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
52209,SRR8992787,SRX5771765,SRS4705624,SRP194294,PRJNA540521,Fate plasticity and reprogramming in genetically distinct populations of Danio leucophores,GSE130526,Other,Understanding genetic and cellular bases of adult form remains a fundamental goal at the intersection of developmental and evolutionary biology. The skin pigment cells of vertebrates  derived from embryonic neural crest  are a useful system for elucidating mechanisms of fate specification  pattern formation  and how particular phenotypes impact organismal behavior and ecology. In a survey of Danio fishes  including zebrafish Danio rerio  we identified two populations of white pigment cells—leucophores—one of which arises by transdifferentiation of adult melanophores and another that develops from a yellow/orange xanthophore like progenitor. Single cell transcriptomic  mutational  chemical and ultrastructural analyses of zebrafish leucophores revealed cell type specific chemical compositions  organelle configurations and genetic requirements. At the organismal level  we identified distinct physiological responses of leucophores during environmental background matching and we show that leucophore complement influences behavior. Together  our studies revealed new  independently arisen pigment cell types and mechanisms of fate acquisition in zebrafish  and illustrate how concerted analyses across hierarchical levels can provide insights into phenotypes and their evolution. Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform using zebrafish fin pigment cells FACs sorted for mCherry. For additional details see associated publication,,pubmed:31138706,,Zebrafish fin pigment cells,GSM3741778,,tissue:Dorsal and anal fins|cell type:pigment cells|treatment:Untreated,Zebrafish fin pigment cells,Expression matrix files were generated using cellranger 10X genomics version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Genome build: GRCz11/danRer11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.,Dorsal and anal fins,Fins were amputated from fish expressing both pnp4a:palmmCherry and tyrp1b:palmmCherry. To approximately normalize capture of relevant cell types by quantity and improve the likelihood of recovering cells at intermediate states of differentiation  we extracted distal dorsal fin regions 10 mm standard length  SL; n=20 and proximal interstripe anal fin regions 14 mm SL; n=10. Tissue was enzymatically dissociated with Liberase 0.25 mg/mL in dPBS at 25°C for 15 min followed by manual trituration with a flame polished glass pipette for 5 min. Cell suspensions were then filtered through a 70 μm Nylon cell strainer to obtain a single cell suspension. Liberated cells were re suspended in 1% BSA / 5% FBS in dPBS and DAPI 0.1 μg/mL  15 min before FACS purification. All plastic and glass surfaces of cell contact were coated with 1% BSA in dPBS before to use. Prior to sorting for fluorescence levels  single cells were isolated by sequentially gating cells according to their SSC A vs. FSC A  FSC H vs FSC W and SSC H vs SSC W profiles according to standard flow cytometry practices. Cells with high levels of DAPI staining were excluded as dead or damaged. Cells from wild type zebrafish were used as negative control to determine gates for detection of mCherry and GFP fluorescence  and then cells from transgenic fish were purified according to these gates. All samples were kept on ice  except during Liberase incubation  and then sorted chilled.,10X genomics V1 protocol following manufacturer recommendations.,Fish were maintained at 28.5C with 10 h : 14 h light:dark conditions. Larvae were reared with marine rotifers supplemented with Artemac Aquafauna followed by Artemia and flake food. Adults were maintained on Artemia and flake food. Fish stocks of Danio rerio: WTABb  a derivative of inbred ABwp  Tgtyrp1b:palm mCherrywp.rt11  Tgpnp4a:palmmCherrywp.rt10,cell type:pigment cells|treatment:Untreated,GSM3741778,GSM3741778: Zebrafish fin pigment cells; Danio rerio; RNA Seq,GSM3741778,,1,10X genomics V1 protocol following manufacturer recommendations.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP194294,,,leucophore_S9_L003_R2_001.fastq.gz leucophore_S9_L004_R1_001.fastq.gz,fastq fastq,424061944.0,10241510.0,GSM3741778 r1,0:26 1:57,A:119042142;C:89897538;G:98172861;T:116716009;N:233394,26,57,,,119042142,89897538,98172861,116716009,233394,SRX5771765,SRS4705624,SRA881136,GEO,"Parichy Lab, Biology, University of Washington",1,0.33934,,0.07693,,0.8742,,0.51425,,57,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-04-30,Multi-stage,Multi-stage,Fin,Surface Structure
55221,SRR10182211,SRX6902836,SRS5434733,SRP223244,PRJNA574059,Cellular diversity of the regenerating caudal fin,GSE137971,Transcriptome Analysis,single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies  filtered through 40 µm cell strainers  and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging  alignment to zebrafish reference genome GRCz10  and feature counting based on Ensembl release 91 cellranger count.,,pubmed:32851162,,1dpa fin1 scRNA,GSM4095395,,source name:1dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:1 day post amputation,1dpa fin1 scRNA,All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly  sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.,1dpa caudal fin,,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility  with system water temperature at 28.5˚C  and a day night cycle controlled as 14 hr light/10 hr dark.,strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:1 day post amputation,GSM4095395,GSM4095395: 1dpa fin1 scRNA; Danio rerio; RNA Seq,GSM4095395,,1,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,GEO Accession:GSM4095395,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP223244,,,1dpa1_S1_L002_R1_001.fastq.gz 1dpa1_S1_L002_R2_001.fastq.gz,fastq fastq,3515690517.0,34808817.0,GSM4095395 r1,0:26 1:75,A:1021208515;C:750623954;G:773148636;T:968849435;N:1859977,26,75,,,1021208515,750623954,773148636,968849435,1859977,SRX6902836,SRS5434733,SRA968154,GEO,"Ting Wang, Genetics, Washington University St Louis",2,0.00195,0.91495,0.00089,0.10966,0.99699,0.84855,0.35643,0.59738,26,75,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-09-25,Adult,Adult,Fin,Surface Structure
55222,SRR10182210,SRX6902835,SRS5434732,SRP223244,PRJNA574059,Cellular diversity of the regenerating caudal fin,GSE137971,Transcriptome Analysis,single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies  filtered through 40 µm cell strainers  and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging  alignment to zebrafish reference genome GRCz10  and feature counting based on Ensembl release 91 cellranger count.,,pubmed:32851162,,preinjury fin2 scRNA,GSM4095394,,source name:Preinjury caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:preinjury,preinjury fin2 scRNA,All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly  sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.,Preinjury caudal fin,,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility  with system water temperature at 28.5˚C  and a day night cycle controlled as 14 hr light/10 hr dark.,strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:preinjury,GSM4095394,GSM4095394: preinjury fin2 scRNA; Danio rerio; RNA Seq,GSM4095394,,1,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,GEO Accession:GSM4095394,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP223244,,,samp2_S2_L002_R2_001.fastq.gz samp2_S2_L002_R1_001.fastq.gz,fastq fastq,14313306001.0,141715901.0,GSM4095394 r1,0:26 1:75,A:4080921082;C:3121900376;G:3341495424;T:3761528384;N:7460735,26,75,,,4080921082,3121900376,3341495424,3761528384,7460735,SRX6902835,SRS5434732,SRA968154,GEO,"Ting Wang, Genetics, Washington University St Louis",2,0.0029,0.89943,0.00115,0.07948,0.99543,0.8714,0.29607,0.47916,26,75,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-09-25,Adult,Adult,Fin,Surface Structure
55223,SRR10182209,SRX6902834,SRS5434731,SRP223244,PRJNA574059,Cellular diversity of the regenerating caudal fin,GSE137971,Transcriptome Analysis,single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies  filtered through 40 µm cell strainers  and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging  alignment to zebrafish reference genome GRCz10  and feature counting based on Ensembl release 91 cellranger count.,,pubmed:32851162,,preinjury fin1 scRNA,GSM4095393,,source name:Preinjury caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:preinjury,preinjury fin1 scRNA,All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly  sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.,Preinjury caudal fin,,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility  with system water temperature at 28.5˚C  and a day night cycle controlled as 14 hr light/10 hr dark.,strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:preinjury,GSM4095393,GSM4095393: preinjury fin1 scRNA; Danio rerio; RNA Seq,GSM4095393,,1,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,GEO Accession:GSM4095393,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP223244,,,samp1_S1_L001_R1_001.fastq.gz samp1_S1_L001_R2_001.fastq.gz,fastq fastq,14610147425.0,144654925.0,GSM4095393 r1,0:26 1:75,A:4066051353;C:3189039694;G:3388950081;T:3856651906;N:109454391,26,75,,,4066051353,3189039694,3388950081,3856651906,109454391,SRX6902834,SRS5434731,SRA968154,GEO,"Ting Wang, Genetics, Washington University St Louis",2,0.0024,0.87757,0.00072,0.08379,0.99504,0.85269,0.34276,0.52515,26,75,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-09-25,Adult,Adult,Fin,Surface Structure
55224,SRR10182216,SRX6902833,SRS5434730,SRP223244,PRJNA574059,Cellular diversity of the regenerating caudal fin,GSE137971,Transcriptome Analysis,single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies  filtered through 40 µm cell strainers  and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging  alignment to zebrafish reference genome GRCz10  and feature counting based on Ensembl release 91 cellranger count.,,pubmed:32851162,,4dpa fin2 scRNA,GSM4095400,,source name:4dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:4 day post amputation,4dpa fin2 scRNA,All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly  sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.,4dpa caudal fin,,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility  with system water temperature at 28.5˚C  and a day night cycle controlled as 14 hr light/10 hr dark.,strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:4 day post amputation,GSM4095400,GSM4095400: 4dpa fin2 scRNA; Danio rerio; RNA Seq,GSM4095400,,1,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,GEO Accession:GSM4095400,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP223244,,,4dpa2_S2_L002_R1_001.fastq.gz 4dpa2_S2_L002_R2_001.fastq.gz,fastq fastq,12205232082.0,120843882.0,GSM4095400 r1,0:26 1:75,A:3462691218;C:2662402586;G:2782962664;T:3293833482;N:3342132,26,75,,,3462691218,2662402586,2782962664,3293833482,3342132,SRX6902833,SRS5434730,SRA968154,GEO,"Ting Wang, Genetics, Washington University St Louis",2,0.00216,0.90418,0.00058,0.09381,0.99488,0.82666,0.33993,0.51619,26,75,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-09-25,Adult,Adult,Fin,Surface Structure
55225,SRR10182215,SRX6902832,SRS5434729,SRP223244,PRJNA574059,Cellular diversity of the regenerating caudal fin,GSE137971,Transcriptome Analysis,single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies  filtered through 40 µm cell strainers  and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging  alignment to zebrafish reference genome GRCz10  and feature counting based on Ensembl release 91 cellranger count.,,pubmed:32851162,,4dpa fin1 scRNA,GSM4095399,,source name:4dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:4 day post amputation,4dpa fin1 scRNA,All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly  sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.,4dpa caudal fin,,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility  with system water temperature at 28.5˚C  and a day night cycle controlled as 14 hr light/10 hr dark.,strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:4 day post amputation,GSM4095399,GSM4095399: 4dpa fin1 scRNA; Danio rerio; RNA Seq,GSM4095399,,1,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,GEO Accession:GSM4095399,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP223244,,,4dpa1_S1_L001_R1_001.fastq.gz 4dpa1_S1_L001_R2_001.fastq.gz,fastq fastq,14335848494.0,141939094.0,GSM4095399 r1,0:26 1:75,A:4028586492;C:3145713740;G:3334469278;T:3823390760;N:3688224,26,75,,,4028586492,3145713740,3334469278,3823390760,3688224,SRX6902832,SRS5434729,SRA968154,GEO,"Ting Wang, Genetics, Washington University St Louis",2,0.00214,0.90496,0.00068,0.10148,0.99494,0.82014,0.36363,0.54339,26,75,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-09-25,Adult,Adult,Fin,Surface Structure
55226,SRR10182214,SRX6902831,SRS5434728,SRP223244,PRJNA574059,Cellular diversity of the regenerating caudal fin,GSE137971,Transcriptome Analysis,single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies  filtered through 40 µm cell strainers  and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging  alignment to zebrafish reference genome GRCz10  and feature counting based on Ensembl release 91 cellranger count.,,pubmed:32851162,,2dpa fin2 scRNA,GSM4095398,,source name:2dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:2 day post amputation,2dpa fin2 scRNA,All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly  sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.,2dpa caudal fin,,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility  with system water temperature at 28.5˚C  and a day night cycle controlled as 14 hr light/10 hr dark.,strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:2 day post amputation,GSM4095398,GSM4095398: 2dpa fin2 scRNA; Danio rerio; RNA Seq,GSM4095398,,1,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,GEO Accession:GSM4095398,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP223244,,,2dpa2_S2_L002_R1_001.fastq.gz 2dpa2_S2_L002_R2_001.fastq.gz,fastq fastq,14592805725.0,144483225.0,GSM4095398 r1,0:26 1:75,A:4087287462;C:3228369053;G:3401290297;T:3861324848;N:14534065,26,75,,,4087287462,3228369053,3401290297,3861324848,14534065,SRX6902831,SRS5434728,SRA968154,GEO,"Ting Wang, Genetics, Washington University St Louis",2,0.00231,0.91223,0.00055,0.08705,0.99452,0.82627,0.30769,0.5211,26,75,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-09-25,Adult,Adult,Fin,Surface Structure
55227,SRR10182213,SRX6902830,SRS5434727,SRP223244,PRJNA574059,Cellular diversity of the regenerating caudal fin,GSE137971,Transcriptome Analysis,single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies  filtered through 40 µm cell strainers  and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging  alignment to zebrafish reference genome GRCz10  and feature counting based on Ensembl release 91 cellranger count.,,pubmed:32851162,,2dpa fin1 scRNA,GSM4095397,,source name:2dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:2 day post amputation,2dpa fin1 scRNA,All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly  sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.,2dpa caudal fin,,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility  with system water temperature at 28.5˚C  and a day night cycle controlled as 14 hr light/10 hr dark.,strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:2 day post amputation,GSM4095397,GSM4095397: 2dpa fin1 scRNA; Danio rerio; RNA Seq,GSM4095397,,1,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,GEO Accession:GSM4095397,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP223244,,,2dpa1_S1_L001_R1_001.fastq.gz 2dpa1_S1_L001_R2_001.fastq.gz,fastq fastq,15317979261.0,151663161.0,GSM4095397 r1,0:26 1:75,A:4303056842;C:3349998898;G:3533853775;T:4116083703;N:14986043,26,75,,,4303056842,3349998898,3533853775,4116083703,14986043,SRX6902830,SRS5434727,SRA968154,GEO,"Ting Wang, Genetics, Washington University St Louis",2,0.0022,0.9122,0.0006,0.09555,0.99504,0.82203,0.33222,0.52299,26,75,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-09-25,Adult,Adult,Fin,Surface Structure
55228,SRR10182212,SRX6902829,SRS5434726,SRP223244,PRJNA574059,Cellular diversity of the regenerating caudal fin,GSE137971,Transcriptome Analysis,single cell transcriptomics of preinjury and regenerating caudal fin tissue revealed cell type consistency and cell type specific genetic program during regeneration Overall design: Preinjury and 1/2/4 day post amputation caudal fin tissues were collected and digested by Accumax Innovative Cell Technologies  filtered through 40 µm cell strainers  and washed with 1× Dulbecco's phosphate buffered saline DPBS–0.04% bovine serum albumin to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution three prime v2 10x Genomics and were subsequently sequenced on HiSeq2500 Illumina with read lengths of 26 + 75 Read1 + Read2. Raw reads were processed by Cell Ranger 10x Genomics with default parameters for read tagging  alignment to zebrafish reference genome GRCz10  and feature counting based on Ensembl release 91 cellranger count.,,pubmed:32851162,,1dpa fin2 scRNA,GSM4095396,,source name:1dpa caudal fin|strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:1 day post amputation,1dpa fin2 scRNA,All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter trimmed with cutadapt. RNA reads were aligned to Zv10 genome using STAR. Genome build: Zv10 Supplementary files format and content: Digital gene expression matrices were generated by cellranger count. Briefly  sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.,1dpa caudal fin,,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,Tgsp7:EGFP strains are maintained under standard husbandry in the Washington University Fish Facility  with system water temperature at 28.5˚C  and a day night cycle controlled as 14 hr light/10 hr dark.,strain:Tgsp7:egfp|age:1 year|tissue:caudal fin|timepoint:1 day post amputation,GSM4095396,GSM4095396: 1dpa fin2 scRNA; Danio rerio; RNA Seq,GSM4095396,,1,We anesthetized one year old fish with 0.16g/L MS 222 in system water  and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ ICT  filtered through 40µm cell strainers  and washed with 1xDPBS 0.04%BSA to generate single cell suspensions. Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution 10xGenomics,GEO Accession:GSM4095396,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP223244,,,1dpa2_S2_L002_R2_001.fastq.gz 1dpa2_S2_L002_R1_001.fastq.gz,fastq fastq,10934230609.0,108259709.0,GSM4095396 r1,0:26 1:75,A:3111673507;C:2358969825;G:2438293271;T:3019487882;N:5806124,26,75,,,3111673507,2358969825,2438293271,3019487882,5806124,SRX6902829,SRS5434726,SRA968154,GEO,"Ting Wang, Genetics, Washington University St Louis",2,0.00198,0.92416,0.00054,0.08626,0.99596,0.83808,0.29818,0.52586,26,75,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-09-25,Adult,Adult,Fin,Surface Structure
61429,SRR12749699,SRX9221655,SRS7455356,SRP285950,PRJNA666695,Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae,GSE158851,Transcriptome Analysis,Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation.  Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform  and sequenced using Illumina NovaSeq 6000.  Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets  previously described by our group to govern zebrafish fin regeneration  and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform  and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP.,,pubmed:34732706;pubmed:35664055,,Uncut caudal fin scRNA,GSM4812244,,source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation,Uncut caudal fin scRNA,Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format : the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination ; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv  barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'.,caudal fin,,Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer’s instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.,,tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation,GSM4812244,GSM4812244: Uncut caudal fin scRNA; Danio rerio; RNA Seq,GSM4812244,,1,Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.,GEO Accession:GSM4812244,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP285950,,loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=Uncut S8 L001 R1 001.fastq.gz   read2PairFiles=Uncut S8 L001 R2 001.fastq.gz   read3PairFiles=Uncut S8 L001 I1 001.fastq.gz,Uncut_S8_L001_I1_001.fastq.gz Uncut_S8_L001_R1_001.fastq.gz Uncut_S8_L001_R2_001.fastq.gz,fastq fastq fastq,18909629967.0,153736829.0,GSM4812244 r1,0:28 1:87 2:8,A:5220924848;C:4279280050;G:4788532540;T:4619612909;N:1279620,28,87,8,,5220924848,4279280050,4788532540,4619612909,1279620,SRX9221655,SRS7455356,SRA1136463,GEO,"Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm",1,0.63376,,0.11724,,0.8393,,0.55679,,87,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,France,2020-09-30,Larval,Larval,Fin,Surface Structure
61430,SRR12749700,SRX9221655,SRS7455356,SRP285950,PRJNA666695,Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae,GSE158851,Transcriptome Analysis,Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation.  Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform  and sequenced using Illumina NovaSeq 6000.  Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets  previously described by our group to govern zebrafish fin regeneration  and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform  and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP.,,pubmed:34732706;pubmed:35664055,,Uncut caudal fin scRNA,GSM4812244,,source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation,Uncut caudal fin scRNA,Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format : the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination ; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv  barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'.,caudal fin,,Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer’s instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.,,tissue:caudal fin|developmental stage:larvae|treatment:uncut|time:24 hours post amputation,GSM4812244,GSM4812244: Uncut caudal fin scRNA; Danio rerio; RNA Seq,GSM4812244,,1,Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.,GEO Accession:GSM4812244,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP285950,,loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=Uncut S8 L002 R1 001.fastq.gz   read2PairFiles=Uncut S8 L002 R2 001.fastq.gz   read3PairFiles=Uncut S8 L002 I1 001.fastq.gz,Uncut_S8_L002_I1_001.fastq.gz Uncut_S8_L002_R1_001.fastq.gz Uncut_S8_L002_R2_001.fastq.gz,fastq fastq fastq,18967585107.0,154208009.0,GSM4812244 r2,0:28 1:87 2:8,A:5236542259;C:4292274179;G:4804216460;T:4633355352;N:1196857,28,87,8,,5236542259,4292274179,4804216460,4633355352,1196857,SRX9221655,SRS7455356,SRA1136463,GEO,"Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm",1,0.63437,,0.11726,,0.83857,,0.5661,,87,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,France,2020-09-30,Larval,Larval,Fin,Surface Structure
61431,SRR12749697,SRX9221654,SRS7455355,SRP285950,PRJNA666695,Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae,GSE158851,Transcriptome Analysis,Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation.  Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform  and sequenced using Illumina NovaSeq 6000.  Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets  previously described by our group to govern zebrafish fin regeneration  and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform  and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP.,,pubmed:34732706;pubmed:35664055,,Cut caudal fin scRNA,GSM4812243,,source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:cut|time:24 hours,Cut caudal fin scRNA,Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format : the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination ; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv  barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'.,caudal fin,,Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer’s instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.,,tissue:caudal fin|developmental stage:larvae|treatment:cut|time:24 hours,GSM4812243,GSM4812243: Cut caudal fin scRNA; Danio rerio; RNA Seq,GSM4812243,,1,Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.,GEO Accession:GSM4812243,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP285950,,loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=Cut S7 L001 R1 001.fastq.gz   read2PairFiles=Cut S7 L001 R2 001.fastq.gz   read3PairFiles=Cut S7 L001 I1 001.fastq.gz,Cut_S7_L001_I1_001.fastq.gz Cut_S7_L001_R1_001.fastq.gz Cut_S7_L001_R2_001.fastq.gz,fastq fastq fastq,17453571711.0,141898957.0,GSM4812243 r1,0:28 1:87 2:8,A:4820960991;C:3908308491;G:4347557585;T:4375565175;N:1179469,28,87,8,,4820960991,3908308491,4347557585,4375565175,1179469,SRX9221654,SRS7455355,SRA1136463,GEO,"Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm",1,0.63902,,0.11232,,0.82235,,0.50797,,87,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,France,2020-09-30,Larval,Larval,Fin,Surface Structure
61432,SRR12749698,SRX9221654,SRS7455355,SRP285950,PRJNA666695,Single cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae,GSE158851,Transcriptome Analysis,Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single cell RNA sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation.  Methods: 150 of regenerating caudal fin cut and intact caudal fine uncut samples were dissociated and loaded into the 10x Genomics Chromium Platform  and sequenced using Illumina NovaSeq 6000.  Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single molecule based sequencing technology for high throughput profiling of both intact uncut and regenerating caudal fin samples cut at 24hpA. We confirmed the presence of macrophage subsets  previously described by our group to govern zebrafish fin regeneration  and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single cell RNA sequencing 10xGenomics Chromium Platform  and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection UMAP.,,pubmed:34732706;pubmed:35664055,,Cut caudal fin scRNA,GSM4812243,,source name:caudal fin|tissue:caudal fin|developmental stage:larvae|treatment:cut|time:24 hours,Cut caudal fin scRNA,Image analyses and base calling were performed using the NovaSeq Control Software and Real Time Analysis component Illumina. Demultiplexing was performed using cellranger mkfastq v3.1.0. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV Sequencing Analysis Viewer. cellranger count v3.1.0 was used to align reads to the reference genome and generate the raw and filtered gene barcodes matrices. cellranger aggr v3.1.0 was used to combine the results of the two samples. Genome build: danRer11 Supplementary files format and content: MEX file format : the matrix.mtx file contains the filtered gene barcode matrix total UMI count per cell and gene combination ; the .tsv files contain all annotated genes and cell barcodes represented in the mtx file. In the file Aggregation barcodes.tsv  barcodes appended with ' 1' represent the sample 'Cut' and barcodes appended with ' 2' represent the sample 'UnCut'.,caudal fin,,Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer’s instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.,,tissue:caudal fin|developmental stage:larvae|treatment:cut|time:24 hours,GSM4812243,GSM4812243: Cut caudal fin scRNA; Danio rerio; RNA Seq,GSM4812243,,1,Caudal fin amputation was performed with a sterile scalpel under anaesthesia with 0.016% Tricaine MS222  Sigma in zebrafish water. Approximately  150 of regenerating caudal fin cut and intact caudal fin uncut samples were collected at 24 hours post amputation hpA and dissociated into a single cell suspension. The concentration of freshly dissociated cells was adjusted to 700 800 cells/μl in PBS aiming to capture 4 000 cells by the 10X genomics device. Libraries were constructed according to the manufacturer's instructions using Chromium™ Single Cell three prime v3.1 Reagent Kits and a Chromium instrument.,GEO Accession:GSM4812243,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP285950,,loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=Cut S7 L002 R1 001.fastq.gz   read2PairFiles=Cut S7 L002 R2 001.fastq.gz   read3PairFiles=Cut S7 L002 I1 001.fastq.gz,Cut_S7_L002_I1_001.fastq.gz Cut_S7_L002_R1_001.fastq.gz Cut_S7_L002_R2_001.fastq.gz,fastq fastq fastq,17511283926.0,142368162.0,GSM4812243 r2,0:28 1:87 2:8,A:4836849959;C:3920920286;G:4362769830;T:4389644044;N:1099807,28,87,8,,4836849959,3920920286,4362769830,4389644044,1099807,SRX9221654,SRS7455355,SRA1136463,GEO,"Institute for Regenerative Medecine and Biotherapy, University Hospital of Montpellier, Inserm",1,0.63847,,0.11249,,0.82231,,0.51524,,87,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,France,2020-09-30,Larval,Larval,Fin,Surface Structure
65589,SRR15390211,SRX11692441,SRS9724035,SRP331755,PRJNA753151,scRNA seq of fin and body zebrafish melanocytes,GSE181748,Transcriptome Analysis,Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here  we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body  whereas the acral subtype arises on the palms of the hands  soles of the feet  or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs  indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes  compared to body melanocytes  revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma  which was generated by injecting Casper fish with MniCoopR GFP  mitfa:hsCRKL  mitfa:hsGAB2  mitfa:hsTERT  mitfa:Cas9 mCherry;U6nf1a gRNA  mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins  digested using liberase  and then FACS sorted for GFP+ melanocytes and GFP  microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total  GFP+ body cells  GFP  body cells  GFP+ fin cells  GFP  fin cells. Data was then analyzed and pooled together  taking note of their sample origin.,,pubmed:35355015,,XFN,GSM5510267,,source name:Zebrafish fins|model:Acral melanoma model Caspers with MiniCoopR eGFP  mitfa:hsCRKL  mitfa:hsGAB2  mitfa:hsTERT  mitfa:Cas9 mCherry;U6 nf1a gRNA  mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP ,XFN,Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao  Hao et al.  2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija  2019. Principal component analysis Joliffe  1986 and UMAP dimensionality reduction McInnes  2018 were performed using default parameters  with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al.  2020; Hunter  Moncada et al.  2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output,Zebrafish fins,,Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics,,model:Acral melanoma model Caspers with MiniCoopR eGFP  mitfa:hsCRKL  mitfa:hsGAB2  mitfa:hsTERT  mitfa:Cas9 mCherry;U6 nf1a gRNA  mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP ,GSM5510267,GSM5510267: XFN; Danio rerio; RNA Seq,GSM5510267,,1,Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics,GEO Accession:GSM5510267,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP331755,,,2385_XFN_IGO_11718_4_S4_L001_R1_001.fastq.gz 2385_XFN_IGO_11718_4_S4_L001_R2_001.fastq.gz,fastq fastq,20452607604.0,174808612.0,GSM5510267 r1,0:29 1:88,A:5729911089;C:4526353776;G:4631244451;T:5564405432;N:692856,29,88,,,5729911089,4526353776,4631244451,5564405432,692856,SRX11692441,SRS9724035,SRA1274997,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.00608,0.85139,0.00196,0.14282,0.99093,0.78543,0.42676,0.53168,29,88,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-09,Undetermined,Adult,Fin,Surface Structure
65590,SRR15390212,SRX11692441,SRS9724035,SRP331755,PRJNA753151,scRNA seq of fin and body zebrafish melanocytes,GSE181748,Transcriptome Analysis,Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here  we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body  whereas the acral subtype arises on the palms of the hands  soles of the feet  or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs  indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes  compared to body melanocytes  revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma  which was generated by injecting Casper fish with MniCoopR GFP  mitfa:hsCRKL  mitfa:hsGAB2  mitfa:hsTERT  mitfa:Cas9 mCherry;U6nf1a gRNA  mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins  digested using liberase  and then FACS sorted for GFP+ melanocytes and GFP  microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total  GFP+ body cells  GFP  body cells  GFP+ fin cells  GFP  fin cells. Data was then analyzed and pooled together  taking note of their sample origin.,,pubmed:35355015,,XFN,GSM5510267,,source name:Zebrafish fins|model:Acral melanoma model Caspers with MiniCoopR eGFP  mitfa:hsCRKL  mitfa:hsGAB2  mitfa:hsTERT  mitfa:Cas9 mCherry;U6 nf1a gRNA  mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP ,XFN,Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao  Hao et al.  2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija  2019. Principal component analysis Joliffe  1986 and UMAP dimensionality reduction McInnes  2018 were performed using default parameters  with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al.  2020; Hunter  Moncada et al.  2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output,Zebrafish fins,,Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics,,model:Acral melanoma model Caspers with MiniCoopR eGFP  mitfa:hsCRKL  mitfa:hsGAB2  mitfa:hsTERT  mitfa:Cas9 mCherry;U6 nf1a gRNA  mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP ,GSM5510267,GSM5510267: XFN; Danio rerio; RNA Seq,GSM5510267,,1,Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics,GEO Accession:GSM5510267,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP331755,,,2385_XFN_IGO_11718_4_S4_L002_R1_001.fastq.gz 2385_XFN_IGO_11718_4_S4_L002_R2_001.fastq.gz,fastq fastq,20056571028.0,171423684.0,GSM5510267 r2,0:29 1:88,A:5624358913;C:4435209829;G:4536840173;T:5459497012;N:665101,29,88,,,5624358913,4435209829,4536840173,5459497012,665101,SRX11692441,SRS9724035,SRA1274997,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.00636,0.85263,0.00229,0.14314,0.99113,0.78206,0.42564,0.53095,29,88,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-09,Undetermined,Adult,Fin,Surface Structure
65591,SRR15390209,SRX11692439,SRS9724039,SRP331755,PRJNA753151,scRNA seq of fin and body zebrafish melanocytes,GSE181748,Transcriptome Analysis,Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here  we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body  whereas the acral subtype arises on the palms of the hands  soles of the feet  or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs  indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes  compared to body melanocytes  revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma  which was generated by injecting Casper fish with MniCoopR GFP  mitfa:hsCRKL  mitfa:hsGAB2  mitfa:hsTERT  mitfa:Cas9 mCherry;U6nf1a gRNA  mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins  digested using liberase  and then FACS sorted for GFP+ melanocytes and GFP  microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total  GFP+ body cells  GFP  body cells  GFP+ fin cells  GFP  fin cells. Data was then analyzed and pooled together  taking note of their sample origin.,,pubmed:35355015,,XFG,GSM5510266,,source name:Zebrafish fins|model:Acral melanoma model Caspers with MiniCoopR eGFP  mitfa:hsCRKL  mitfa:hsGAB2  mitfa:hsTERT  mitfa:Cas9 mCherry;U6 nf1a gRNA  mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP+,XFG,Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao  Hao et al.  2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija  2019. Principal component analysis Joliffe  1986 and UMAP dimensionality reduction McInnes  2018 were performed using default parameters  with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al.  2020; Hunter  Moncada et al.  2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output,Zebrafish fins,,Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics,,model:Acral melanoma model Caspers with MiniCoopR eGFP  mitfa:hsCRKL  mitfa:hsGAB2  mitfa:hsTERT  mitfa:Cas9 mCherry;U6 nf1a gRNA  mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP+,GSM5510266,GSM5510266: XFG; Danio rerio; RNA Seq,GSM5510266,,1,Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics,GEO Accession:GSM5510266,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP331755,,,2384_XFG_IGO_11718_3_S3_L001_R1_001.fastq.gz 2384_XFG_IGO_11718_3_S3_L001_R2_001.fastq.gz,fastq fastq,21239736102.0,181536206.0,GSM5510266 r1,0:29 1:88,A:6013451435;C:4631285818;G:4786546365;T:5807740759;N:711725,29,88,,,6013451435,4631285818,4786546365,5807740759,711725,SRX11692439,SRS9724039,SRA1274997,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.00797,0.89811,0.00258,0.14942,0.9889,0.79259,0.38209,0.54357,29,88,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-09,Undetermined,Adult,Fin,Surface Structure
65592,SRR15390210,SRX11692439,SRS9724039,SRP331755,PRJNA753151,scRNA seq of fin and body zebrafish melanocytes,GSE181748,Transcriptome Analysis,Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre existing transcriptional programs in the cell of origin. Here  we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body  whereas the acral subtype arises on the palms of the hands  soles of the feet  or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs  indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes  compared to body melanocytes  revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults. Overall design: For this experiment we used our zebrafish transgenic model of Acral melanoma  which was generated by injecting Casper fish with MniCoopR GFP  mitfa:hsCRKL  mitfa:hsGAB2  mitfa:hsTERT  mitfa:Cas9 mCherry;U6nf1a gRNA  mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins  digested using liberase  and then FACS sorted for GFP+ melanocytes and GFP  microenviornmental cells. Each sample constituted a pooling of 2 males and 2 females that were 6 mpf This led to generation of 4 samples total  GFP+ body cells  GFP  body cells  GFP+ fin cells  GFP  fin cells. Data was then analyzed and pooled together  taking note of their sample origin.,,pubmed:35355015,,XFG,GSM5510266,,source name:Zebrafish fins|model:Acral melanoma model Caspers with MiniCoopR eGFP  mitfa:hsCRKL  mitfa:hsGAB2  mitfa:hsTERT  mitfa:Cas9 mCherry;U6 nf1a gRNA  mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP+,XFG,Data was processed using R version 4.0.4 and Seurat version 4.0.3 Hao  Hao et al.  2021. Each of the four reactions were processed separately before merging into a single object. Cells with fewer than 200 unique genes were filtered out. Expression data was normalized with SCTransform Hafemeister and Satija  2019. Principal component analysis Joliffe  1986 and UMAP dimensionality reduction McInnes  2018 were performed using default parameters  with 15 principal components used for UMAP calculations. Clustering was done using the Seurat function FindMarkers with a resolution of 0.2. Clusters were annotated based on expression of zebrafish cell type marker genes as done previously Baron et al.  2020; Hunter  Moncada et al.  2021. Genome build: GRCz10 Supplementary files format and content: csv file containing counts from all 4 samples Supplementary files format and content: Cell ranger output,Zebrafish fins,,Droplet based scRNA seq was performed using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics,,model:Acral melanoma model Caspers with MiniCoopR eGFP  mitfa:hsCRKL  mitfa:hsGAB2  mitfa:hsTERT  mitfa:Cas9 mCherry;U6 nf1a gRNA  mitfa:Cas9 mCherry;U6 nf1b gRNA|tissue:Fin|cell type:GFP+,GSM5510266,GSM5510266: XFG; Danio rerio; RNA Seq,GSM5510266,,1,Droplet based scRNA seq was performed using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 10 000 cells were encapsulated per each of the four reactions. GEM generation and library preparation was performed according to kit instructions. Libraries were sequenced on a NovaSeq S4 flow cell. Sequencing parameters were: Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 40 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger version 5.0.1 10X Genomics. scRNA seq 10X genomics,GEO Accession:GSM5510266,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP331755,,,2384_XFG_IGO_11718_3_S3_L002_R1_001.fastq.gz 2384_XFG_IGO_11718_3_S3_L002_R2_001.fastq.gz,fastq fastq,20799675234.0,177775002.0,GSM5510266 r2,0:29 1:88,A:5894902894;C:4531100030;G:4681582244;T:5691398362;N:691704,29,88,,,5894902894,4531100030,4681582244,5691398362,691704,SRX11692439,SRS9724039,SRA1274997,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.00787,0.89764,0.00227,0.14926,0.98821,0.78928,0.40092,0.53114,29,88,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-09,Undetermined,Adult,Fin,Surface Structure