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 54188,SRR10095964,SRX6828145,SRS5370320,SRP221273,PRJNA564810,A Single Cell Transcriptome Atlas for Zebrafish Development,PRJNA564810,Other,The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.,,,,,5b,,strain:Tgolig2:GFPvu12|age:5 dpf|sex:unknown|tissue:whole embryo|Replicate name:5b|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish embryos,5b,5b,10X v2 chromium cDNA library,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP221273,,loader:latf load,olig2gfp120hb_S5_L001_R1_001.fastq olig2gfp120hb_S5_L001_R2_001.fastq olig2gfp120hb_S5_L002_R1_001.fastq olig2gfp120hb_S5_L002_R2_001.fastq olig2gfp120hb_S5_L003_R1_001.fastq olig2gfp120hb_S5_L003_R2_001.fastq olig2gfp120hb_S5_L004_R1_001.fastq olig2gfp120hb_S5_L004_R2_001.fastq olig2gfp120hb_S5_L005_R1_001.fastq olig2gfp120hb_S5_L005_R2_001.fastq olig2gfp120hb_S5_L006_R1_001.fastq olig2gfp120hb_S5_L006_R2_001.fastq olig2gfp120hb_S5_L007_R1_001.fastq olig2gfp120hb_S5_L007_R2_001.fastq olig2gfp120hb_S5_L008_R1_001.fastq olig2gfp120hb_S5_L008_R2_001.fastq,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,90080193105.0,566542095.0,5b.gz,0:26 1:133,A:25143336916;C:20071432223;G:20537826191;T:24313961041;N:13636734,26,133,,,25143336916,20071432223,20537826191,24313961041,13636734,SRX6828145,SRS5370320,SRA960102,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.00976,0.95301,0.00215,0.10077,0.97926,0.77851,0.44407,0.5221,26,133,T,B,sc-like readlen,illumina,hiseq_era,unknown,unknown,unknown,sc,single_cell_droplet,10x,,United States,2019-12-10,Larval,Larval,Whole Organism,All anatomical structures 54189,SRR10095965,SRX6828144,SRS5370319,SRP221273,PRJNA564810,A Single Cell Transcriptome Atlas for Zebrafish Development,PRJNA564810,Other,The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.,,,,,5a,,strain:Tgolig2:GFPvu12|age:5 dpf|sex:unknown|tissue:whole embryo|Replicate name:5a|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish embryos,5a,5a,10X v2 chromium cDNA library,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP221273,,loader:latf load,olig2gfp120ha_S4_L001_R1_001.fastq olig2gfp120ha_S4_L001_R2_001.fastq olig2gfp120ha_S4_L002_R1_001.fastq olig2gfp120ha_S4_L002_R2_001.fastq olig2gfp120ha_S4_L003_R1_001.fastq olig2gfp120ha_S4_L003_R2_001.fastq olig2gfp120ha_S4_L004_R1_001.fastq olig2gfp120ha_S4_L004_R2_001.fastq olig2gfp120ha_S4_L005_R1_001.fastq olig2gfp120ha_S4_L005_R2_001.fastq olig2gfp120ha_S4_L006_R1_001.fastq olig2gfp120ha_S4_L006_R2_001.fastq olig2gfp120ha_S4_L007_R1_001.fastq olig2gfp120ha_S4_L007_R2_001.fastq olig2gfp120ha_S4_L008_R1_001.fastq olig2gfp120ha_S4_L008_R2_001.fastq,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,106640540616.0,670695224.0,5a.gz,0:26 1:133,A:29532468637;C:23968826821;G:24791831474;T:28331248539;N:16165145,26,133,,,29532468637,23968826821,24791831474,28331248539,16165145,SRX6828144,SRS5370319,SRA960102,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.01014,0.95016,0.00222,0.09527,0.97855,0.78212,0.41929,0.50263,26,133,T,B,sc-like readlen,illumina,hiseq_era,unknown,unknown,unknown,sc,single_cell_droplet,10x,,United States,2019-12-10,Larval,Larval,Whole Organism,All anatomical structures 54190,SRR10095966,SRX6828143,SRS5370318,SRP221273,PRJNA564810,A Single Cell Transcriptome Atlas for Zebrafish Development,PRJNA564810,Other,The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.,,,,,2b,,strain:Tgolig2:GFPvu12|age:2 dpf|sex:unknown|tissue:whole embryo|Replicate name:2b|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish embryos,2b,2b,10X v2 chromium cDNA library,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP221273,,loader:latf load,olig2gfp48ha_S3_L003_R2_001.fastq olig2gfp48ha_S3_L004_R1_001.fastq olig2gfp48ha_S3_L004_R2_001.fastq olig2gfp48ha_S3_L005_R1_001.fastq olig2gfp48ha_S3_L005_R2_001.fastq olig2gfp48ha_S3_L006_R1_001.fastq olig2gfp48ha_S3_L006_R2_001.fastq olig2gfp48ha_S3_L007_R1_001.fastq olig2gfp48ha_S3_L007_R2_001.fastq olig2gfp48ha_S3_L008_R1_001.fastq olig2gfp48ha_S3_L008_R2_001.fastq olig2gfp48ha_S3_L003_R1_001.fastq olig2gfp48ha_S3_L002_R2_001.fastq olig2gfp48ha_S3_L002_R1_001.fastq olig2gfp48ha_S3_L001_R2_001.fastq olig2gfp48ha_S3_L001_R1_001.fastq,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,100194025377.0,630151103.0,2b.gz,0:26 1:133,A:27235389395;C:22388810842;G:23041272930;T:27513445748;N:15106462,26,133,,,27235389395,22388810842,23041272930,27513445748,15106462,SRX6828143,SRS5370318,SRA960102,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.0127,0.95456,0.00215,0.09469,0.97463,0.79308,0.43287,0.50046,26,133,T,B,sc-like readlen,illumina,hiseq_era,unknown,unknown,unknown,sc,single_cell_droplet,10x,,United States,2019-12-10,Hatching,Embryo,Whole Organism,All anatomical structures 54191,SRR10095967,SRX6828142,SRS5370317,SRP221273,PRJNA564810,A Single Cell Transcriptome Atlas for Zebrafish Development,PRJNA564810,Other,The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.,,,,,2a,,strain:Tgelavl3:GCaMP6s|age:2 dpf|sex:unknown|tissue:whole embryo|Replicate name:2a|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish embryos,2a,2a,10X v2 chromium cDNA library,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,NextSeq 500,,SRP221273,,loader:latf load,2a elav_gcamp_48h_S1_L001_R1_001.fastq elav_gcamp_48h_S1_L001_R2_001.fastq elav_gcamp_48h_S1_L002_R1_001.fastq elav_gcamp_48h_S1_L002_R2_001.fastq elav_gcamp_48h_S1_L003_R1_001.fastq elav_gcamp_48h_S1_L003_R2_001.fastq elav_gcamp_48h_S1_L004_R1_001.fastq elav_gcamp_48h_S1_L004_R2_001.fastq,fastq fastq fastq fastq fastq fastq fastq fastq fastq,30654488793.0,192795527.0,2a.gz,0:26 1:133,A:8922702024;C:6370087682;G:7321183700;T:8019014142;N:21501245,26,133,,,8922702024,6370087682,7321183700,8019014142,21501245,SRX6828142,SRS5370317,SRA960102,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.00427,0.91705,0.00106,0.08701,0.98999,0.8198,0.35255,0.50555,26,133,T,B,sc-like readlen,illumina,nextseq,unknown,unknown,unknown,sc,single_cell_droplet,10x,,United States,2019-12-10,Hatching,Embryo,Whole Organism,All anatomical structures 54192,SRR10095968,SRX6828141,SRS5370316,SRP221273,PRJNA564810,A Single Cell Transcriptome Atlas for Zebrafish Development,PRJNA564810,Other,The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.,,,,,1b,,strain:Tgolig2:GFPvu12|age:1 dpf|sex:unknown|tissue:whole embryo|Replicate name:1b|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish embryos,1b,1b,10X v2 chromium cDNA library,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP221273,,loader:latf load,olig2gfp24hb_S2_L001_R1_001.fastq olig2gfp24hb_S2_L001_R2_001.fastq olig2gfp24hb_S2_L002_R1_001.fastq olig2gfp24hb_S2_L002_R2_001.fastq olig2gfp24hb_S2_L003_R1_001.fastq olig2gfp24hb_S2_L003_R2_001.fastq olig2gfp24hb_S2_L004_R1_001.fastq olig2gfp24hb_S2_L004_R2_001.fastq olig2gfp24hb_S2_L005_R1_001.fastq olig2gfp24hb_S2_L005_R2_001.fastq olig2gfp24hb_S2_L006_R1_001.fastq olig2gfp24hb_S2_L006_R2_001.fastq olig2gfp24hb_S2_L007_R1_001.fastq olig2gfp24hb_S2_L007_R2_001.fastq olig2gfp24hb_S2_L008_R1_001.fastq olig2gfp24hb_S2_L008_R2_001.fastq,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,98193351273.0,617568247.0,1b.gz,0:26 1:133,A:27237053473;C:21828277485;G:22951157364;T:26162156154;N:14706797,26,133,,,27237053473,21828277485,22951157364,26162156154,14706797,SRX6828141,SRS5370316,SRA960102,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.01479,0.95138,0.00273,0.12104,0.97327,0.78293,0.39405,0.4998,26,133,T,B,sc-like readlen,illumina,hiseq_era,unknown,unknown,unknown,sc,single_cell_droplet,10x,,United States,2019-12-10,Pharyngula,Embryo,Whole Organism,All anatomical structures 54193,SRR10095969,SRX6828140,SRS5370315,SRP221273,PRJNA564810,A Single Cell Transcriptome Atlas for Zebrafish Development,PRJNA564810,Other,The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.,,,,,1a,,strain:Tgolig2:GFPvu12|age:1 dpf|sex:unknown|tissue:whole embryo|Replicate name:1a|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish embryos,1a,1a,10X v2 chromium cDNA library,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP221273,,loader:latf load,olig2gfp24ha_S1_L001_R1_001.fastq olig2gfp24ha_S1_L001_R2_001.fastq olig2gfp24ha_S1_L002_R1_001.fastq olig2gfp24ha_S1_L002_R2_001.fastq olig2gfp24ha_S1_L003_R1_001.fastq olig2gfp24ha_S1_L003_R2_001.fastq olig2gfp24ha_S1_L004_R1_001.fastq olig2gfp24ha_S1_L004_R2_001.fastq olig2gfp24ha_S1_L005_R1_001.fastq olig2gfp24ha_S1_L005_R2_001.fastq olig2gfp24ha_S1_L006_R1_001.fastq olig2gfp24ha_S1_L006_R2_001.fastq olig2gfp24ha_S1_L007_R1_001.fastq olig2gfp24ha_S1_L007_R2_001.fastq olig2gfp24ha_S1_L008_R1_001.fastq olig2gfp24ha_S1_L008_R2_001.fastq,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,99552249225.0,626114775.0,1a.gz,0:26 1:133,A:27540748865;C:22111148705;G:23108024457;T:26777444676;N:14882522,26,133,,,27540748865,22111148705,23108024457,26777444676,14882522,SRX6828140,SRS5370315,SRA960102,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.01166,0.95413,0.002,0.08635,0.9779,0.80034,0.44044,0.48046,26,133,T,B,sc-like readlen,illumina,hiseq_era,unknown,unknown,unknown,sc,single_cell_droplet,10x,,United States,2019-12-10,Pharyngula,Embryo,Whole Organism,All anatomical structures 54727,SRR10150436,SRX6875873,SRS5411730,SRP222654,PRJNA571187,single cell RNA Seq of juvenile zebrafish,PRJNA571187,Other,single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit,,,,whole organism single cell RNA seq of juvenile zebrafish,SC2S3,,strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal,,,,,,,,,single cell RNA Seq of zebrafish: whole organism of juvenile,I4S2,I4S2,A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP222654,,,S3-I4-Hiseq_S2_L001_R1_001.fastq.gz S3-I4-Hiseq_S2_L001_R2_001.fastq.gz,fastq fastq,3487596300.0,11625321.0,S3 I4 Hiseq S2 L001 R1 001.fastq.gz,0:150 1:150,A:892777135;C:554604922;G:602698080;T:1437353489;N:162674,150,150,,,892777135,554604922,602698080,1437353489,162674,SRX6875873,SRS5411730,SRA965192,Sun Yat- sen University|Life Sicence School,Sun Yat- sen University,2,0.20171,0.89797,0.05294,0.15018,0.98557,0.78865,0.5155,0.57581,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2019-09-20,Juvenile,Juvenile,Whole Organism,All anatomical structures 54728,SRR10150437,SRX6875872,SRS5411730,SRP222654,PRJNA571187,single cell RNA Seq of juvenile zebrafish,PRJNA571187,Other,single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit,,,,whole organism single cell RNA seq of juvenile zebrafish,SC2S3,,strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal,,,,,,,,,single cell RNA Seq of zebrafish: whole organism of juvenile,I4S1,I4S1,A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP222654,,,S3-I4-Hiseq_S1_L001_R1_001.fastq.gz S3-I4-Hiseq_S1_L001_R2_001.fastq.gz,fastq fastq,7508763300.0,25029211.0,S3 I4 Hiseq S1 L001 R1 001.fastq.gz,0:150 1:150,A:1913388616;C:1347525105;G:1432782100;T:2815014523;N:52956,150,150,,,1913388616,1347525105,1432782100,2815014523,52956,SRX6875872,SRS5411730,SRA965192,Sun Yat- sen University|Life Sicence School,Sun Yat- sen University,2,0.07221,0.85601,0.01751,0.14578,0.98569,0.78642,0.49143,0.56028,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2019-09-20,Juvenile,Juvenile,Whole Organism,All anatomical structures 54729,SRR10150438,SRX6875871,SRS5411730,SRP222654,PRJNA571187,single cell RNA Seq of juvenile zebrafish,PRJNA571187,Other,single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit,,,,whole organism single cell RNA seq of juvenile zebrafish,SC2S3,,strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal,,,,,,,,,single cell RNA Seq of zebrafish: whole organism of juvenile,I3S2,I3S2,A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP222654,,,S3-I3-Hiseq_S2_L001_R1_001.fastq.gz S3-I3-Hiseq_S2_L001_R2_001.fastq.gz,fastq fastq,4273728900.0,14245763.0,S3 I3 Hiseq S2 L001 R1 001.fastq.gz,0:150 1:150,A:1093044190;C:680068409;G:740119940;T:1760292389;N:203972,150,150,,,1093044190,680068409,740119940,1760292389,203972,SRX6875871,SRS5411730,SRA965192,Sun Yat- sen University|Life Sicence School,Sun Yat- sen University,2,0.20465,0.90036,0.05289,0.14865,0.98553,0.7877,0.49162,0.55234,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2019-09-20,Juvenile,Juvenile,Whole Organism,All anatomical structures 54730,SRR10150439,SRX6875870,SRS5411730,SRP222654,PRJNA571187,single cell RNA Seq of juvenile zebrafish,PRJNA571187,Other,single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit,,,,whole organism single cell RNA seq of juvenile zebrafish,SC2S3,,strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal,,,,,,,,,single cell RNA Seq of zebrafish: whole organism of juvenile,I3S1,I3S1,A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP222654,,,S3-I3-Hiseq_S1_L001_R1_001.fastq.gz S3-I3-Hiseq_S1_L001_R2_001.fastq.gz,fastq fastq,9027772200.0,30092574.0,S3 I3 Hiseq S1 L001 R1 001.fastq.gz,0:150 1:150,A:2295058606;C:1618993604;G:1725968569;T:3387689160;N:62261,150,150,,,2295058606,1618993604,1725968569,3387689160,62261,SRX6875870,SRS5411730,SRA965192,Sun Yat- sen University|Life Sicence School,Sun Yat- sen University,2,0.07429,0.86204,0.01816,0.14367,0.98638,0.78754,0.51152,0.56418,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2019-09-20,Juvenile,Juvenile,Whole Organism,All anatomical structures 54731,SRR10150440,SRX6875869,SRS5411730,SRP222654,PRJNA571187,single cell RNA Seq of juvenile zebrafish,PRJNA571187,Other,single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit,,,,whole organism single cell RNA seq of juvenile zebrafish,SC2S3,,strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal,,,,,,,,,single cell RNA Seq of zebrafish: whole organism of juvenile,I2S2,I2S2,A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP222654,,,S3-I2-Hiseq_S2_L001_R1_001.fastq.gz S3-I2-Hiseq_S2_L001_R2_001.fastq.gz,fastq fastq,3198554400.0,10661848.0,S3 I2 Hiseq S2 L001 R1 001.fastq.gz,0:150 1:150,A:818748615;C:508568675;G:554517575;T:1316569216;N:150319,150,150,,,818748615,508568675,554517575,1316569216,150319,SRX6875869,SRS5411730,SRA965192,Sun Yat- sen University|Life Sicence School,Sun Yat- sen University,2,0.2074,0.89961,0.05315,0.14953,0.98514,0.78849,0.48568,0.56678,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2019-09-20,Juvenile,Juvenile,Whole Organism,All anatomical structures 54732,SRR10150441,SRX6875868,SRS5411730,SRP222654,PRJNA571187,single cell RNA Seq of juvenile zebrafish,PRJNA571187,Other,single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit,,,,whole organism single cell RNA seq of juvenile zebrafish,SC2S3,,strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal,,,,,,,,,single cell RNA Seq of zebrafish: whole organism of juvenile,I2S1,I2S1,A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP222654,,,S3-I2-Hiseq_S1_L001_R1_001.fastq.gz S3-I2-Hiseq_S1_L001_R2_001.fastq.gz,fastq fastq,7025021100.0,23416737.0,S3 I2 Hiseq S1 L001 R1 001.fastq.gz,0:150 1:150,A:1791257403;C:1265471598;G:1350119282;T:2618125524;N:47293,150,150,,,1791257403,1265471598,1350119282,2618125524,47293,SRX6875868,SRS5411730,SRA965192,Sun Yat- sen University|Life Sicence School,Sun Yat- sen University,2,0.0595,0.8397,0.01378,0.14017,0.98602,0.78618,0.49684,0.57243,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2019-09-20,Juvenile,Juvenile,Whole Organism,All anatomical structures 54733,SRR10150442,SRX6875867,SRS5411730,SRP222654,PRJNA571187,single cell RNA Seq of juvenile zebrafish,PRJNA571187,Other,single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit,,,,whole organism single cell RNA seq of juvenile zebrafish,SC2S3,,strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal,,,,,,,,,single cell RNA Seq of zebrafish: whole organism of juvenile,I1S2,I1S2,A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP222654,,,S3-I1-Hiseq_S2_L001_R1_001.fastq.gz S3-I1-Hiseq_S2_L001_R2_001.fastq.gz,fastq fastq,3657667800.0,12192226.0,S3 I1 Hiseq S2 L001 R1 001.fastq.gz,0:150 1:150,A:936855915;C:580324428;G:630608753;T:1509707910;N:170794,150,150,,,936855915,580324428,630608753,1509707910,170794,SRX6875867,SRS5411730,SRA965192,Sun Yat- sen University|Life Sicence School,Sun Yat- sen University,2,0.20478,0.89817,0.05194,0.15048,0.98543,0.78817,0.49956,0.57664,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2019-09-20,Juvenile,Juvenile,Whole Organism,All anatomical structures 54734,SRR10150443,SRX6875866,SRS5411730,SRP222654,PRJNA571187,single cell RNA Seq of juvenile zebrafish,PRJNA571187,Other,single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit,,,,whole organism single cell RNA seq of juvenile zebrafish,SC2S3,,strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal,,,,,,,,,single cell RNA Seq of zebrafish: whole organism of juvenile,I1S1,I1S1,A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP222654,,,S3-I1-Hiseq_S1_L001_R1_001.fastq.gz S3-I1-Hiseq_S1_L001_R2_001.fastq.gz,fastq fastq,7809763800.0,26032546.0,S3 I1 Hiseq S1 L001 R1 001.fastq.gz,0:150 1:150,A:1991021603;C:1400155384;G:1489635110;T:2928896892;N:54811,150,150,,,1991021603,1400155384,1489635110,2928896892,54811,SRX6875866,SRS5411730,SRA965192,Sun Yat- sen University|Life Sicence School,Sun Yat- sen University,2,0.06891,0.85095,0.01881,0.14251,0.98555,0.78772,0.49154,0.57233,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2019-09-20,Juvenile,Juvenile,Whole Organism,All anatomical structures 64514,SRR17137062,SRX13321492,SRS11229253,SRP324000,PRJNA737474,Construction the larval and adult zebrafish cell atlas at single cell resolution,GSE178150,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping the current cell type classification system. In previous studies we built the mouse cell atlas MCA and human cell landscape HCL to catalog all cell types by collecting scRNA seq data. However systematically study for zebrafish Danio rerio and fruit fly Drosophila melanogaster are still lacking. Here we construct the zebrafish and Drosophila cell atlas with Microwell seq protocols which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila and studying difference between vertebrates and Invertebrates at single cell level. Overall design: Over 550 000 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 72 hpf 3 replicates 10 fish for each replicate and adult 90 day 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA737471,pubmed:36229673,,Microwell seq datasets of Zebrafish 72hpf COL104,GSM5718328,,source name:Zebrafish 72hpf sample3|strain:AB|age:72 hours|tissue:whole organism,Microwell seq datasets of Zebrafish 72hpf COL104,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Genome build: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.,Zebrafish 72hpf sample3,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:72 hours|tissue:whole organism,GSM5718328,GSM5718328: Microwell seq datasets of Zebrafish 72hpf COL104; Danio rerio; RNA Seq,GSM5718328,,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP324000,,assembly:GRCz11|intentional duplicate,Zebrafish_72hpf_COL104.bam,10X Genomics bam file,90497447328.0,520100272.0,GSM5718328 r1,0:24 1:150,A:26568037621;C:19526761960;G:20762820842;T:23593883403;N:45943502,24,150,,,26568037621,19526761960,20762820842,23593883403,45943502,SRX13321492,SRS11229253,SRA1244752,GEO,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00219,0.7651,0.00205,0.0914,0.99981,0.79953,0.5,0.51979,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-12-05,Larval,Larval,Whole Organism,All anatomical structures 67725,SRR17247473,SRX13426482,SRS11327468,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,rosa brad aug2019 zf 4E,GSM5737706,,source name:dissociated zebrafish embryos|Stage:96 hpf|class:cxcl8|tissue:whole embryo|geo loc name:missing|collection date:missing,rosa brad aug2019 zf 4E,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,dissociated zebrafish embryos,No treatments,Embryos were euthanized minced and cells digested with Liberase before filtering and isolation using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Embryos were grown in E3. embryo medium at 28C.,Stage:96 hpf|class:cxcl8|tissue:whole embryo,GSM5737706,GSM5737706: rosa brad aug2019 zf 4E; Danio rerio; RNA Seq,GSM5737706 r1,GSM5737706,1,Embryos were euthanized minced and cells digested with Liberase before filtering and isolation using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,ZF_4E_S2_L001_R1_001.fastq.gz ZF_4E_S2_L001_R2_001.fastq.gz,fastq fastq,29236231628.0,96808714.0,GSM5737706 r1,0:151 1:151,A:9334627873;C:4386190824;G:4741532026;T:10773738549;N:142356,151,151,,,9334627873,4386190824,4741532026,10773738549,142356,SRX13426482,SRS11327468,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.37216,0.92956,0.05597,0.06942,0.98565,0.83522,0.5073,0.38552,151,151,B,B,mate1-mate2 similar by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Larval,Larval,Whole Organism,All anatomical structures 67726,SRR17247474,SRX13426482,SRS11327468,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,rosa brad aug2019 zf 4E,GSM5737706,,source name:dissociated zebrafish embryos|Stage:96 hpf|class:cxcl8|tissue:whole embryo|geo loc name:missing|collection date:missing,rosa brad aug2019 zf 4E,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,dissociated zebrafish embryos,No treatments,Embryos were euthanized minced and cells digested with Liberase before filtering and isolation using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Embryos were grown in E3. embryo medium at 28C.,Stage:96 hpf|class:cxcl8|tissue:whole embryo,GSM5737706,GSM5737706: rosa brad aug2019 zf 4E; Danio rerio; RNA Seq,GSM5737706 r1,GSM5737706,1,Embryos were euthanized minced and cells digested with Liberase before filtering and isolation using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,ZF_4E_S2_L002_R1_001.fastq.gz ZF_4E_S2_L002_R2_001.fastq.gz,fastq fastq,28006461052.0,92736626.0,GSM5737706 r2,0:151 1:151,A:8927070583;C:4167814184;G:4546529982;T:10364933489;N:112814,151,151,,,8927070583,4167814184,4546529982,10364933489,112814,SRX13426482,SRS11327468,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.38545,0.92932,0.05633,0.06951,0.98597,0.83709,0.51364,0.38726,151,151,B,B,mate1-mate2 similar by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Larval,Larval,Whole Organism,All anatomical structures 67727,SRR17247475,SRX13426481,SRS11327467,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,rosa brad aug2019 zf 4C,GSM5737705,,source name:dissociated zebrafish embryos|Stage:96 hpf|class:control|tissue:whole embryo|geo loc name:missing|collection date:missing,rosa brad aug2019 zf 4C,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,dissociated zebrafish embryos,No treatments,Embryos were euthanized minced and cells digested with Liberase before filtering and isolation using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Embryos were grown in E3. embryo medium at 28C.,Stage:96 hpf|class:control|tissue:whole embryo,GSM5737705,GSM5737705: rosa brad aug2019 zf 4C; Danio rerio; RNA Seq,GSM5737705 r1,GSM5737705,1,Embryos were euthanized minced and cells digested with Liberase before filtering and isolation using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,ZF_4C_S1_L001_R1_001.fastq.gz ZF_4C_S1_L001_R2_001.fastq.gz,fastq fastq,26611314974.0,88116937.0,GSM5737705 r1,0:151 1:151,A:8486328361;C:4017347730;G:4318309315;T:9789199999;N:129569,151,151,,,8486328361,4017347730,4318309315,9789199999,129569,SRX13426481,SRS11327467,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.31384,0.92912,0.04442,0.07551,0.98664,0.83899,0.52158,0.42131,151,151,B,B,mate1-mate2 similar by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Larval,Larval,Whole Organism,All anatomical structures 67728,SRR17247476,SRX13426481,SRS11327467,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,rosa brad aug2019 zf 4C,GSM5737705,,source name:dissociated zebrafish embryos|Stage:96 hpf|class:control|tissue:whole embryo|geo loc name:missing|collection date:missing,rosa brad aug2019 zf 4C,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,dissociated zebrafish embryos,No treatments,Embryos were euthanized minced and cells digested with Liberase before filtering and isolation using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Embryos were grown in E3. embryo medium at 28C.,Stage:96 hpf|class:control|tissue:whole embryo,GSM5737705,GSM5737705: rosa brad aug2019 zf 4C; Danio rerio; RNA Seq,GSM5737705 r1,GSM5737705,1,Embryos were euthanized minced and cells digested with Liberase before filtering and isolation using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,ZF_4C_S1_L002_R1_001.fastq.gz ZF_4C_S1_L002_R2_001.fastq.gz,fastq fastq,25351458252.0,83945226.0,GSM5737705 r2,0:151 1:151,A:8070939404;C:3796877993;G:4118811149;T:9364727163;N:102543,151,151,,,8070939404,3796877993,4118811149,9364727163,102543,SRX13426481,SRS11327467,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.31605,0.92745,0.04064,0.07668,0.98664,0.83615,0.51053,0.41348,151,151,B,B,mate1-mate2 similar by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Larval,Larval,Whole Organism,All anatomical structures 67729,SRR17247477,SRX13426480,SRS11327469,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,2 runx cxcl8 2a mcherry,GSM5737704,,source name:dissociated zebrafish embryos|Stage:96 hpf|class:cxcl8|tissue:whole embryo|geo loc name:missing|collection date:missing,2 runx cxcl8 2a mcherry,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,dissociated zebrafish embryos,No treatments,Embryos were euthanized minced and cells digested with Liberase before filtering and isolation using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Embryos were grown in E3. embryo medium at 28C.,Stage:96 hpf|class:cxcl8|tissue:whole embryo,GSM5737704,GSM5737704: 2 runx cxcl8 2a mcherry; Danio rerio; RNA Seq,GSM5737704 r1,GSM5737704,1,Embryos were euthanized minced and cells digested with Liberase before filtering and isolation using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,2-runx-cxcl8-2a-mcherry_S2_L008_R1_001.fastq.gz 2-runx-cxcl8-2a-mcherry_S2_L008_R2_001.fastq.gz,fastq fastq,44617802536.0,147741068.0,GSM5737704 r1,0:151 1:151,A:10676744103;C:7945886652;G:8556558310;T:17429992688;N:8620783,151,151,,,10676744103,7945886652,8556558310,17429992688,8620783,SRX13426480,SRS11327469,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.01846,0.9114,0.00566,0.10728,0.99646,0.82729,0.47435,0.46396,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Larval,Larval,Whole Organism,All anatomical structures 67730,SRR17247478,SRX13426479,SRS11327466,SRP351089,PRJNA789478,Microenvironmental Control of Hematopoietic Niche Capacity via CXCL8 and Protein Kinase C,GSE191029,Other,Altered hematopoietic stem cell HSC fate underlies primary blood disorders but microenvironmental factors controlling HSC fate are poorly understood. Genetically barcoded GESTALT zebrafish were used to screen for factors expressed by the sinusoidal vascular niche that alter the phylogenetic distribution of the HSC pool under native conditions. Dysregulated expression of protein kinase C delta PKC d encoded by prkcda increased the number of HSC clones by approximately 50% and expanded polyclonal populations of immature neutrophil and erythroid precursors. PKC agonists such as cxcl8 augmented HSC competition for residency within the niche and expanded defined niche populations. Cxcl8 induced association of PKC d with the focal adhesion complex activating MEK/ERK signaling and expression of niche factors in human endothelial cells. Our findings demonstrate the existence of reserve capacity within the niche which is controlled by PKC and has significant impact on HSC phylogenetic and phenotypic fate. Overall design: Single Cell RNA seq and Single Cell ATAC seq from zebrafish embryos and zebrafish kidney marrow. Bulk RNA seq and bulk ATAC seq from HUVEC cells transduced with adenovirus E4ORF1.,,pubmed:37209097,,1 runx clover,GSM5737703,,source name:dissociated zebrafish embryos|Stage:96 hpf|class:control|tissue:whole embryo|geo loc name:missing|collection date:missing,1 runx clover,scRNA seq data were processed from FASTQs to gene cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome. scATAC seq data were processed from FASTQs to peak cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome RNA seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. ATAC seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome. Genome build: GRCz11 GRCh38 Supplementary files format and content: scRNAseq: hdf5 file format containing gene cell barcode matrices. scATACseq: hdf5 file format containing peak cell barcode matrices. RNA seq: Normalized abundance table from RSEM with TPM FPKM and other metrics per gene. ATAC seq: bigwig file with genome weide accessibility tracks and narrowPeak files standard BED6+4 format.,dissociated zebrafish embryos,No treatments,Embryos were euthanized minced and cells digested with Liberase before filtering and isolation using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,Embryos were grown in E3. embryo medium at 28C.,Stage:96 hpf|class:control|tissue:whole embryo,GSM5737703,GSM5737703: 1 runx clover; Danio rerio; RNA Seq,GSM5737703 r1,GSM5737703,1,Embryos were euthanized minced and cells digested with Liberase before filtering and isolation using the 10X Chromium System. Libraries were constructed using the 10X Single Cell three prime protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP351089,,,1-runx-clover_S1_L008_R1_001.fastq.gz 1-runx-clover_S1_L008_R2_001.fastq.gz,fastq fastq,39209720926.0,129833513.0,GSM5737703 r1,0:151 1:151,A:9431797064;C:6936682144;G:7365275696;T:15468331501;N:7634521,151,151,,,9431797064,6936682144,7365275696,15468331501,7634521,SRX13426479,SRS11327466,SRA1347311,"Blaser Lab, Comprehensive Cancer Center, Ohio State University","Blaser Lab, Comprehensive Cancer Center, Ohio State University",2,0.01416,0.89936,0.00452,0.10988,0.99646,0.81542,0.49056,0.49889,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-16,Larval,Larval,Whole Organism,All anatomical structures 69032,SRR18915949,SRX14993867,SRS12743200,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 21d COL79,GSM6065255,,source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism,Micorwell seq datasets of Zebrafish 21d COL79,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.,Zebrafish 21d sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:21 day|tissue:whole organism,GSM6065255,GSM6065255: Micorwell seq datasets of Zebrafish 21d COL79; Danio rerio; RNA Seq,GSM6065255 r1,GSM6065255,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP363983,,assembly:GRCz11|intentional duplicate,Zebrafish_21d_COL79.bam,10X Genomics bam file,141397811748.0,812631102.0,GSM6065255 r1,0:24 1:150,A:42419601578;C:30491813752;G:32301586155;T:36094049456;N:90760807,24,150,,,42419601578,30491813752,32301586155,36094049456,90760807,SRX14993867,SRS12743200,SRA1409755,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00187,0.69179,0.00172,0.07347,0.99975,0.82231,0.33333,0.52514,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-04-25,Larval,Larval,Whole Organism,All anatomical structures 69035,SRR18915952,SRX14993864,SRS12743197,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 21d COL76,GSM6065252,,source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism,Micorwell seq datasets of Zebrafish 21d COL76,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.,Zebrafish 21d sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:21 day|tissue:whole organism,GSM6065252,GSM6065252: Micorwell seq datasets of Zebrafish 21d COL76; Danio rerio; RNA Seq,GSM6065252 r1,GSM6065252,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP363983,,assembly:GRCz11|intentional duplicate,Zebrafish_21d_COL76.bam,10X Genomics bam file,111633243510.0,641570365.0,GSM6065252 r1,0:24 1:150,A:33972927532;C:23914299609;G:25579933876;T:28104989997;N:61092496,24,150,,,33972927532,23914299609,25579933876,28104989997,61092496,SRX14993864,SRS12743197,SRA1409755,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00193,0.6842,0.00182,0.07841,0.99983,0.82059,0.375,0.55944,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-04-25,Larval,Larval,Whole Organism,All anatomical structures 69038,SRR18642995,SRX14746259,SRS12507764,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 21d COL73,GSM6019658,,source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism,Micorwell seq datasets of Zebrafish 21d COL73,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.,Zebrafish 21d sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:21 day|tissue:whole organism,GSM6019658,GSM6019658: Micorwell seq datasets of Zebrafish 21d COL73; Danio rerio; RNA Seq,GSM6019658 r1,GSM6019658,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP363983,,assembly:GRCz11|intentional duplicate,Zebrafish_21d_COL73.bam,10X Genomics bam file,94495251666.0,543076159.0,GSM6019658 r1,0:24 1:150,A:28813859102;C:20196407259;G:21422570931;T:24009240216;N:53174158,24,150,,,28813859102,20196407259,21422570931,24009240216,53174158,SRX14746259,SRS12507764,SRA1398049,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.002,0.68935,0.00186,0.07467,0.99977,0.82392,0.45454,0.54871,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-04-05,Larval,Larval,Whole Organism,All anatomical structures 69040,SRR18642997,SRX14746257,SRS12507765,SRP363983,PRJNA816047,Mapping the zebrafish developmental and aging atlas by single cell mRNA seq,GSE198571,Transcriptome Analysis,Single cell mRNA sequencing scRNA seq technologies are reshaping current cell type classification system. In previous studies we constructed the Mouse Cell Atlas MCA and Human Cell Landscape HCL to catalog all cell types by collecting scRNA seq data. Howerver the systematic study for organism level dynamic changes of cellular states across zebrafish life span are still lacking. Here we constructed the zebrafish cell Landscape covering different development periods using Microwell seq protocol. The zebrafish cell landscape provides a valuable resource for studying cross sepciess development maturation and aging. Overall design: Over 452 878 cells derived from zebrafish whole body single cell dissociation and profiling at the larval stage 21 day 3 replicates and 10 fish for each replicate and adult 22 month 6 replicates 1 fish for each replicate.,parent bioproject:PRJNA817101,pubmed:35929025,,Micorwell seq datasets of Zebrafish 21d COL71,GSM6019656,,source name:Zebrafish 21d sample1|strain:AB|age:21 day|tissue:whole organism,Micorwell seq datasets of Zebrafish 21d COL71,Base call files were performed with Illumina bcl2fastq. Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12. The reads quality under 10 were removed. For raw file 1 in each COL cellbarcode: in read1 the bases 1 6 22 27 43 48 are merged 18bp; UMI: in read1 the bases 49 54 6bp. For raw file 2 5 in each COL cellbarcode: in read1 the bases 1 6 7 12 13 18 are merged 18bp; UMI: in read1 the bases 19 24 6bp. scRNA seq reads were aligned to the Danio rerio GRCz11 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix DGE based on UMI counts. The cell barcode is tagged with XC the UMI is tagged with XM and the gene is tagged with GE. Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab delimited text files of digital expression matrix DGE based on raw UMI counts with genes as rows and cells as columns.,Zebrafish 21d sample1,,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,strain:AB|age:21 day|tissue:whole organism,GSM6019656,GSM6019656: Micorwell seq datasets of Zebrafish 21d COL71; Danio rerio; RNA Seq,GSM6019656 r1,GSM6019656,1,Whole body single cell dissociation and lysate Library preparations were performed with the Microwell seq protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP363983,,assembly:GRCz11|intentional duplicate,Zebrafish_21d_COL71.bam,10X Genomics bam file,141830365482.0,815117043.0,GSM6019656 r1,0:24 1:150,A:43213881758;C:30298104199;G:32190676130;T:36046592777;N:81110618,24,150,,,43213881758,30298104199,32190676130,36046592777,81110618,SRX14746257,SRS12507765,SRA1398049,"Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine","Zhejiang University School of Medicine, Center for Stem Cell and Regenerative Medicine",2,0.00172,0.68841,0.00159,0.06954,0.99977,0.82351,0.54545,0.55717,24,150,T,B,sc-like readlen,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2022-04-05,Larval,Larval,Whole Organism,All anatomical structures 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,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,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,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,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,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