution consisted of HBSS no mag no cal plus phenol red HEPES 15mM D Glucose 25mM 2% Sterile Goat Serum Collagenase IV 2.5mg/ml. Groups of 50 larvae were submerged in 2ml of Dissociation Solution prewarmed to 28 degrees and transferred to a 12 well plate. Each well was incubated at 28 degrees with shaking for 5 minutes followed by 1 minute of rapid pipetting through a P1000 filter tip. Incubation and pipetting were repeated a further two times until a single cell suspension was obtained. For each sample 5 wells were pooled into a single falcon tube then washed and resuspended in 500ul of Dissociation Solution sans collagenase. Samples were filtered and stained with DAPI shortly prior to sorting using a FACS Fusion Becton Dickson. Keratinocytes/preneoplastic cells and myeloid cells were sorted into a single tube for each sample on the basis of mcherry and EGFP expression respectively. Freshly collected cells were washed once in HBSS at 4 degrees. Cells were counted and checked for viability with a cytometer and approx. 7000 cells were loaded to the 10X chromium chip. Library preparation was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly cells were resuspended in master mix and loaded onto the 10X chip alongside partitioning oil and beads to form GEMs gel beads in emulsion. A poly A capture method was used to reverse transcribe each transcript within each GEM whilst adding a Unique Molecular Identifier UMI cell barcode and Illumina R1 primer sequence. The resulting cDNA was captured on Silane DynaBeads and washed prior to amplification by PCR. To prepare the libraries further rounds of PCR were carried out in which the Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added. | tissue:whole larvae|cell types:keratinocytes and myeloid cells|strain:Tgkrtt1c19e:KALTA44 ERT2; UAS:mCherry CAAX;mpeg1.1:EGFP|treatment:4 OH Tamoxifen | GSM7389050 | GSM7389050: CAAX control 8hpi; Danio rerio; RNA Seq | GSM7389050 r1 | GSM7389050 | 1 | Whole larvae were dissociated by collagenase and rapid pipetting. Dissociation Solution consisted of HBSS no mag no cal plus phenol red HEPES 15mM D Glucose 25mM 2% Sterile Goat Serum Collagenase IV 2.5mg/ml. Groups of 50 larvae were submerged in 2ml of Dissociation Solution prewarmed to 28 degrees and transferred to a 12 well plate. Each well was incubated at 28 degrees with shaking for 5 minutes followed by 1 minute of rapid pipetting through a P1000 filter tip. Incubation and pipetting were repeated a further two times until a single cell suspension was obtained. For each sample 5 wells were pooled into a single falcon tube then washed and resuspended in 500ul of Dissociation Solution sans collagenase. Samples were filtered and stained with DAPI shortly prior to sorting using a FACS Fusion Becton Dickson. Keratinocytes/preneoplastic cells and myeloid cells were sorted into a single tube for each sample on the basis of mcherry and EGFP expression respectively. Freshly collected cells were washed once in HBSS at 4 degrees. Cells were counted and checked for viability with a cytometer and approx. 7000 cells were loaded to the 10X chromium chip. Library preparation was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly cells were resuspended in master mix and loaded onto the 10X chip alongside partitioning oil and beads to form GEMs gel beads in emulsion. A poly A capture method was used to reverse transcribe each transcript within each GEM whilst adding a Unique Molecular Identifier UMI cell barcode and Illumina R1 primer sequence. The resulting cDNA was captured on Silane DynaBeads and washed prior to amplification by PCR. To prepare the libraries further rounds of PCR were carried out in which the Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP438621 | C8_S1_L001_R1_001.fastq.gz C8_S1_L001_R2_001.fastq.gz | fastq fastq | 16431760320.0 | 136931336.0 | GSM7389050 r1 | 0:29 1:91 | A:4578216787;C:3611412540;G:3630222244;T:4611494621;N:414128 | 29 | 91 | 4578216787 | 3611412540 | 3630222244 | 4611494621 | 414128 | SRX20438400 | SRS17745024 | SRA1641488 | University of Edinburgh | University of Edinburgh | 2 | 0.00718 | 0.93832 | 0.00157 | 0.11575 | 0.98573 | 0.78498 | 0.38295 | 0.51244 | 29 | 91 | T | B | sc-like readlen | illumina | novaseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2023-05-19 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;