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
25297,SRR25764099,SRX21486772,SRS18719072,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,Adult itgb4+ basal cells,GSM7734879,,tissue:epidermal cells|cell type:adult fin epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing,Adult itgb4+ basal cells,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:adult fin epidermal basal cells|genotype:Tgitgb4:mcherry,GSM7734879,GSM7734879: Adult itgb4+ basal cells; Danio rerio; RNA Seq,GSM7734879 r1,GSM7734879,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,Adult_itgb4mcherry_S230_R1_001.fastq.gz Adult_itgb4mcherry_S230_R2_001.fastq.gz,fastq fastq,5035430000.0,12588575.0,GSM7734879 r1,0:200 1:200,A:1339392170;C:1117195164;G:1254708952;T:1323174485;N:959229,200,200,,,1339392170,1117195164,1254708952,1323174485,959229,SRX21486772,SRS18719072,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.01543,0.02468,0.00098,0.00102,0.99318,0.99387,0.47878,0.31718,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Adult,Adult,Skin,Surface Structure
25298,SRR25764100,SRX21486771,SRS18719071,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,1 dpf itgb4+ embryonic basal precursors rep2,GSM7734878,,tissue:epidermal cells|cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing,1 dpf itgb4+ embryonic basal precursors rep2,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry,GSM7734878,GSM7734878: 1 dpf itgb4+ embryonic basal precursors rep2; Danio rerio; RNA Seq,GSM7734878 r1,GSM7734878,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,itgb4mcherry_2_S229_R1_001.fastq.gz itgb4mcherry_2_S229_R2_001.fastq.gz,fastq fastq,6040245600.0,15100614.0,GSM7734878 r1,0:200 1:200,A:1588346322;C:1356558310;G:1524614760;T:1569583583;N:1142625,200,200,,,1588346322,1356558310,1524614760,1569583583,1142625,SRX21486771,SRS18719071,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.0156,0.0191,0.00074,0.00093,0.99024,0.99088,0.47058,0.47838,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Multi-stage,Multi-stage,Skin,Surface Structure
25299,SRR25764101,SRX21486770,SRS18719070,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,1 dpf itgb4+ embryonic basal precursors rep1,GSM7734877,,tissue:epidermal cells|cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing,1 dpf itgb4+ embryonic basal precursors rep1,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry,GSM7734877,GSM7734877: 1 dpf itgb4+ embryonic basal precursors rep1; Danio rerio; RNA Seq,GSM7734877 r1,GSM7734877,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,itgb4mcherry_1_S20_R1_001.fastq.gz itgb4mcherry_1_S20_R2_001.fastq.gz,fastq fastq,7055215600.0,17638039.0,GSM7734877 r1,0:200 1:200,A:1894635584;C:1556854856;G:1769420212;T:1825520802;N:8784146,200,200,,,1894635584,1556854856,1769420212,1825520802,8784146,SRX21486770,SRS18719070,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.01135,0.01881,0.00043,0.00016,0.9932,0.99543,0.46234,0.43106,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Multi-stage,Multi-stage,Skin,Surface Structure
25300,SRR25764102,SRX21486769,SRS18719069,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,1 dpf krt4+ embryonic periderm cells rep2,GSM7734876,,tissue:epidermal cells|cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp|geo loc name:missing|collection date:missing,1 dpf krt4+ embryonic periderm cells rep2,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp,GSM7734876,GSM7734876: 1 dpf krt4+ embryonic periderm cells rep2; Danio rerio; RNA Seq,GSM7734876 r1,GSM7734876,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,krt4cre-gfp_2_S4_R2_001.fastq.gz krt4cre-gfp_2_S4_R1_001.fastq.gz,fastq fastq,9439207600.0,23598019.0,GSM7734876 r1,0:200 1:200,A:2499982675;C:2086665360;G:2395002073;T:2454282285;N:3275207,200,200,,,2499982675,2086665360,2395002073,2454282285,3275207,SRX21486769,SRS18719069,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.44931,0.01877,0.02236,0.00115,0.80012,0.99032,0.45473,0.49453,200,200,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Multi-stage,Multi-stage,Skin,Surface Structure
25301,SRR25764103,SRX21486768,SRS18719066,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,1 dpf krt4+ embryonic periderm cells rep1,GSM7734875,,tissue:epidermal cells|cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp|geo loc name:missing|collection date:missing,1 dpf krt4+ embryonic periderm cells rep1,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp,GSM7734875,GSM7734875: 1 dpf krt4+ embryonic periderm cells rep1; Danio rerio; RNA Seq,GSM7734875 r1,GSM7734875,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,krt4cre-gfp_1_S19_R2_001.fastq.gz krt4cre-gfp_1_S19_R1_001.fastq.gz,fastq fastq,6119547200.0,15298868.0,GSM7734875 r1,0:200 1:200,A:1642059769;C:1349462427;G:1535937964;T:1584527048;N:7559992,200,200,,,1642059769,1349462427,1535937964,1584527048,7559992,SRX21486768,SRS18719066,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.01112,0.01017,0.0003,0.00014,0.9931,0.99586,0.43605,0.40821,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Multi-stage,Multi-stage,Skin,Surface Structure
33892,SRR30866052,SRX26263961,SRS22803217,SRP536276,PRJNA1168147,Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [scRNA seq],GSE278654,Transcriptome Analysis,Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To understand how selective N glycosylation modification performed by mgat4b promote melanocyte development  we performed single cell RNA sequencing of mitfa+ve melanophores sorted from the 36hpf staged zebrafish.,,,,m4b mut,GSM8552316,,tissue:melanocytes|cell type:melanocytes|age:36 hpf|genotype:mgat4b mutant|treatment:No|geo loc name:missing|collection date:missing,m4b mut,Cellranger mkfastq pipeline was used to generate fastq files The fastq files were then aligned with custom zebrafish reference assembly GRCz11 using cellranger. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including barcodes and features  and matrix files,melanocytes,,The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction,,cell type:melanocytes|age:36 hpf|genotype:mgat4b mutant|treatment:No,GSM8552316,GSM8552316: m4b mut; Danio rerio; RNA Seq,GSM8552316 r1,GSM8552316,1,The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536276,,loader:fastq load.py,m4b_mut_S2_L001_I1_001.fastq.gz m4b_mut_S2_L001_I2_001.fastq.gz m4b_mut_S2_L001_R1_001.fastq.gz m4b_mut_S2_L001_R2_001.fastq.gz,fastq fastq fastq fastq,18274385040.0,132423080.0,GSM8552316 r1,0:10 1:10 2:28 3:90,A:3788703303;C:2355223955;G:2645521958;T:3126630009;N:1997975,10,10,28,90,3788703303,2355223955,2645521958,3126630009,1997975,SRX26263961,SRS22803217,SRA1984944,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,India,2024-10-02,Pharyngula,Embryo,Skin,Surface Structure
33893,SRR30866053,SRX26263960,SRS22803216,SRP536276,PRJNA1168147,Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [scRNA seq],GSE278654,Transcriptome Analysis,Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To understand how selective N glycosylation modification performed by mgat4b promote melanocyte development  we performed single cell RNA sequencing of mitfa+ve melanophores sorted from the 36hpf staged zebrafish.,,,,Control,GSM8552315,,tissue:melanocytes|cell type:melanocytes|age:36 hpf|genotype:control|treatment:No|geo loc name:missing|collection date:missing,Control,Cellranger mkfastq pipeline was used to generate fastq files The fastq files were then aligned with custom zebrafish reference assembly GRCz11 using cellranger. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including barcodes and features  and matrix files,melanocytes,,The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction,,cell type:melanocytes|age:36 hpf|genotype:control|treatment:No,GSM8552315,GSM8552315: Control; Danio rerio; RNA Seq,GSM8552315 r1,GSM8552315,1,The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536276,,loader:fastq load.py,con_S1_L001_I1_001.fastq.gz con_S1_L001_I2_001.fastq.gz con_S1_L001_R1_001.fastq.gz con_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,15825218034.0,114675493.0,GSM8552315 r1,0:10 1:10 2:28 3:90,A:3074750870;C:2137365424;G:2401965854;T:2704984993;N:1727229,10,10,28,90,3074750870,2137365424,2401965854,2704984993,1727229,SRX26263960,SRS22803216,SRA1984944,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,India,2024-10-02,Pharyngula,Embryo,Skin,Surface Structure
33894,SRR30866028,SRX26263941,SRS22803195,SRP536275,PRJNA1168148,Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq],GSE278653,Transcriptome Analysis,Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.,,,,m4b mut melanoma  biol rep 2,GSM8552314,,source name:skin|tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI|geo loc name:missing|collection date:missing,m4b mut melanoma  biol rep 2,Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample,skin,,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI,GSM8552314,GSM8552314: m4b mut melanoma  biol rep 2; Danio rerio; RNA Seq,GSM8552314 r1,GSM8552314,1,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536275,,,MKO2_S39_R1_001.fastq.gz MKO2_S39_R2_001.fastq.gz,fastq fastq,3705364625.0,14164066.0,GSM8552314 r1,0:126.72 1:134.89,A:785806700;C:949078797;G:1178279032;T:784972987;N:7227109,126,134,,,785806700,949078797,1178279032,784972987,7227109,SRX26263941,SRS22803195,SRA1984938,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,trueseq,sc_generic,bulk,bulk,,India,2024-10-02,Undetermined,Undetermined,Skin,Surface Structure
33895,SRR30866029,SRX26263940,SRS22803194,SRP536275,PRJNA1168148,Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq],GSE278653,Transcriptome Analysis,Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.,,,,m4b mut melanoma  biol rep 1,GSM8552313,,source name:skin|tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI|geo loc name:missing|collection date:missing,m4b mut melanoma  biol rep 1,Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample,skin,,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI,GSM8552313,GSM8552313: m4b mut melanoma  biol rep 1; Danio rerio; RNA Seq,GSM8552313 r1,GSM8552313,1,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536275,,,MKO1_S38_R1_001.fastq.gz MKO1_S38_R2_001.fastq.gz,fastq fastq,4779377372.0,18058294.0,GSM8552313 r1,0:128.72 1:135.94,A:1016908920;C:1236613888;G:1502465334;T:1018053808;N:5335422,128,135,,,1016908920,1236613888,1502465334,1018053808,5335422,SRX26263940,SRS22803194,SRA1984938,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,trueseq,sc_generic,bulk,bulk,,India,2024-10-02,Undetermined,Undetermined,Skin,Surface Structure
33896,SRR30866030,SRX26263939,SRS22803193,SRP536275,PRJNA1168148,Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq],GSE278653,Transcriptome Analysis,Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.,,,,wild type melanoma control  biol rep 2,GSM8552312,,source name:skin|tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI|geo loc name:missing|collection date:missing,wild type melanoma control  biol rep 2,Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample,skin,,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI,GSM8552312,GSM8552312: wild type melanoma control  biol rep 2; Danio rerio; RNA Seq,GSM8552312 r1,GSM8552312,1,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536275,,,EV2_S37_R1_001.fastq.gz EV2_S37_R2_001.fastq.gz,fastq fastq,5427379509.0,19981504.0,GSM8552312 r1,0:133.16 1:138.46,A:1136639418;C:1414638483;G:1736492639;T:1137614638;N:1994331,133,138,,,1136639418,1414638483,1736492639,1137614638,1994331,SRX26263939,SRS22803193,SRA1984938,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,trueseq,sc_generic,bulk,bulk,,India,2024-10-02,Undetermined,Undetermined,Skin,Surface Structure
33897,SRR30866031,SRX26263938,SRS22803192,SRP536275,PRJNA1168148,Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq],GSE278653,Transcriptome Analysis,Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.,,,,wild type melanoma control  biol rep 1,GSM8552311,,source name:skin|tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI|geo loc name:missing|collection date:missing,wild type melanoma control  biol rep 1,Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample,skin,,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI,GSM8552311,GSM8552311: wild type melanoma control  biol rep 1; Danio rerio; RNA Seq,GSM8552311 r1,GSM8552311,1,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536275,,,EV1_S36_R1_001.fastq.gz EV1_S36_R2_001.fastq.gz,fastq fastq,5248108957.0,19087024.0,GSM8552311 r1,0:135.12 1:139.84,A:1112163842;C:1354895660;G:1658732932;T:1120342985;N:1973538,135,139,,,1112163842,1354895660,1658732932,1120342985,1973538,SRX26263938,SRS22803192,SRA1984938,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,trueseq,sc_generic,bulk,bulk,,India,2024-10-02,Undetermined,Undetermined,Skin,Surface Structure
33898,SRR30866032,SRX26263937,SRS22803191,SRP536275,PRJNA1168148,Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq],GSE278653,Transcriptome Analysis,Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.,,,,melanophore  biol rep 2,GSM8552310,,source name:skin|tissue:skin|cell type:melanophore|genotype:WT|treatment:No|geo loc name:missing|collection date:missing,melanophore  biol rep 2,Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample,skin,,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,tissue:skin|cell type:melanophore|genotype:WT|treatment:No,GSM8552310,GSM8552310: melanophore  biol rep 2; Danio rerio; RNA Seq,GSM8552310 r1,GSM8552310,1,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536275,,,WT2_S41_R1_001.fastq.gz WT2_S41_R2_001.fastq.gz,fastq fastq,4636631881.0,16340506.0,GSM8552310 r1,0:140.47 1:143.28,A:1114533149;C:1104066636;G:1293649625;T:1122672029;N:1710442,140,143,,,1114533149,1104066636,1293649625,1122672029,1710442,SRX26263937,SRS22803191,SRA1984938,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,trueseq,sc_generic,bulk,bulk,,India,2024-10-02,Undetermined,Undetermined,Skin,Surface Structure
33899,SRR30866033,SRX26263936,SRS22803190,SRP536275,PRJNA1168148,Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq],GSE278653,Transcriptome Analysis,Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.,,,,melanophore  biol rep 1,GSM8552309,,source name:skin|tissue:skin|cell type:melanophore|genotype:WT|treatment:No|geo loc name:missing|collection date:missing,melanophore  biol rep 1,Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample,skin,,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,tissue:skin|cell type:melanophore|genotype:WT|treatment:No,GSM8552309,GSM8552309: melanophore  biol rep 1; Danio rerio; RNA Seq,GSM8552309 r1,GSM8552309,1,The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536275,,,WT1_S40_R1_001.fastq.gz WT1_S40_R2_001.fastq.gz,fastq fastq,5185761246.0,18118534.0,GSM8552309 r1,0:141.81 1:144.40,A:1231235669;C:1235759770;G:1476864583;T:1240636871;N:1264353,141,144,,,1231235669,1235759770,1476864583,1240636871,1264353,SRX26263936,SRS22803190,SRA1984938,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,trueseq,sc_generic,bulk,bulk,,India,2024-10-02,Undetermined,Undetermined,Skin,Surface Structure
36717,SRR835162,SRX271958,SRS416254,SRP021517,PRJNA198908,Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin,GSE46387,Transcriptome Analysis,In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing,,pubmed:23874447,,dm 77h 28 399s62,GSM1129620,,tissue:melanocytes|hpf,dm 77h 28 399s62,Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library,melanocytes,,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,,hpf,GSM1129620,GSM1129620: dm 77h 28 399s62; Danio rerio; RNA Seq,GSM1129620 1,,1,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,GEO Accession:GSM1129620,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP021517,,,,,731276158.0,3620179.0,GSM1129620 r1,0:101 1:101,A:173989639;C:199270484;G:188281318;T:169725601;N:9116,101,101,,,173989639,199270484,188281318,169725601,9116,SRX271958,SRS416254,SRA074390,GEO,"Rob Mitra, Genetics, Washington University",2,0.84122,0.79964,0.02274,0.02168,0.89645,0.89073,0.63341,0.63015,101,101,B,B,biological fallback assumption,illumina,hiseq_era,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2013-04-25,Larval,Larval,Skin,Surface Structure
36718,SRR835161,SRX271957,SRS416253,SRP021517,PRJNA198908,Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin,GSE46387,Transcriptome Analysis,In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing,,pubmed:23874447,,dm 77h 28 399s61,GSM1129619,,tissue:melanocytes|hpf,dm 77h 28 399s61,Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library,melanocytes,,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,,hpf,GSM1129619,GSM1129619: dm 77h 28 399s61; Danio rerio; RNA Seq,GSM1129619 1,,1,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,GEO Accession:GSM1129619,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP021517,,,dm_77h_28_399s61_CACT.fq.bz2 dm_77h_28_399s62_CACT.fq.bz2,fastq fastq,731276158.0,3620179.0,GSM1129619 r1,0:101 1:101,A:173989639;C:199270484;G:188281318;T:169725601;N:9116,101,101,,,173989639,199270484,188281318,169725601,9116,SRX271957,SRS416253,SRA074390,GEO,"Rob Mitra, Genetics, Washington University",2,0.84121,0.79968,0.02287,0.02141,0.89658,0.89051,0.63318,0.63061,101,101,B,B,biological fallback assumption,illumina,hiseq_era,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2013-04-25,Larval,Larval,Skin,Surface Structure
36725,SRR835154,SRX271950,SRS416245,SRP021517,PRJNA198908,Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin,GSE46387,Transcriptome Analysis,In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing,,pubmed:23874447,,dm 77h 25 399s62,GSM1129612,,tissue:melanocytes|hpf,dm 77h 25 399s62,Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library,melanocytes,,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,,hpf,GSM1129612,GSM1129612: dm 77h 25 399s62; Danio rerio; RNA Seq,GSM1129612 1,,1,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,GEO Accession:GSM1129612,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP021517,,,,,1715809008.0,8494104.0,GSM1129612 r1,0:101 1:101,A:405310561;C:444474389;G:467897835;T:398105078;N:21145,101,101,,,405310561,444474389,467897835,398105078,21145,SRX271950,SRS416245,SRA074390,GEO,"Rob Mitra, Genetics, Washington University",2,0.66327,0.58026,0.07911,0.07288,0.91721,0.9083,0.56907,0.5363,101,101,B,B,biological fallback assumption,illumina,hiseq_era,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2013-04-25,Larval,Larval,Skin,Surface Structure
36726,SRR835153,SRX271949,SRS416246,SRP021517,PRJNA198908,Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin,GSE46387,Transcriptome Analysis,In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing,,pubmed:23874447,,dm 77h 25 399s61,GSM1129611,,tissue:melanocytes|hpf,dm 77h 25 399s61,Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library,melanocytes,,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,,hpf,GSM1129611,GSM1129611: dm 77h 25 399s61; Danio rerio; RNA Seq,GSM1129611 1,,1,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,GEO Accession:GSM1129611,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP021517,,,dm_77h_25_399s61_TCTT.fq.bz2 dm_77h_25_399s62_TCTT.fq.bz2,fastq fastq,1715809008.0,8494104.0,GSM1129611 r1,0:101 1:101,A:405310561;C:444474389;G:467897835;T:398105078;N:21145,101,101,,,405310561,444474389,467897835,398105078,21145,SRX271949,SRS416246,SRA074390,GEO,"Rob Mitra, Genetics, Washington University",2,0.66325,0.58027,0.0792,0.07327,0.91741,0.90847,0.56374,0.53632,101,101,B,B,biological fallback assumption,illumina,hiseq_era,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2013-04-25,Larval,Larval,Skin,Surface Structure
51228,SRR8591752,SRX5391965,SRS4379795,SRP186291,PRJNA523219,Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs,GSE126763,Transcriptome Analysis,In order to have a comprehensive comparison of  locally restricted mpeg1+ cells MLCs and cLCs  we isolated  locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls  keratinocytes  T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis  including locally restricted mpeg1+ cells  cLCs  keratinocytes  T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol  library construction and whole transcriptome RNA sequencing were proformed by Novogene.,,pubmed:31006648,,T cells 3,GSM3612324,,source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx,T cells 3,Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample,specific cells types in zebrafish epidermis,,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,,tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx,GSM3612324,GSM3612324: T cells 3; Danio rerio; RNA Seq,GSM3612324,,1,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,GEO Accession:GSM3612324,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP186291,,,T_cells_3_R2.fq.gz T_cells_3_R1.fq.gz,fastq fastq,11144333100.0,37147777.0,GSM3612324 r1,0:150 1:150,A:3499952862;C:2003192621;G:2060397654;T:3580454183;N:335780,150,150,,,3499952862,2003192621,2060397654,3580454183,335780,SRX5391965,SRS4379795,SRA850414,GEO,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.7813,0.78015,0.18285,0.17813,0.83978,0.84051,0.5593,0.449,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,nebnext,sc,single_cell_plate,smartseq,,China,2019-02-19,Adult,Adult,Skin,Surface Structure
51229,SRR8591751,SRX5391964,SRS4379794,SRP186291,PRJNA523219,Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs,GSE126763,Transcriptome Analysis,In order to have a comprehensive comparison of  locally restricted mpeg1+ cells MLCs and cLCs  we isolated  locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls  keratinocytes  T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis  including locally restricted mpeg1+ cells  cLCs  keratinocytes  T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol  library construction and whole transcriptome RNA sequencing were proformed by Novogene.,,pubmed:31006648,,T cells 2,GSM3612323,,source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx,T cells 2,Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample,specific cells types in zebrafish epidermis,,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,,tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx,GSM3612323,GSM3612323: T cells 2; Danio rerio; RNA Seq,GSM3612323,,1,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,GEO Accession:GSM3612323,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP186291,,,T_cells_2_R2.fq.gz T_cells_2_R1.fq.gz,fastq fastq,7919587200.0,26398624.0,GSM3612323 r1,0:150 1:150,A:2465301954;C:1441444830;G:1480576895;T:2531979045;N:284476,150,150,,,2465301954,1441444830,1480576895,2531979045,284476,SRX5391964,SRS4379794,SRA850414,GEO,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.78322,0.78133,0.14641,0.14616,0.8547,0.8537,0.46251,0.56483,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,nebnext,sc,single_cell_plate,smartseq,,China,2019-02-19,Adult,Adult,Skin,Surface Structure
51230,SRR8591750,SRX5391963,SRS4379793,SRP186291,PRJNA523219,Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs,GSE126763,Transcriptome Analysis,In order to have a comprehensive comparison of  locally restricted mpeg1+ cells MLCs and cLCs  we isolated  locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls  keratinocytes  T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis  including locally restricted mpeg1+ cells  cLCs  keratinocytes  T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol  library construction and whole transcriptome RNA sequencing were proformed by Novogene.,,pubmed:31006648,,T cells 1,GSM3612322,,source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx,T cells 1,Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample,specific cells types in zebrafish epidermis,,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,,tissue:epidermis|Stage:adult|transgenic line:Tglck:DsRedx,GSM3612322,GSM3612322: T cells 1; Danio rerio; RNA Seq,GSM3612322,,1,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,GEO Accession:GSM3612322,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP186291,,,T_cells_1_R2.fq.gz T_cells_1_R1.fq.gz,fastq fastq,10355072400.0,34516908.0,GSM3612322 r1,0:150 1:150,A:2939445450;C:2059218859;G:2124006194;T:3229931547;N:2470350,150,150,,,2939445450,2059218859,2124006194,3229931547,2470350,SRX5391963,SRS4379793,SRA850414,GEO,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.82838,0.8272,0.19005,0.18949,0.81128,0.81227,0.52045,0.51858,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,nebnext,sc,single_cell_plate,smartseq,,China,2019-02-19,Adult,Adult,Skin,Surface Structure
51231,SRR8591749,SRX5391962,SRS4379792,SRP186291,PRJNA523219,Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs,GSE126763,Transcriptome Analysis,In order to have a comprehensive comparison of  locally restricted mpeg1+ cells MLCs and cLCs  we isolated  locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls  keratinocytes  T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis  including locally restricted mpeg1+ cells  cLCs  keratinocytes  T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol  library construction and whole transcriptome RNA sequencing were proformed by Novogene.,,pubmed:31006648,,Neutrophils 3,GSM3612321,,source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP,Neutrophils 3,Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample,specific cells types in zebrafish epidermis,,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,,tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP,GSM3612321,GSM3612321: Neutrophils 3; Danio rerio; RNA Seq,GSM3612321,,1,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,GEO Accession:GSM3612321,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP186291,,,Neutrophils_3_R1.fq.gz Neutrophils_3_R2.fq.gz,fastq fastq,8692700700.0,28975669.0,GSM3612321 r1,0:150 1:150,A:2652684352;C:1652069995;G:1735457120;T:2652129934;N:359299,150,150,,,2652684352,1652069995,1735457120,2652129934,359299,SRX5391962,SRS4379792,SRA850414,GEO,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.8145,0.81686,0.10965,0.10808,0.92713,0.92744,0.55607,0.57186,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,nebnext,sc,single_cell_plate,smartseq,,China,2019-02-19,Adult,Adult,Skin,Surface Structure
51232,SRR8591748,SRX5391961,SRS4379791,SRP186291,PRJNA523219,Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs,GSE126763,Transcriptome Analysis,In order to have a comprehensive comparison of  locally restricted mpeg1+ cells MLCs and cLCs  we isolated  locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls  keratinocytes  T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis  including locally restricted mpeg1+ cells  cLCs  keratinocytes  T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol  library construction and whole transcriptome RNA sequencing were proformed by Novogene.,,pubmed:31006648,,Neutrophils 2,GSM3612320,,source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP,Neutrophils 2,Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample,specific cells types in zebrafish epidermis,,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,,tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP,GSM3612320,GSM3612320: Neutrophils 2; Danio rerio; RNA Seq,GSM3612320,,1,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,GEO Accession:GSM3612320,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP186291,,,Neutrophils_2_R1.fq.gz Neutrophils_2_R2.fq.gz,fastq fastq,7327680000.0,24425600.0,GSM3612320 r1,0:150 1:150,A:2187183417;C:1429377098;G:1474177623;T:2236324081;N:617781,150,150,,,2187183417,1429377098,1474177623,2236324081,617781,SRX5391961,SRS4379791,SRA850414,GEO,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.84825,0.84925,0.11406,0.11367,0.91244,0.91277,0.54443,0.52025,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,nebnext,sc,single_cell_plate,smartseq,,China,2019-02-19,Adult,Adult,Skin,Surface Structure
51233,SRR8591747,SRX5391960,SRS4379790,SRP186291,PRJNA523219,Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs,GSE126763,Transcriptome Analysis,In order to have a comprehensive comparison of  locally restricted mpeg1+ cells MLCs and cLCs  we isolated  locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls  keratinocytes  T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis  including locally restricted mpeg1+ cells  cLCs  keratinocytes  T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol  library construction and whole transcriptome RNA sequencing were proformed by Novogene.,,pubmed:31006648,,Neutrophils 1,GSM3612319,,source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP,Neutrophils 1,Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample,specific cells types in zebrafish epidermis,,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,,tissue:epidermis|Stage:adult|transgenic line:Tglyz:GFP,GSM3612319,GSM3612319: Neutrophils 1; Danio rerio; RNA Seq,GSM3612319,,1,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,GEO Accession:GSM3612319,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP186291,,,Neutrophils_1_R1.fq.gz Neutrophils_1_R2.fq.gz,fastq fastq,12087825300.0,40292751.0,GSM3612319 r1,0:150 1:150,A:3327151170;C:2523891980;G:2588985485;T:3644916170;N:2880495,150,150,,,3327151170,2523891980,2588985485,3644916170,2880495,SRX5391960,SRS4379790,SRA850414,GEO,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.88642,0.88127,0.10539,0.10565,0.85151,0.85451,0.45008,0.4553,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,nebnext,sc,single_cell_plate,smartseq,,China,2019-02-19,Adult,Adult,Skin,Surface Structure
51234,SRR8591746,SRX5391959,SRS4379789,SRP186291,PRJNA523219,Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs,GSE126763,Transcriptome Analysis,In order to have a comprehensive comparison of  locally restricted mpeg1+ cells MLCs and cLCs  we isolated  locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls  keratinocytes  T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis  including locally restricted mpeg1+ cells  cLCs  keratinocytes  T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol  library construction and whole transcriptome RNA sequencing were proformed by Novogene.,,pubmed:31006648,,MLCs 4,GSM3612318,,source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP,MLCs 4,Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample,specific cells types in zebrafish epidermis,,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,,tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP,GSM3612318,GSM3612318: MLCs 4; Danio rerio; RNA Seq,GSM3612318,,1,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,GEO Accession:GSM3612318,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP186291,,,MLCs_4_R2.fq.gz MLCs_4_R1.fq.gz,fastq fastq,8636325300.0,28787751.0,GSM3612318 r1,0:150 1:150,A:2653500651;C:1647706630;G:1681001556;T:2652196955;N:1919508,150,150,,,2653500651,1647706630,1681001556,2652196955,1919508,SRX5391959,SRS4379789,SRA850414,GEO,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.82279,0.82455,0.10092,0.10051,0.87625,0.87411,0.64616,0.67509,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,nebnext,sc,single_cell_plate,smartseq,,China,2019-02-19,Adult,Adult,Skin,Surface Structure
51235,SRR8591745,SRX5391958,SRS4379788,SRP186291,PRJNA523219,Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs,GSE126763,Transcriptome Analysis,In order to have a comprehensive comparison of  locally restricted mpeg1+ cells MLCs and cLCs  we isolated  locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls  keratinocytes  T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis  including locally restricted mpeg1+ cells  cLCs  keratinocytes  T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol  library construction and whole transcriptome RNA sequencing were proformed by Novogene.,,pubmed:31006648,,MLCs 3,GSM3612317,,source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP,MLCs 3,Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample,specific cells types in zebrafish epidermis,,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,,tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP,GSM3612317,GSM3612317: MLCs 3; Danio rerio; RNA Seq,GSM3612317,,1,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,GEO Accession:GSM3612317,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP186291,,,MLCs_3_R1.fq.gz MLCs_3_R2.fq.gz,fastq fastq,9768968700.0,32563229.0,GSM3612317 r1,0:150 1:150,A:2993731360;C:1868928141;G:1920209904;T:2983932349;N:2166946,150,150,,,2993731360,1868928141,1920209904,2983932349,2166946,SRX5391958,SRS4379788,SRA850414,GEO,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.80623,0.80159,0.09971,0.09865,0.85754,0.85677,0.57368,0.57722,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,nebnext,sc,single_cell_plate,smartseq,,China,2019-02-19,Adult,Adult,Skin,Surface Structure
51236,SRR8591744,SRX5391957,SRS4379787,SRP186291,PRJNA523219,Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs,GSE126763,Transcriptome Analysis,In order to have a comprehensive comparison of  locally restricted mpeg1+ cells MLCs and cLCs  we isolated  locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls  keratinocytes  T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis  including locally restricted mpeg1+ cells  cLCs  keratinocytes  T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol  library construction and whole transcriptome RNA sequencing were proformed by Novogene.,,pubmed:31006648,,MLCs 2,GSM3612316,,source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP,MLCs 2,Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample,specific cells types in zebrafish epidermis,,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,,tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP,GSM3612316,GSM3612316: MLCs 2; Danio rerio; RNA Seq,GSM3612316,,1,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,GEO Accession:GSM3612316,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP186291,,,MLCs_2_R2.fq.gz MLCs_2_R1.fq.gz,fastq fastq,13514398200.0,45047994.0,GSM3612316 r1,0:150 1:150,A:3741759684;C:2708870921;G:2854612129;T:4207496675;N:1658791,150,150,,,3741759684,2708870921,2854612129,4207496675,1658791,SRX5391957,SRS4379787,SRA850414,GEO,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.85592,0.84009,0.10566,0.10231,0.85904,0.86689,0.46757,0.54817,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,nebnext,sc,single_cell_plate,smartseq,,China,2019-02-19,Adult,Adult,Skin,Surface Structure
51237,SRR8591743,SRX5391956,SRS4379786,SRP186291,PRJNA523219,Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs,GSE126763,Transcriptome Analysis,In order to have a comprehensive comparison of  locally restricted mpeg1+ cells MLCs and cLCs  we isolated  locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls  keratinocytes  T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis  including locally restricted mpeg1+ cells  cLCs  keratinocytes  T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol  library construction and whole transcriptome RNA sequencing were proformed by Novogene.,,pubmed:31006648,,MLCs 1,GSM3612315,,source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP,MLCs 1,Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample,specific cells types in zebrafish epidermis,,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,,tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP,GSM3612315,GSM3612315: MLCs 1; Danio rerio; RNA Seq,GSM3612315,,1,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,GEO Accession:GSM3612315,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP186291,,,MLCs_1_R1.fq.gz MLCs_1_R2.fq.gz,fastq fastq,6037864832.0,20003506.0,GSM3612315 r1,0:150.92 1:150.92,A:1818516368;C:1085016023;G:1139951931;T:1985307132;N:9073378,150,150,,,1818516368,1085016023,1139951931,1985307132,9073378,SRX5391956,SRS4379786,SRA850414,GEO,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.74163,0.65034,0.20675,0.17721,0.85285,0.87409,0.66103,0.66629,151,151,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,nebnext,sc,single_cell_plate,smartseq,,China,2019-02-19,Adult,Adult,Skin,Surface Structure
51238,SRR8591742,SRX5391955,SRS4379784,SRP186291,PRJNA523219,Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs,GSE126763,Transcriptome Analysis,In order to have a comprehensive comparison of  locally restricted mpeg1+ cells MLCs and cLCs  we isolated  locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls  keratinocytes  T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis  including locally restricted mpeg1+ cells  cLCs  keratinocytes  T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol  library construction and whole transcriptome RNA sequencing were proformed by Novogene.,,pubmed:31006648,,Keratinocytes 3,GSM3612314,,source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP,Keratinocytes 3,Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample,specific cells types in zebrafish epidermis,,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,,tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP,GSM3612314,GSM3612314: Keratinocytes 3; Danio rerio; RNA Seq,GSM3612314,,1,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,GEO Accession:GSM3612314,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP186291,,,Keratinocytes_3_R1.fq.gz Keratinocytes_3_R2.fq.gz,fastq fastq,7155019200.0,23850064.0,GSM3612314 r1,0:150 1:150,A:2267290727;C:1304084105;G:1335196968;T:2248029844;N:417556,150,150,,,2267290727,1304084105,1335196968,2248029844,417556,SRX5391955,SRS4379784,SRA850414,GEO,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.77684,0.75758,0.12563,0.12043,0.87606,0.87618,0.63846,0.64712,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,nebnext,sc,single_cell_plate,smartseq,,China,2019-02-19,Adult,Adult,Skin,Surface Structure
51239,SRR8591741,SRX5391954,SRS4379785,SRP186291,PRJNA523219,Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs,GSE126763,Transcriptome Analysis,In order to have a comprehensive comparison of  locally restricted mpeg1+ cells MLCs and cLCs  we isolated  locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls  keratinocytes  T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis  including locally restricted mpeg1+ cells  cLCs  keratinocytes  T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol  library construction and whole transcriptome RNA sequencing were proformed by Novogene.,,pubmed:31006648,,Keratinocytes 2,GSM3612313,,source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP,Keratinocytes 2,Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample,specific cells types in zebrafish epidermis,,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,,tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP,GSM3612313,GSM3612313: Keratinocytes 2; Danio rerio; RNA Seq,GSM3612313,,1,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,GEO Accession:GSM3612313,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP186291,,,Keratinocytes_2_R1.fq.gz Keratinocytes_2_R2.fq.gz,fastq fastq,6456398100.0,21521327.0,GSM3612313 r1,0:150 1:150,A:2077468795;C:1142603883;G:1144675726;T:2084897858;N:6751838,150,150,,,2077468795,1142603883,1144675726,2084897858,6751838,SRX5391954,SRS4379785,SRA850414,GEO,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.74005,0.73114,0.1187,0.11653,0.8604,0.85985,0.56777,0.56778,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,nebnext,sc,single_cell_plate,smartseq,,China,2019-02-19,Adult,Adult,Skin,Surface Structure
51240,SRR8591740,SRX5391953,SRS4379783,SRP186291,PRJNA523219,Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs,GSE126763,Transcriptome Analysis,In order to have a comprehensive comparison of  locally restricted mpeg1+ cells MLCs and cLCs  we isolated  locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls  keratinocytes  T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis  including locally restricted mpeg1+ cells  cLCs  keratinocytes  T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol  library construction and whole transcriptome RNA sequencing were proformed by Novogene.,,pubmed:31006648,,Keratinocytes 1,GSM3612312,,source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP,Keratinocytes 1,Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample,specific cells types in zebrafish epidermis,,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,,tissue:epidermis|Stage:adult|transgenic line:Tgkrt4:lyn GFP,GSM3612312,GSM3612312: Keratinocytes 1; Danio rerio; RNA Seq,GSM3612312,,1,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,GEO Accession:GSM3612312,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP186291,,,Keratinocytes_1_R2.fq.gz Keratinocytes_1_R1.fq.gz,fastq fastq,13235365200.0,44117884.0,GSM3612312 r1,0:150 1:150,A:3733277705;C:2648363624;G:2742826351;T:4109351172;N:1546348,150,150,,,3733277705,2648363624,2742826351,4109351172,1546348,SRX5391953,SRS4379783,SRA850414,GEO,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.83183,0.82563,0.13916,0.13781,0.86048,0.86517,0.46753,0.45399,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,nebnext,sc,single_cell_plate,smartseq,,China,2019-02-19,Adult,Adult,Skin,Surface Structure
51241,SRR8591739,SRX5391952,SRS4379782,SRP186291,PRJNA523219,Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs,GSE126763,Transcriptome Analysis,In order to have a comprehensive comparison of  locally restricted mpeg1+ cells MLCs and cLCs  we isolated  locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls  keratinocytes  T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis  including locally restricted mpeg1+ cells  cLCs  keratinocytes  T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol  library construction and whole transcriptome RNA sequencing were proformed by Novogene.,,pubmed:31006648,,cLCs 4,GSM3612311,,source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP,cLCs 4,Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample,specific cells types in zebrafish epidermis,,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,,tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP,GSM3612311,GSM3612311: cLCs 4; Danio rerio; RNA Seq,GSM3612311,,1,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,GEO Accession:GSM3612311,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP186291,,,cLCs_4_R1.fq.gz cLCs_4_R2.fq.gz,fastq fastq,8713251600.0,29044172.0,GSM3612311 r1,0:150 1:150,A:2637859361;C:1663768374;G:1739990329;T:2671283369;N:350167,150,150,,,2637859361,1663768374,1739990329,2671283369,350167,SRX5391952,SRS4379782,SRA850414,GEO,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.82506,0.82564,0.14826,0.14636,0.92133,0.92194,0.64203,0.64155,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,nebnext,sc,single_cell_plate,smartseq,,China,2019-02-19,Adult,Adult,Skin,Surface Structure
51242,SRR8591738,SRX5391951,SRS4379781,SRP186291,PRJNA523219,Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs,GSE126763,Transcriptome Analysis,In order to have a comprehensive comparison of  locally restricted mpeg1+ cells MLCs and cLCs  we isolated  locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls  keratinocytes  T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis  including locally restricted mpeg1+ cells  cLCs  keratinocytes  T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol  library construction and whole transcriptome RNA sequencing were proformed by Novogene.,,pubmed:31006648,,cLCs 3,GSM3612310,,source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP,cLCs 3,Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample,specific cells types in zebrafish epidermis,,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,,tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP,GSM3612310,GSM3612310: cLCs 3; Danio rerio; RNA Seq,GSM3612310,,1,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,GEO Accession:GSM3612310,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP186291,,,cLCs_3_R2.fq.gz cLCs_3_R1.fq.gz,fastq fastq,8085762300.0,26952541.0,GSM3612310 r1,0:150 1:150,A:2358914181;C:1670033364;G:1711269394;T:2345255094;N:290267,150,150,,,2358914181,1670033364,1711269394,2345255094,290267,SRX5391951,SRS4379781,SRA850414,GEO,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.80361,0.80478,0.06011,0.06067,0.90666,0.90613,0.43542,0.42737,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,nebnext,sc,single_cell_plate,smartseq,,China,2019-02-19,Adult,Adult,Skin,Surface Structure
51243,SRR8591737,SRX5391950,SRS4379780,SRP186291,PRJNA523219,Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs,GSE126763,Transcriptome Analysis,In order to have a comprehensive comparison of  locally restricted mpeg1+ cells MLCs and cLCs  we isolated  locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls  keratinocytes  T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis  including locally restricted mpeg1+ cells  cLCs  keratinocytes  T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol  library construction and whole transcriptome RNA sequencing were proformed by Novogene.,,pubmed:31006648,,cLCs 2,GSM3612309,,source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP,cLCs 2,Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample,specific cells types in zebrafish epidermis,,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,,tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP,GSM3612309,GSM3612309: cLCs 2; Danio rerio; RNA Seq,GSM3612309,,1,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,GEO Accession:GSM3612309,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP186291,,,cLCs_2_R2.fq.gz cLCs_2_R1.fq.gz,fastq fastq,14035834800.0,46786116.0,GSM3612309 r1,0:150 1:150,A:3886956713;C:2808123594;G:3002545528;T:4337287271;N:921694,150,150,,,3886956713,2808123594,3002545528,4337287271,921694,SRX5391950,SRS4379780,SRA850414,GEO,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.80521,0.79346,0.13916,0.13314,0.88061,0.88872,0.5212,0.54523,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,nebnext,sc,single_cell_plate,smartseq,,China,2019-02-19,Adult,Adult,Skin,Surface Structure
51244,SRR8591736,SRX5391949,SRS4379779,SRP186291,PRJNA523219,Whole transcriptome RNA seq analysis of zebrafish epidemal MLCs,GSE126763,Transcriptome Analysis,In order to have a comprehensive comparison of  locally restricted mpeg1+ cells MLCs and cLCs  we isolated  locally restricted mpeg1+ cells and cLCs from heat shock labeled zebrafish epidermis and performed whole transcriptome RNA sequencing. As the controls  keratinocytes  T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile. Overall design: Different cell types form zebrafish epidemis  including locally restricted mpeg1+ cells  cLCs  keratinocytes  T cells and neutrophils were isolated by manually picking. Each cell types contain 3 4 replicated from 3 4 indipendent experiments. cDNA libraries were generated using Smart seq2 protocol  library construction and whole transcriptome RNA sequencing were proformed by Novogene.,,pubmed:31006648,,cLCs 1,GSM3612308,,source name:specific cells types in zebrafish epidermis|tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP,cLCs 1,Raw reads were first aligned to zebrafish reference genome danRer10 using STAR aligner with default parameters. Read count per gene was then calculated using the FeatureCount program with default parameters. TPMtranscripts per million was calculated according to standard formula. Genome build: danRer10  Supplementary files format and content: comma separated values file including read counts and TPM values for each sample,specific cells types in zebrafish epidermis,,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,,tissue:epidermis|Stage:adult|transgenic line:Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP,GSM3612308,GSM3612308: cLCs 1; Danio rerio; RNA Seq,GSM3612308,,1,Different fluorescence labeled cell types from Tgkrt4:lyn GFP  Tglck:DsRedx  Tglyz:GFP and Tghsp70:mCherry T2a CreERT2;mpeg1:loxP DsRedx loxP GFP fish epidermis were picked into lysis buffer 1% Triton X 100 for direct reverse transcription and cDNA amplification. cDNA library was generated based on SMART seq2 protocol. Library construction were done by Novogene using NEBNext kit.,GEO Accession:GSM3612308,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP186291,,,cLCs_1_R1.fq.gz cLCs_1_R2.fq.gz,fastq fastq,6917825858.0,22926042.0,GSM3612308 r1,0:150.87 1:150.87,A:2168007671;C:1152140252;G:1228288198;T:2358773829;N:10615908,150,150,,,2168007671,1152140252,1228288198,2358773829,10615908,SRX5391949,SRS4379779,SRA850414,GEO,"Room 6319, Division of Life Science, Hong Kong University of Science and Technology",2,0.6965,0.66301,0.20956,0.19509,0.8521,0.86218,0.6102,0.59061,151,151,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,nebnext,sc,single_cell_plate,smartseq,,China,2019-02-19,Adult,Adult,Skin,Surface Structure
52154,SRR18181452,SRX14328416,SRS12144047,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.,,pubmed:34660600,,Skin6,GSM5924290,,source name:skin|strain:Tubingen|tissue:skin|genotype:wild type,Skin6,Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Mus musculus.GRCm38.88 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 based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.,skin,,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:skin|genotype:wild type,GSM5924290,GSM5924290: Skin6; Danio rerio; RNA Seq,GSM5924290,,1,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924290,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Skin6.bam,bam,25513490100.0,85044967.0,GSM5924290 r1,0:150 1:150,A:6925113942;C:3968740165;G:4171395948;T:10445470654;N:2769391,150,150,,,6925113942,3968740165,4171395948,10445470654,2769391,SRX14328416,SRS12144047,SRA880843,GEO,Zhejiang University,2,2e-05,0.59157,0.0,0.06443,0.99997,0.87677,1.0,0.63522,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Skin,Surface Structure
52155,SRR18181451,SRX14328415,SRS12144046,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.,,pubmed:34660600,,Skin5,GSM5924289,,source name:skin|strain:Tubingen|tissue:skin|genotype:wild type,Skin5,Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Mus musculus.GRCm38.88 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 based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.,skin,,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:skin|genotype:wild type,GSM5924289,GSM5924289: Skin5; Danio rerio; RNA Seq,GSM5924289,,1,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924289,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Skin5.bam,bam,28489208700.0,94964029.0,GSM5924289 r1,0:150 1:150,A:8246685822;C:4290659458;G:4422543987;T:11526089448;N:3229985,150,150,,,8246685822,4290659458,4422543987,11526089448,3229985,SRX14328415,SRS12144046,SRA880843,GEO,Zhejiang University,2,0.0,0.52,0.0,0.05199,1.0,0.89509,,0.61209,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Skin,Surface Structure
52156,SRR18181450,SRX14328414,SRS12144045,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.,,pubmed:34660600,,Skin3,GSM5924288,,source name:skin|strain:Tubingen|tissue:skin|genotype:wild type,Skin3,Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Mus musculus.GRCm38.88 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 based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.,skin,,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:skin|genotype:wild type,GSM5924288,GSM5924288: Skin3; Danio rerio; RNA Seq,GSM5924288,,1,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924288,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Skin3.bam,bam,22656818700.0,75522729.0,GSM5924288 r1,0:150 1:150,A:5656101080;C:3775541088;G:3901788913;T:9321421770;N:1965849,150,150,,,5656101080,3775541088,3901788913,9321421770,1965849,SRX14328414,SRS12144045,SRA880843,GEO,Zhejiang University,2,2e-05,0.77804,0.0,0.0376,0.99997,0.77275,1.0,0.58426,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Skin,Surface Structure
52201,SRR8991405,SRX5770473,SRS4704582,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.,,pubmed:34660600,,Skin4,GSM3740958,,source name:skin|strain:Tubingen|genotype:wild type|tissue:skin,Skin4,The drop seq core computational tool was used for preprocessing of the Microwell seq data. The implementation is described in the Drop seq computational cookbook http://mccarrolllab.org/dropseq/. Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 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 based on UMI counts. Genome build: http://dec2017.archive.ensembl.org/Danio rerio/Info/Index Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.,skin,,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype:wild type|tissue:skin,GSM3740958,GSM3740958: Skin4; Danio rerio; RNA Seq,GSM3740958,,1,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3740958,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10,Skin4.bam,bam,33628232728.0,111351764.0,GSM3740958 r1,0:151 1:151,A:8460681247;C:5738320863;G:5953293918;T:13386336300;N:89600400,151,151,,,8460681247,5738320863,5953293918,13386336300,89600400,SRX5770473,SRS4704582,SRA880843,GEO,Zhejiang University,2,0.0,0.73034,0.0,0.03701,1.0,0.80454,,0.53563,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-04-30,Undetermined,Multi-stage,Skin,Surface Structure
52249,SRR9050626,SRX5827017,SRS4754831,SRP198298,PRJNA542704,Thyroid hormone regulates distinct paths to maturation in pigment cell lineages,GSE131136,Transcriptome Analysis,Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted  Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.,,pubmed:31140974;pubmed:33933422,,Neural crest derived cells from hypothyroid  post embryonic zebrafish skins  biological replicate 2,GSM3764573,,tissue:sox10:Cre+ cells from post embryonic zebrafish skin tissue|cell type:3033 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid,Neural crest derived cells from hypothyroid  post embryonic zebrafish skins  biological replicate 2,Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.,sox10:Cre+ cells from post embryonic zebrafish skin tissue,Transgenic zebrafish  Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia  rotifers enriched with TH free Algamac Aquafauna  and bloodworms.,cell type:3033 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 7.2 10.4 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid,GSM3764573,GSM3764573: Neural crest derived cells from hypothyroid  post embryonic zebrafish skins  biological replicate 2; Danio rerio; RNA Seq,GSM3764573,,1,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP198298,,dangling references:treat as unmapped,hypo6_possorted_genome_bam.bam,10X Genomics bam file,7642585251.0,134080443.0,GSM3764573 r1,0:57,A:2330102138;C:1530481079;G:1741129436;T:2036914417;N:3958181,57,,,,2330102138,1530481079,1741129436,2036914417,3958181,SRX5827017,SRS4754831,SRA886020,GEO,"Biology, University of Virginia",1,0.92859,,0.20322,,0.83019,,0.51386,,57,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-05-13,Larval,Larval,Skin,Surface Structure
52255,SRR9050620,SRX5827011,SRS4754825,SRP198298,PRJNA542704,Thyroid hormone regulates distinct paths to maturation in pigment cell lineages,GSE131136,Transcriptome Analysis,Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted  Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.,,pubmed:31140974;pubmed:33933422,,Neural crest derived cells from euthyroid  post embryonic zebrafish skins  biological replicate 2,GSM3764567,,tissue:sox10:Cre+ cells from post embryonic zebrafish skin tissue|cell type:3008 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from skins. Zebrafish range in stage from 7.2 10.4 SSL.|treatment:Euthyroid,Neural crest derived cells from euthyroid  post embryonic zebrafish skins  biological replicate 2,Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.,sox10:Cre+ cells from post embryonic zebrafish skin tissue,Transgenic zebrafish  Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia  rotifers enriched with TH free Algamac Aquafauna  and bloodworms.,cell type:3008 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from skins. Zebrafish  range in stage from 7.2 10.4 SSL.|treatment:Euthyroid,GSM3764567,GSM3764567: Neural crest derived cells from euthyroid  post embryonic zebrafish skins  biological replicate 2; Danio rerio; RNA Seq,GSM3764567,,1,10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP198298,,dangling references:treat as unmapped,eu5_possorted_genome_bam.bam,10X Genomics bam file,7562050749.0,132667557.0,GSM3764567 r1,0:57,A:2291130941;C:1508834109;G:1752506997;T:2005478206;N:4100496,57,,,,2291130941,1508834109,1752506997,2005478206,4100496,SRX5827011,SRS4754825,SRA886020,GEO,"Biology, University of Virginia",1,0.92351,,0.19606,,0.82913,,0.5204,,57,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-05-13,Larval,Larval,Skin,Surface Structure
53011,SRR9662028,SRX6422904,SRS5079694,SRP213938,PRJNA553572,A map of cis regulatory elements and 3D genome structures in zebrafish,GSE134055,Other,The zebrafish has been widely used for the study of human disease and development  as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome  however  has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects  we performed RNA seq  ATAC seq  ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall  we have identified 235 596 cis regulatory elements  which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish  human  and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore  through the analysis of Hi C data in zebrafish brain and muscle  we observed different levels of 3D genome organization  including compartment  topological associating domains TADs  and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and  embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3  RNA Seq  11 of them were examined using ATAC seq  WGBS and ChIP seq H3K9me3 and H3K9me2  and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that  for the samples GSM4661977 GSM4662088  [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.,,pubmed:33239788;pubmed:35649578,,YueLab RNA Seq Skin rep2,GSM3934896,,source name:Tissue|strain:Tuebingen|tissue:Skin,YueLab RNA Seq Skin rep2,RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following  setting: ChIP seq q value <10e 2  p value<10e 5  Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged,Tissue,,For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.,Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions,strain:Tuebingen|tissue:Skin,GSM3934896,GSM3934896: YueLab RNA Seq Skin rep2; Danio rerio; RNA Seq,GSM3934896,,1,For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.,GEO Accession:GSM3934896,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer,,SRP213938,,,YueLab-RNA-Seq-Skin-rep2_1.fastq.gz YueLab-RNA-Seq-Skin-rep2_2.fastq.gz,fastq fastq,3369540489.0,27929926.0,GSM3934896 r1,0:60.47 1:60.17,A:881257889;C:784720097;G:773160075;T:930047288;N:355140,60,60,,,881257889,784720097,773160075,930047288,355140,SRX6422904,SRS5079694,SRA919194,GEO,"Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine",2,0.96098,0.96359,0.1219,0.11985,0.69962,0.70161,0.48503,0.4877,61,60,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-07-09,Pharyngula,Embryo,Skin,Surface Structure
53012,SRR9662027,SRX6422903,SRS5079693,SRP213938,PRJNA553572,A map of cis regulatory elements and 3D genome structures in zebrafish,GSE134055,Other,The zebrafish has been widely used for the study of human disease and development  as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome  however  has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects  we performed RNA seq  ATAC seq  ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall  we have identified 235 596 cis regulatory elements  which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish  human  and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore  through the analysis of Hi C data in zebrafish brain and muscle  we observed different levels of 3D genome organization  including compartment  topological associating domains TADs  and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and  embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3  RNA Seq  11 of them were examined using ATAC seq  WGBS and ChIP seq H3K9me3 and H3K9me2  and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that  for the samples GSM4661977 GSM4662088  [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.,,pubmed:33239788;pubmed:35649578,,YueLab RNA Seq Skin rep1,GSM3934895,,source name:Tissue|strain:Tuebingen|tissue:Skin,YueLab RNA Seq Skin rep1,RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following  setting: ChIP seq q value <10e 2  p value<10e 5  Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged,Tissue,,For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.,Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions,strain:Tuebingen|tissue:Skin,GSM3934895,GSM3934895: YueLab RNA Seq Skin rep1; Danio rerio; RNA Seq,GSM3934895,,1,For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.,GEO Accession:GSM3934895,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer,,SRP213938,,,YueLab-RNA-Seq-Skin-rep1_1.fastq.gz YueLab-RNA-Seq-Skin-rep1_2.fastq.gz,fastq fastq,2565035707.0,21260839.0,GSM3934895 r1,0:60.48 1:60.17,A:670789880;C:599392091;G:585931498;T:708654706;N:267532,60,60,,,670789880,599392091,585931498,708654706,267532,SRX6422903,SRS5079693,SRA919194,GEO,"Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine",2,0.96148,0.96283,0.12215,0.11903,0.70015,0.70114,0.47321,0.47375,60,60,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-07-09,Pharyngula,Embryo,Skin,Surface Structure
56585,SRR11015125,SRX7670824,SRS6098560,SRP247126,PRJNA604753,IN SITU DIFFERENTIATION OF IRIDOPHORE CRYSTALLOTYPES UNDERLIES ZEBRAFISH STRIPING,GSE144734,Transcriptome Analysis,Skin color patterns are ubiquitous in nature  evolve rapidly  and impact social behavior  predator avoidance  and protection from ultraviolet irradiation. A leading model system for vertebrate skin patterning is the zebrafish; its alternating blue stripes and yellow interstripes depend on guanine crystal containing cells called iridophores that reflect light. It was suggested that the zebrafish's alternating color pattern arises from a single type of iridophore migrating differentially to stripes and interstripes. When we tracked iridophores  however  we found they did not migrate between stripes and interstripes but instead differentiated and proliferated in place based on their micro environment. RNA sequencing analysis further revealed that stripe and interstripe iridophores had different transcriptomic states with many differences in gene expression and pathway enrichment  while cryogenic scanning electron microscopy and micro X ray diffraction identified different guanine crystal organizations and responsiveness to norepinephrine  all indicating that stripe and interstripe iridophores are different cell types. Based on these results  we present a new model of skin patterning in zebrafish in which distinct iridophore crystallotypes containing specialized  physiologically responsive  subcellular organelles arise in stripe and interstripe zones by in situ differentiation. In this model  pattern phenotype depends not only on interactions among pigment cells that affect their arrangements  but also on factors that specify subcellular organization and physiological responsiveness of specialized organelles. Overall design: Unbiased classification of iridophores  based solely on their RNA profiles obtained by single cell RNA sequencing,,pubmed:33319779,,Dvir zebrafish Light 7 010919,GSM4294473,,source name:Flank dermis|tissue:Flank dermis|stripe pattern:light|reporter:Adult pnp4a:palmmCherry and pnp4a:nlsEos postive cells,Dvir zebrafish Light 7 010919,The libraries were pooled and sequenced on an Illumina NextSeq 550 high output flowcell with 26 base pair read1  50 base pair read 2  8 base pair i7 index.  Samples were demultiplexed using bcl2fastq v2.20 software from Illumina with default settings. Barcode and UMI sequences were extracted from read 1 using custom python scripts.  Barcode error correction was done using starcode v1.1 Zorita et al.  2015 with the following additional parameters: “ d 1  q   print clusters”. Read 2 sequences were renamed using the error corrected barcode from starcode and UMI sequences from read 1  and were aligned to the Danio rerio GRCz11.94 genome assembly from Ensembl ensemble.org using STAR Dobin et al.  2013 with the following additional parameters: “  alignIntronMax 200000   outSAMattributes All   outSAMunmapped Within   outSAMtype BAM Unsorted”.  An alignment is considered valid if it aligns to an exon feature on the correct strand and is unique.  Valid alignments that had at least 50% of the read aligned to an exon feature were used to create gene level counts using a custom python script to collapse UMIs by gene.  All custom scripts are available by request. Genome build: Danio rerio GRCz11.94 genome assembly from Ensembl.org Supplementary files format and content: single Microsoft Excel file that includes counts per million CPM and correct p values for each sample and gene,Flank dermis,Untreated fish,Fish were euthanized in MS222 and the stripe and interstiped regions were micro dissected from fish expressing both pnp4a:palmmCherry and pnp4a:nlsEos. Stripe and interstipe regions were enzymatically dissociated separately with Liberase 0.25 mg/ml in dPBS at 25°C for 15 min followed by manual trituration with increasingly narrower flame polished glass pipette for 3 min at a time for three times. Cells 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 before FACS purification. The flow cytometry experiments were performed on a BD FACSAria II SORP sorter BD Biosciences  San Jose  CA  USA coupled with BD FACSDiva software BD Biosciences for instrument operation  data acquisition  and analysis. A 637 nm and a 488 nm laser were utilized for fluorophore excitation and a 100 μm nozzle was used to generate single droplets under 20PSI sheath pressure. The applied settings were as follows: forward light scatter FSC detector photomultiplier tube PMT gain setting = 80 V with a 1.5 neutral density filter; side light scatter SSC detector PMT gain setting = 90 V; FSC threshold = 10 000; PE Texas Red PE TX Red channel PMT gain setting = 280 V; fluorescein isothiocyanate FITC channel PMT gain setting = 280 V. Sample dilution and flow rate were adjusted to optimal event recordings for 96 well plate single cell sorts below 500 processed events per sec. The population of zebrafish skin iridophores was designated based on their FSC and SSC characteristics and back gating on fluorescence. Control zebrafish skin samples were used to gate out the highly auto fluorescent cells among the members of this population. Fluorescently labeled PNP4 mCherry Eos from either the stripe or interstripe skin samples were sorted separately.  Single cells with high mCherry and Eos expression were collected into 3uL of smart scrb lysis buffer 0.2% Triton X 100 [Sigma]  0.1 U/ul RNAse inhibitor [NEB] using „single cell” indexed sorting mode. Five indexed 96 well plates were collected for each skin band. post sorting  the samples were spun down at 3166 rcf at 4ºC for 2 minutes in an Eppendorf tabletop 5810R centrifuge Eppendorf AG  Hamburg  Germany and stored at  80ºC until further processing. Four plates of each skin band were selected for sequencing.  cDNA was prepared from sorted cells as described previously Cembrowski et al.  2018 with minor modifications to the sequencing configuration.  Reverse transcription  PCR  purification  tagmentation  and library quantification were performed as described.,Zebrafish were housed at 28 °C  14L:10D  fed rotifers  Artemia and flake food,tissue:Flank dermis|stripe pattern:light|reporter:Adult pnp4a:palmmCherry and pnp4a:nlsEos postive cells,GSM4294473,GSM4294473: Dvir zebrafish Light 7 010919; Danio rerio; RNA Seq,GSM4294473,,1,Fish were euthanized in MS222 and the stripe and interstiped regions were micro dissected from fish expressing both pnp4a:palmmCherry and pnp4a:nlsEos. Stripe and interstipe regions were enzymatically dissociated separately with Liberase 0.25 mg/ml in dPBS at 25°C for 15 min followed by manual trituration with increasingly narrower flame polished glass pipette for 3 min at a time for three times. Cells 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 before FACS purification. The flow cytometry experiments were performed on a BD FACSAria II SORP sorter BD Biosciences  San Jose  CA  USA coupled with BD FACSDiva software BD Biosciences for instrument operation  data acquisition  and analysis. A 637 nm and a 488 nm laser were utilized for fluorophore excitation and a 100 μm nozzle was used to generate single droplets under 20PSI sheath pressure. The applied settings were as follows: forward light scatter FSC detector photomultiplier tube PMT gain setting = 80 V with a 1.5 neutral density filter; side light scatter SSC detector PMT gain setting = 90 V; FSC threshold = 10 000; PE Texas Red PE TX Red channel PMT gain setting = 280 V; fluorescein isothiocyanate FITC channel PMT gain setting = 280 V. Sample dilution and flow rate were adjusted to optimal event recordings for 96 well plate single cell sorts below 500 processed events per sec. The population of zebrafish skin iridophores was designated based on their FSC and SSC characteristics and back gating on fluorescence. Control zebrafish skin samples were used to gate out the highly auto fluorescent cells among the members of this population. Fluorescently labeled PNP4 mCherry Eos from either the stripe or interstripe skin samples were sorted separately.  Single cells with high mCherry and Eos expression were collected into 3uL of smart scrb lysis buffer 0.2% Triton X 100 [Sigma]  0.1 U/ul RNAse inhibitor [NEB] using „single cell” indexed sorting mode. Five indexed 96 well plates were collected for each skin band. post sorting  the samples were spun down at 3166 rcf at 4ºC for 2 minutes in an Eppendorf tabletop 5810R centrifuge Eppendorf AG  Hamburg  Germany and stored at  80ºC until further processing. Four plates of each skin band were selected for sequencing.  cDNA was prepared from sorted cells as described previously Cembrowski et al.  2018 with minor modifications to the sequencing configuration.  Reverse transcription  PCR  purification  tagmentation  and library quantification were performed as described.,GEO Accession:GSM4294473,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP247126,,,Plate_301_Q6_1.fastq.gz Plate_301_Q6_2.fastq.gz,fastq fastq,4242367348.0,55820623.0,GSM4294473 r1,0:26 1:50,A:1294749632;C:790142762;G:973860904;T:1182269517;N:1344533,26,50,,,1294749632,790142762,973860904,1182269517,1344533,SRX7670824,SRS6098560,SRA1037187,GEO,"JLS, HHMI Janelia Research Campus",2,0.01168,0.49695,0.01107,0.41291,0.99868,0.93803,0.57407,0.56961,26,50,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2020-02-04,Adult,Adult,Skin,Surface Structure
56586,SRR11015124,SRX7670823,SRS6098558,SRP247126,PRJNA604753,IN SITU DIFFERENTIATION OF IRIDOPHORE CRYSTALLOTYPES UNDERLIES ZEBRAFISH STRIPING,GSE144734,Transcriptome Analysis,Skin color patterns are ubiquitous in nature  evolve rapidly  and impact social behavior  predator avoidance  and protection from ultraviolet irradiation. A leading model system for vertebrate skin patterning is the zebrafish; its alternating blue stripes and yellow interstripes depend on guanine crystal containing cells called iridophores that reflect light. It was suggested that the zebrafish's alternating color pattern arises from a single type of iridophore migrating differentially to stripes and interstripes. When we tracked iridophores  however  we found they did not migrate between stripes and interstripes but instead differentiated and proliferated in place based on their micro environment. RNA sequencing analysis further revealed that stripe and interstripe iridophores had different transcriptomic states with many differences in gene expression and pathway enrichment  while cryogenic scanning electron microscopy and micro X ray diffraction identified different guanine crystal organizations and responsiveness to norepinephrine  all indicating that stripe and interstripe iridophores are different cell types. Based on these results  we present a new model of skin patterning in zebrafish in which distinct iridophore crystallotypes containing specialized  physiologically responsive  subcellular organelles arise in stripe and interstripe zones by in situ differentiation. In this model  pattern phenotype depends not only on interactions among pigment cells that affect their arrangements  but also on factors that specify subcellular organization and physiological responsiveness of specialized organelles. Overall design: Unbiased classification of iridophores  based solely on their RNA profiles obtained by single cell RNA sequencing,,pubmed:33319779,,Dvir zebrafish Dark 9 010919,GSM4294472,,source name:Flank dermis|tissue:Flank dermis|stripe pattern:dark|reporter:Adult pnp4a:palmmCherry and pnp4a:nlsEos postive cells,Dvir zebrafish Dark 9 010919,The libraries were pooled and sequenced on an Illumina NextSeq 550 high output flowcell with 26 base pair read1  50 base pair read 2  8 base pair i7 index.  Samples were demultiplexed using bcl2fastq v2.20 software from Illumina with default settings. Barcode and UMI sequences were extracted from read 1 using custom python scripts.  Barcode error correction was done using starcode v1.1 Zorita et al.  2015 with the following additional parameters: “ d 1  q   print clusters”. Read 2 sequences were renamed using the error corrected barcode from starcode and UMI sequences from read 1  and were aligned to the Danio rerio GRCz11.94 genome assembly from Ensembl ensemble.org using STAR Dobin et al.  2013 with the following additional parameters: “  alignIntronMax 200000   outSAMattributes All   outSAMunmapped Within   outSAMtype BAM Unsorted”.  An alignment is considered valid if it aligns to an exon feature on the correct strand and is unique.  Valid alignments that had at least 50% of the read aligned to an exon feature were used to create gene level counts using a custom python script to collapse UMIs by gene.  All custom scripts are available by request. Genome build: Danio rerio GRCz11.94 genome assembly from Ensembl.org Supplementary files format and content: single Microsoft Excel file that includes counts per million CPM and correct p values for each sample and gene,Flank dermis,Untreated fish,Fish were euthanized in MS222 and the stripe and interstiped regions were micro dissected from fish expressing both pnp4a:palmmCherry and pnp4a:nlsEos. Stripe and interstipe regions were enzymatically dissociated separately with Liberase 0.25 mg/ml in dPBS at 25°C for 15 min followed by manual trituration with increasingly narrower flame polished glass pipette for 3 min at a time for three times. Cells 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 before FACS purification. The flow cytometry experiments were performed on a BD FACSAria II SORP sorter BD Biosciences  San Jose  CA  USA coupled with BD FACSDiva software BD Biosciences for instrument operation  data acquisition  and analysis. A 637 nm and a 488 nm laser were utilized for fluorophore excitation and a 100 μm nozzle was used to generate single droplets under 20PSI sheath pressure. The applied settings were as follows: forward light scatter FSC detector photomultiplier tube PMT gain setting = 80 V with a 1.5 neutral density filter; side light scatter SSC detector PMT gain setting = 90 V; FSC threshold = 10 000; PE Texas Red PE TX Red channel PMT gain setting = 280 V; fluorescein isothiocyanate FITC channel PMT gain setting = 280 V. Sample dilution and flow rate were adjusted to optimal event recordings for 96 well plate single cell sorts below 500 processed events per sec. The population of zebrafish skin iridophores was designated based on their FSC and SSC characteristics and back gating on fluorescence. Control zebrafish skin samples were used to gate out the highly auto fluorescent cells among the members of this population. Fluorescently labeled PNP4 mCherry Eos from either the stripe or interstripe skin samples were sorted separately.  Single cells with high mCherry and Eos expression were collected into 3uL of smart scrb lysis buffer 0.2% Triton X 100 [Sigma]  0.1 U/ul RNAse inhibitor [NEB] using „single cell” indexed sorting mode. Five indexed 96 well plates were collected for each skin band. post sorting  the samples were spun down at 3166 rcf at 4ºC for 2 minutes in an Eppendorf tabletop 5810R centrifuge Eppendorf AG  Hamburg  Germany and stored at  80ºC until further processing. Four plates of each skin band were selected for sequencing.  cDNA was prepared from sorted cells as described previously Cembrowski et al.  2018 with minor modifications to the sequencing configuration.  Reverse transcription  PCR  purification  tagmentation  and library quantification were performed as described.,Zebrafish were housed at 28 °C  14L:10D  fed rotifers  Artemia and flake food,tissue:Flank dermis|stripe pattern:dark|reporter:Adult pnp4a:palmmCherry and pnp4a:nlsEos postive cells,GSM4294472,GSM4294472: Dvir zebrafish Dark 9 010919; Danio rerio; RNA Seq,GSM4294472,,1,Fish were euthanized in MS222 and the stripe and interstiped regions were micro dissected from fish expressing both pnp4a:palmmCherry and pnp4a:nlsEos. Stripe and interstipe regions were enzymatically dissociated separately with Liberase 0.25 mg/ml in dPBS at 25°C for 15 min followed by manual trituration with increasingly narrower flame polished glass pipette for 3 min at a time for three times. Cells 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 before FACS purification. The flow cytometry experiments were performed on a BD FACSAria II SORP sorter BD Biosciences  San Jose  CA  USA coupled with BD FACSDiva software BD Biosciences for instrument operation  data acquisition  and analysis. A 637 nm and a 488 nm laser were utilized for fluorophore excitation and a 100 μm nozzle was used to generate single droplets under 20PSI sheath pressure. The applied settings were as follows: forward light scatter FSC detector photomultiplier tube PMT gain setting = 80 V with a 1.5 neutral density filter; side light scatter SSC detector PMT gain setting = 90 V; FSC threshold = 10 000; PE Texas Red PE TX Red channel PMT gain setting = 280 V; fluorescein isothiocyanate FITC channel PMT gain setting = 280 V. Sample dilution and flow rate were adjusted to optimal event recordings for 96 well plate single cell sorts below 500 processed events per sec. The population of zebrafish skin iridophores was designated based on their FSC and SSC characteristics and back gating on fluorescence. Control zebrafish skin samples were used to gate out the highly auto fluorescent cells among the members of this population. Fluorescently labeled PNP4 mCherry Eos from either the stripe or interstripe skin samples were sorted separately.  Single cells with high mCherry and Eos expression were collected into 3uL of smart scrb lysis buffer 0.2% Triton X 100 [Sigma]  0.1 U/ul RNAse inhibitor [NEB] using „single cell” indexed sorting mode. Five indexed 96 well plates were collected for each skin band. post sorting  the samples were spun down at 3166 rcf at 4ºC for 2 minutes in an Eppendorf tabletop 5810R centrifuge Eppendorf AG  Hamburg  Germany and stored at  80ºC until further processing. Four plates of each skin band were selected for sequencing.  cDNA was prepared from sorted cells as described previously Cembrowski et al.  2018 with minor modifications to the sequencing configuration.  Reverse transcription  PCR  purification  tagmentation  and library quantification were performed as described.,GEO Accession:GSM4294472,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP247126,,,Plate_300_Q5_2.fastq.gz Plate_300_Q5_1.fastq.gz,fastq fastq,3438545520.0,45244020.0,GSM4294472 r1,0:26 1:50,A:974738478;C:653512868;G:736374899;T:1072822842;N:1096433,26,50,,,974738478,653512868,736374899,1072822842,1096433,SRX7670823,SRS6098558,SRA1037187,GEO,"JLS, HHMI Janelia Research Campus",2,0.01009,0.71984,0.00955,0.53187,0.99843,0.8994,0.52083,0.59736,26,50,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2020-02-04,Adult,Adult,Skin,Surface Structure
56587,SRR11015123,SRX7670822,SRS6098555,SRP247126,PRJNA604753,IN SITU DIFFERENTIATION OF IRIDOPHORE CRYSTALLOTYPES UNDERLIES ZEBRAFISH STRIPING,GSE144734,Transcriptome Analysis,Skin color patterns are ubiquitous in nature  evolve rapidly  and impact social behavior  predator avoidance  and protection from ultraviolet irradiation. A leading model system for vertebrate skin patterning is the zebrafish; its alternating blue stripes and yellow interstripes depend on guanine crystal containing cells called iridophores that reflect light. It was suggested that the zebrafish's alternating color pattern arises from a single type of iridophore migrating differentially to stripes and interstripes. When we tracked iridophores  however  we found they did not migrate between stripes and interstripes but instead differentiated and proliferated in place based on their micro environment. RNA sequencing analysis further revealed that stripe and interstripe iridophores had different transcriptomic states with many differences in gene expression and pathway enrichment  while cryogenic scanning electron microscopy and micro X ray diffraction identified different guanine crystal organizations and responsiveness to norepinephrine  all indicating that stripe and interstripe iridophores are different cell types. Based on these results  we present a new model of skin patterning in zebrafish in which distinct iridophore crystallotypes containing specialized  physiologically responsive  subcellular organelles arise in stripe and interstripe zones by in situ differentiation. In this model  pattern phenotype depends not only on interactions among pigment cells that affect their arrangements  but also on factors that specify subcellular organization and physiological responsiveness of specialized organelles. Overall design: Unbiased classification of iridophores  based solely on their RNA profiles obtained by single cell RNA sequencing,,pubmed:33319779,,Dvir zebrafish Dark 2 010919,GSM4294471,,source name:Flank dermis|tissue:Flank dermis|stripe pattern:dark|reporter:Adult pnp4a:palmmCherry and pnp4a:nlsEos postive cells,Dvir zebrafish Dark 2 010919,The libraries were pooled and sequenced on an Illumina NextSeq 550 high output flowcell with 26 base pair read1  50 base pair read 2  8 base pair i7 index.  Samples were demultiplexed using bcl2fastq v2.20 software from Illumina with default settings. Barcode and UMI sequences were extracted from read 1 using custom python scripts.  Barcode error correction was done using starcode v1.1 Zorita et al.  2015 with the following additional parameters: “ d 1  q   print clusters”. Read 2 sequences were renamed using the error corrected barcode from starcode and UMI sequences from read 1  and were aligned to the Danio rerio GRCz11.94 genome assembly from Ensembl ensemble.org using STAR Dobin et al.  2013 with the following additional parameters: “  alignIntronMax 200000   outSAMattributes All   outSAMunmapped Within   outSAMtype BAM Unsorted”.  An alignment is considered valid if it aligns to an exon feature on the correct strand and is unique.  Valid alignments that had at least 50% of the read aligned to an exon feature were used to create gene level counts using a custom python script to collapse UMIs by gene.  All custom scripts are available by request. Genome build: Danio rerio GRCz11.94 genome assembly from Ensembl.org Supplementary files format and content: single Microsoft Excel file that includes counts per million CPM and correct p values for each sample and gene,Flank dermis,Untreated fish,Fish were euthanized in MS222 and the stripe and interstiped regions were micro dissected from fish expressing both pnp4a:palmmCherry and pnp4a:nlsEos. Stripe and interstipe regions were enzymatically dissociated separately with Liberase 0.25 mg/ml in dPBS at 25°C for 15 min followed by manual trituration with increasingly narrower flame polished glass pipette for 3 min at a time for three times. Cells 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 before FACS purification. The flow cytometry experiments were performed on a BD FACSAria II SORP sorter BD Biosciences  San Jose  CA  USA coupled with BD FACSDiva software BD Biosciences for instrument operation  data acquisition  and analysis. A 637 nm and a 488 nm laser were utilized for fluorophore excitation and a 100 μm nozzle was used to generate single droplets under 20PSI sheath pressure. The applied settings were as follows: forward light scatter FSC detector photomultiplier tube PMT gain setting = 80 V with a 1.5 neutral density filter; side light scatter SSC detector PMT gain setting = 90 V; FSC threshold = 10 000; PE Texas Red PE TX Red channel PMT gain setting = 280 V; fluorescein isothiocyanate FITC channel PMT gain setting = 280 V. Sample dilution and flow rate were adjusted to optimal event recordings for 96 well plate single cell sorts below 500 processed events per sec. The population of zebrafish skin iridophores was designated based on their FSC and SSC characteristics and back gating on fluorescence. Control zebrafish skin samples were used to gate out the highly auto fluorescent cells among the members of this population. Fluorescently labeled PNP4 mCherry Eos from either the stripe or interstripe skin samples were sorted separately.  Single cells with high mCherry and Eos expression were collected into 3uL of smart scrb lysis buffer 0.2% Triton X 100 [Sigma]  0.1 U/ul RNAse inhibitor [NEB] using „single cell” indexed sorting mode. Five indexed 96 well plates were collected for each skin band. post sorting  the samples were spun down at 3166 rcf at 4ºC for 2 minutes in an Eppendorf tabletop 5810R centrifuge Eppendorf AG  Hamburg  Germany and stored at  80ºC until further processing. Four plates of each skin band were selected for sequencing.  cDNA was prepared from sorted cells as described previously Cembrowski et al.  2018 with minor modifications to the sequencing configuration.  Reverse transcription  PCR  purification  tagmentation  and library quantification were performed as described.,Zebrafish were housed at 28 °C  14L:10D  fed rotifers  Artemia and flake food,tissue:Flank dermis|stripe pattern:dark|reporter:Adult pnp4a:palmmCherry and pnp4a:nlsEos postive cells,GSM4294471,GSM4294471: Dvir zebrafish Dark 2 010919; Danio rerio; RNA Seq,GSM4294471,,1,Fish were euthanized in MS222 and the stripe and interstiped regions were micro dissected from fish expressing both pnp4a:palmmCherry and pnp4a:nlsEos. Stripe and interstipe regions were enzymatically dissociated separately with Liberase 0.25 mg/ml in dPBS at 25°C for 15 min followed by manual trituration with increasingly narrower flame polished glass pipette for 3 min at a time for three times. Cells 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 before FACS purification. The flow cytometry experiments were performed on a BD FACSAria II SORP sorter BD Biosciences  San Jose  CA  USA coupled with BD FACSDiva software BD Biosciences for instrument operation  data acquisition  and analysis. A 637 nm and a 488 nm laser were utilized for fluorophore excitation and a 100 μm nozzle was used to generate single droplets under 20PSI sheath pressure. The applied settings were as follows: forward light scatter FSC detector photomultiplier tube PMT gain setting = 80 V with a 1.5 neutral density filter; side light scatter SSC detector PMT gain setting = 90 V; FSC threshold = 10 000; PE Texas Red PE TX Red channel PMT gain setting = 280 V; fluorescein isothiocyanate FITC channel PMT gain setting = 280 V. Sample dilution and flow rate were adjusted to optimal event recordings for 96 well plate single cell sorts below 500 processed events per sec. The population of zebrafish skin iridophores was designated based on their FSC and SSC characteristics and back gating on fluorescence. Control zebrafish skin samples were used to gate out the highly auto fluorescent cells among the members of this population. Fluorescently labeled PNP4 mCherry Eos from either the stripe or interstripe skin samples were sorted separately.  Single cells with high mCherry and Eos expression were collected into 3uL of smart scrb lysis buffer 0.2% Triton X 100 [Sigma]  0.1 U/ul RNAse inhibitor [NEB] using „single cell” indexed sorting mode. Five indexed 96 well plates were collected for each skin band. post sorting  the samples were spun down at 3166 rcf at 4ºC for 2 minutes in an Eppendorf tabletop 5810R centrifuge Eppendorf AG  Hamburg  Germany and stored at  80ºC until further processing. Four plates of each skin band were selected for sequencing.  cDNA was prepared from sorted cells as described previously Cembrowski et al.  2018 with minor modifications to the sequencing configuration.  Reverse transcription  PCR  purification  tagmentation  and library quantification were performed as described.,GEO Accession:GSM4294471,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP247126,,,Plate_299_Q8_2.fastq.gz Plate_299_Q8_1.fastq.gz,fastq fastq,3127669496.0,41153546.0,GSM4294471 r1,0:26 1:50,A:895815591;C:586306284;G:692521475;T:952037885;N:988261,26,50,,,895815591,586306284,692521475,952037885,988261,SRX7670822,SRS6098555,SRA1037187,GEO,"JLS, HHMI Janelia Research Campus",2,0.01279,0.68363,0.01207,0.50491,0.99795,0.89694,0.45312,0.58388,26,50,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2020-02-04,Adult,Adult,Skin,Surface Structure
56588,SRR11015122,SRX7670821,SRS6098554,SRP247126,PRJNA604753,IN SITU DIFFERENTIATION OF IRIDOPHORE CRYSTALLOTYPES UNDERLIES ZEBRAFISH STRIPING,GSE144734,Transcriptome Analysis,Skin color patterns are ubiquitous in nature  evolve rapidly  and impact social behavior  predator avoidance  and protection from ultraviolet irradiation. A leading model system for vertebrate skin patterning is the zebrafish; its alternating blue stripes and yellow interstripes depend on guanine crystal containing cells called iridophores that reflect light. It was suggested that the zebrafish's alternating color pattern arises from a single type of iridophore migrating differentially to stripes and interstripes. When we tracked iridophores  however  we found they did not migrate between stripes and interstripes but instead differentiated and proliferated in place based on their micro environment. RNA sequencing analysis further revealed that stripe and interstripe iridophores had different transcriptomic states with many differences in gene expression and pathway enrichment  while cryogenic scanning electron microscopy and micro X ray diffraction identified different guanine crystal organizations and responsiveness to norepinephrine  all indicating that stripe and interstripe iridophores are different cell types. Based on these results  we present a new model of skin patterning in zebrafish in which distinct iridophore crystallotypes containing specialized  physiologically responsive  subcellular organelles arise in stripe and interstripe zones by in situ differentiation. In this model  pattern phenotype depends not only on interactions among pigment cells that affect their arrangements  but also on factors that specify subcellular organization and physiological responsiveness of specialized organelles. Overall design: Unbiased classification of iridophores  based solely on their RNA profiles obtained by single cell RNA sequencing,,pubmed:33319779,,Dvir zebrafish Light 6 010919,GSM4294470,,source name:Flank dermis|tissue:Flank dermis|stripe pattern:light|reporter:Adult pnp4a:palmmCherry and pnp4a:nlsEos postive cells,Dvir zebrafish Light 6 010919,The libraries were pooled and sequenced on an Illumina NextSeq 550 high output flowcell with 26 base pair read1  50 base pair read 2  8 base pair i7 index.  Samples were demultiplexed using bcl2fastq v2.20 software from Illumina with default settings. Barcode and UMI sequences were extracted from read 1 using custom python scripts.  Barcode error correction was done using starcode v1.1 Zorita et al.  2015 with the following additional parameters: “ d 1  q   print clusters”. Read 2 sequences were renamed using the error corrected barcode from starcode and UMI sequences from read 1  and were aligned to the Danio rerio GRCz11.94 genome assembly from Ensembl ensemble.org using STAR Dobin et al.  2013 with the following additional parameters: “  alignIntronMax 200000   outSAMattributes All   outSAMunmapped Within   outSAMtype BAM Unsorted”.  An alignment is considered valid if it aligns to an exon feature on the correct strand and is unique.  Valid alignments that had at least 50% of the read aligned to an exon feature were used to create gene level counts using a custom python script to collapse UMIs by gene.  All custom scripts are available by request. Genome build: Danio rerio GRCz11.94 genome assembly from Ensembl.org Supplementary files format and content: single Microsoft Excel file that includes counts per million CPM and correct p values for each sample and gene,Flank dermis,Untreated fish,Fish were euthanized in MS222 and the stripe and interstiped regions were micro dissected from fish expressing both pnp4a:palmmCherry and pnp4a:nlsEos. Stripe and interstipe regions were enzymatically dissociated separately with Liberase 0.25 mg/ml in dPBS at 25°C for 15 min followed by manual trituration with increasingly narrower flame polished glass pipette for 3 min at a time for three times. Cells 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 before FACS purification. The flow cytometry experiments were performed on a BD FACSAria II SORP sorter BD Biosciences  San Jose  CA  USA coupled with BD FACSDiva software BD Biosciences for instrument operation  data acquisition  and analysis. A 637 nm and a 488 nm laser were utilized for fluorophore excitation and a 100 μm nozzle was used to generate single droplets under 20PSI sheath pressure. The applied settings were as follows: forward light scatter FSC detector photomultiplier tube PMT gain setting = 80 V with a 1.5 neutral density filter; side light scatter SSC detector PMT gain setting = 90 V; FSC threshold = 10 000; PE Texas Red PE TX Red channel PMT gain setting = 280 V; fluorescein isothiocyanate FITC channel PMT gain setting = 280 V. Sample dilution and flow rate were adjusted to optimal event recordings for 96 well plate single cell sorts below 500 processed events per sec. The population of zebrafish skin iridophores was designated based on their FSC and SSC characteristics and back gating on fluorescence. Control zebrafish skin samples were used to gate out the highly auto fluorescent cells among the members of this population. Fluorescently labeled PNP4 mCherry Eos from either the stripe or interstripe skin samples were sorted separately.  Single cells with high mCherry and Eos expression were collected into 3uL of smart scrb lysis buffer 0.2% Triton X 100 [Sigma]  0.1 U/ul RNAse inhibitor [NEB] using „single cell” indexed sorting mode. Five indexed 96 well plates were collected for each skin band. post sorting  the samples were spun down at 3166 rcf at 4ºC for 2 minutes in an Eppendorf tabletop 5810R centrifuge Eppendorf AG  Hamburg  Germany and stored at  80ºC until further processing. Four plates of each skin band were selected for sequencing.  cDNA was prepared from sorted cells as described previously Cembrowski et al.  2018 with minor modifications to the sequencing configuration.  Reverse transcription  PCR  purification  tagmentation  and library quantification were performed as described.,Zebrafish were housed at 28 °C  14L:10D  fed rotifers  Artemia and flake food,tissue:Flank dermis|stripe pattern:light|reporter:Adult pnp4a:palmmCherry and pnp4a:nlsEos postive cells,GSM4294470,GSM4294470: Dvir zebrafish Light 6 010919; Danio rerio; RNA Seq,GSM4294470,,1,Fish were euthanized in MS222 and the stripe and interstiped regions were micro dissected from fish expressing both pnp4a:palmmCherry and pnp4a:nlsEos. Stripe and interstipe regions were enzymatically dissociated separately with Liberase 0.25 mg/ml in dPBS at 25°C for 15 min followed by manual trituration with increasingly narrower flame polished glass pipette for 3 min at a time for three times. Cells 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 before FACS purification. The flow cytometry experiments were performed on a BD FACSAria II SORP sorter BD Biosciences  San Jose  CA  USA coupled with BD FACSDiva software BD Biosciences for instrument operation  data acquisition  and analysis. A 637 nm and a 488 nm laser were utilized for fluorophore excitation and a 100 μm nozzle was used to generate single droplets under 20PSI sheath pressure. The applied settings were as follows: forward light scatter FSC detector photomultiplier tube PMT gain setting = 80 V with a 1.5 neutral density filter; side light scatter SSC detector PMT gain setting = 90 V; FSC threshold = 10 000; PE Texas Red PE TX Red channel PMT gain setting = 280 V; fluorescein isothiocyanate FITC channel PMT gain setting = 280 V. Sample dilution and flow rate were adjusted to optimal event recordings for 96 well plate single cell sorts below 500 processed events per sec. The population of zebrafish skin iridophores was designated based on their FSC and SSC characteristics and back gating on fluorescence. Control zebrafish skin samples were used to gate out the highly auto fluorescent cells among the members of this population. Fluorescently labeled PNP4 mCherry Eos from either the stripe or interstripe skin samples were sorted separately.  Single cells with high mCherry and Eos expression were collected into 3uL of smart scrb lysis buffer 0.2% Triton X 100 [Sigma]  0.1 U/ul RNAse inhibitor [NEB] using „single cell” indexed sorting mode. Five indexed 96 well plates were collected for each skin band. post sorting  the samples were spun down at 3166 rcf at 4ºC for 2 minutes in an Eppendorf tabletop 5810R centrifuge Eppendorf AG  Hamburg  Germany and stored at  80ºC until further processing. Four plates of each skin band were selected for sequencing.  cDNA was prepared from sorted cells as described previously Cembrowski et al.  2018 with minor modifications to the sequencing configuration.  Reverse transcription  PCR  purification  tagmentation  and library quantification were performed as described.,GEO Accession:GSM4294470,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP247126,,,Plate_298_Q7_1.fastq.gz Plate_298_Q7_2.fastq.gz,fastq fastq,2559768084.0,33681159.0,GSM4294470 r1,0:26 1:50,A:716945728;C:505642244;G:535898808;T:800467367;N:813937,26,50,,,716945728,505642244,535898808,800467367,813937,SRX7670821,SRS6098554,SRA1037187,GEO,"JLS, HHMI Janelia Research Campus",2,0.00886,0.70125,0.00828,0.44288,0.99829,0.85965,0.50943,0.5945,26,50,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2020-02-04,Adult,Adult,Skin,Surface Structure
56589,SRR11015121,SRX7670820,SRS6098559,SRP247126,PRJNA604753,IN SITU DIFFERENTIATION OF IRIDOPHORE CRYSTALLOTYPES UNDERLIES ZEBRAFISH STRIPING,GSE144734,Transcriptome Analysis,Skin color patterns are ubiquitous in nature  evolve rapidly  and impact social behavior  predator avoidance  and protection from ultraviolet irradiation. A leading model system for vertebrate skin patterning is the zebrafish; its alternating blue stripes and yellow interstripes depend on guanine crystal containing cells called iridophores that reflect light. It was suggested that the zebrafish's alternating color pattern arises from a single type of iridophore migrating differentially to stripes and interstripes. When we tracked iridophores  however  we found they did not migrate between stripes and interstripes but instead differentiated and proliferated in place based on their micro environment. RNA sequencing analysis further revealed that stripe and interstripe iridophores had different transcriptomic states with many differences in gene expression and pathway enrichment  while cryogenic scanning electron microscopy and micro X ray diffraction identified different guanine crystal organizations and responsiveness to norepinephrine  all indicating that stripe and interstripe iridophores are different cell types. Based on these results  we present a new model of skin patterning in zebrafish in which distinct iridophore crystallotypes containing specialized  physiologically responsive  subcellular organelles arise in stripe and interstripe zones by in situ differentiation. In this model  pattern phenotype depends not only on interactions among pigment cells that affect their arrangements  but also on factors that specify subcellular organization and physiological responsiveness of specialized organelles. Overall design: Unbiased classification of iridophores  based solely on their RNA profiles obtained by single cell RNA sequencing,,pubmed:33319779,,Dvir zebrafish Light 5 010919,GSM4294469,,source name:Flank dermis|tissue:Flank dermis|stripe pattern:light|reporter:Adult pnp4a:palmmCherry and pnp4a:nlsEos postive cells,Dvir zebrafish Light 5 010919,The libraries were pooled and sequenced on an Illumina NextSeq 550 high output flowcell with 26 base pair read1  50 base pair read 2  8 base pair i7 index.  Samples were demultiplexed using bcl2fastq v2.20 software from Illumina with default settings. Barcode and UMI sequences were extracted from read 1 using custom python scripts.  Barcode error correction was done using starcode v1.1 Zorita et al.  2015 with the following additional parameters: “ d 1  q   print clusters”. Read 2 sequences were renamed using the error corrected barcode from starcode and UMI sequences from read 1  and were aligned to the Danio rerio GRCz11.94 genome assembly from Ensembl ensemble.org using STAR Dobin et al.  2013 with the following additional parameters: “  alignIntronMax 200000   outSAMattributes All   outSAMunmapped Within   outSAMtype BAM Unsorted”.  An alignment is considered valid if it aligns to an exon feature on the correct strand and is unique.  Valid alignments that had at least 50% of the read aligned to an exon feature were used to create gene level counts using a custom python script to collapse UMIs by gene.  All custom scripts are available by request. Genome build: Danio rerio GRCz11.94 genome assembly from Ensembl.org Supplementary files format and content: single Microsoft Excel file that includes counts per million CPM and correct p values for each sample and gene,Flank dermis,Untreated fish,Fish were euthanized in MS222 and the stripe and interstiped regions were micro dissected from fish expressing both pnp4a:palmmCherry and pnp4a:nlsEos. Stripe and interstipe regions were enzymatically dissociated separately with Liberase 0.25 mg/ml in dPBS at 25°C for 15 min followed by manual trituration with increasingly narrower flame polished glass pipette for 3 min at a time for three times. Cells 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 before FACS purification. The flow cytometry experiments were performed on a BD FACSAria II SORP sorter BD Biosciences  San Jose  CA  USA coupled with BD FACSDiva software BD Biosciences for instrument operation  data acquisition  and analysis. A 637 nm and a 488 nm laser were utilized for fluorophore excitation and a 100 μm nozzle was used to generate single droplets under 20PSI sheath pressure. The applied settings were as follows: forward light scatter FSC detector photomultiplier tube PMT gain setting = 80 V with a 1.5 neutral density filter; side light scatter SSC detector PMT gain setting = 90 V; FSC threshold = 10 000; PE Texas Red PE TX Red channel PMT gain setting = 280 V; fluorescein isothiocyanate FITC channel PMT gain setting = 280 V. Sample dilution and flow rate were adjusted to optimal event recordings for 96 well plate single cell sorts below 500 processed events per sec. The population of zebrafish skin iridophores was designated based on their FSC and SSC characteristics and back gating on fluorescence. Control zebrafish skin samples were used to gate out the highly auto fluorescent cells among the members of this population. Fluorescently labeled PNP4 mCherry Eos from either the stripe or interstripe skin samples were sorted separately.  Single cells with high mCherry and Eos expression were collected into 3uL of smart scrb lysis buffer 0.2% Triton X 100 [Sigma]  0.1 U/ul RNAse inhibitor [NEB] using „single cell” indexed sorting mode. Five indexed 96 well plates were collected for each skin band. post sorting  the samples were spun down at 3166 rcf at 4ºC for 2 minutes in an Eppendorf tabletop 5810R centrifuge Eppendorf AG  Hamburg  Germany and stored at  80ºC until further processing. Four plates of each skin band were selected for sequencing.  cDNA was prepared from sorted cells as described previously Cembrowski et al.  2018 with minor modifications to the sequencing configuration.  Reverse transcription  PCR  purification  tagmentation  and library quantification were performed as described.,Zebrafish were housed at 28 °C  14L:10D  fed rotifers  Artemia and flake food,tissue:Flank dermis|stripe pattern:light|reporter:Adult pnp4a:palmmCherry and pnp4a:nlsEos postive cells,GSM4294469,GSM4294469: Dvir zebrafish Light 5 010919; Danio rerio; RNA Seq,GSM4294469,,1,Fish were euthanized in MS222 and the stripe and interstiped regions were micro dissected from fish expressing both pnp4a:palmmCherry and pnp4a:nlsEos. Stripe and interstipe regions were enzymatically dissociated separately with Liberase 0.25 mg/ml in dPBS at 25°C for 15 min followed by manual trituration with increasingly narrower flame polished glass pipette for 3 min at a time for three times. Cells 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 before FACS purification. The flow cytometry experiments were performed on a BD FACSAria II SORP sorter BD Biosciences  San Jose  CA  USA coupled with BD FACSDiva software BD Biosciences for instrument operation  data acquisition  and analysis. A 637 nm and a 488 nm laser were utilized for fluorophore excitation and a 100 μm nozzle was used to generate single droplets under 20PSI sheath pressure. The applied settings were as follows: forward light scatter FSC detector photomultiplier tube PMT gain setting = 80 V with a 1.5 neutral density filter; side light scatter SSC detector PMT gain setting = 90 V; FSC threshold = 10 000; PE Texas Red PE TX Red channel PMT gain setting = 280 V; fluorescein isothiocyanate FITC channel PMT gain setting = 280 V. Sample dilution and flow rate were adjusted to optimal event recordings for 96 well plate single cell sorts below 500 processed events per sec. The population of zebrafish skin iridophores was designated based on their FSC and SSC characteristics and back gating on fluorescence. Control zebrafish skin samples were used to gate out the highly auto fluorescent cells among the members of this population. Fluorescently labeled PNP4 mCherry Eos from either the stripe or interstripe skin samples were sorted separately.  Single cells with high mCherry and Eos expression were collected into 3uL of smart scrb lysis buffer 0.2% Triton X 100 [Sigma]  0.1 U/ul RNAse inhibitor [NEB] using „single cell” indexed sorting mode. Five indexed 96 well plates were collected for each skin band. post sorting  the samples were spun down at 3166 rcf at 4ºC for 2 minutes in an Eppendorf tabletop 5810R centrifuge Eppendorf AG  Hamburg  Germany and stored at  80ºC until further processing. Four plates of each skin band were selected for sequencing.  cDNA was prepared from sorted cells as described previously Cembrowski et al.  2018 with minor modifications to the sequencing configuration.  Reverse transcription  PCR  purification  tagmentation  and library quantification were performed as described.,GEO Accession:GSM4294469,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP247126,,,Plate_297_Q8_1.fastq.gz Plate_297_Q8_2.fastq.gz,fastq fastq,3221058448.0,42382348.0,GSM4294469 r1,0:26 1:50,A:1008906107;C:582878113;G:692463072;T:935769053;N:1042103,26,50,,,1008906107,582878113,692463072,935769053,1042103,SRX7670820,SRS6098559,SRA1037187,GEO,"JLS, HHMI Janelia Research Campus",2,0.01813,0.58005,0.01743,0.42634,0.99793,0.90972,0.44531,0.58212,26,50,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2020-02-04,Adult,Adult,Skin,Surface Structure
56590,SRR11015120,SRX7670819,SRS6098557,SRP247126,PRJNA604753,IN SITU DIFFERENTIATION OF IRIDOPHORE CRYSTALLOTYPES UNDERLIES ZEBRAFISH STRIPING,GSE144734,Transcriptome Analysis,Skin color patterns are ubiquitous in nature  evolve rapidly  and impact social behavior  predator avoidance  and protection from ultraviolet irradiation. A leading model system for vertebrate skin patterning is the zebrafish; its alternating blue stripes and yellow interstripes depend on guanine crystal containing cells called iridophores that reflect light. It was suggested that the zebrafish's alternating color pattern arises from a single type of iridophore migrating differentially to stripes and interstripes. When we tracked iridophores  however  we found they did not migrate between stripes and interstripes but instead differentiated and proliferated in place based on their micro environment. RNA sequencing analysis further revealed that stripe and interstripe iridophores had different transcriptomic states with many differences in gene expression and pathway enrichment  while cryogenic scanning electron microscopy and micro X ray diffraction identified different guanine crystal organizations and responsiveness to norepinephrine  all indicating that stripe and interstripe iridophores are different cell types. Based on these results  we present a new model of skin patterning in zebrafish in which distinct iridophore crystallotypes containing specialized  physiologically responsive  subcellular organelles arise in stripe and interstripe zones by in situ differentiation. In this model  pattern phenotype depends not only on interactions among pigment cells that affect their arrangements  but also on factors that specify subcellular organization and physiological responsiveness of specialized organelles. Overall design: Unbiased classification of iridophores  based solely on their RNA profiles obtained by single cell RNA sequencing,,pubmed:33319779,,Dvir zebrafish Dark 1 010919,GSM4294468,,source name:Flank dermis|tissue:Flank dermis|stripe pattern:dark|reporter:Adult pnp4a:palmmCherry and pnp4a:nlsEos postive cells,Dvir zebrafish Dark 1 010919,The libraries were pooled and sequenced on an Illumina NextSeq 550 high output flowcell with 26 base pair read1  50 base pair read 2  8 base pair i7 index.  Samples were demultiplexed using bcl2fastq v2.20 software from Illumina with default settings. Barcode and UMI sequences were extracted from read 1 using custom python scripts.  Barcode error correction was done using starcode v1.1 Zorita et al.  2015 with the following additional parameters: “ d 1  q   print clusters”. Read 2 sequences were renamed using the error corrected barcode from starcode and UMI sequences from read 1  and were aligned to the Danio rerio GRCz11.94 genome assembly from Ensembl ensemble.org using STAR Dobin et al.  2013 with the following additional parameters: “  alignIntronMax 200000   outSAMattributes All   outSAMunmapped Within   outSAMtype BAM Unsorted”.  An alignment is considered valid if it aligns to an exon feature on the correct strand and is unique.  Valid alignments that had at least 50% of the read aligned to an exon feature were used to create gene level counts using a custom python script to collapse UMIs by gene.  All custom scripts are available by request. Genome build: Danio rerio GRCz11.94 genome assembly from Ensembl.org Supplementary files format and content: single Microsoft Excel file that includes counts per million CPM and correct p values for each sample and gene,Flank dermis,Untreated fish,Fish were euthanized in MS222 and the stripe and interstiped regions were micro dissected from fish expressing both pnp4a:palmmCherry and pnp4a:nlsEos. Stripe and interstipe regions were enzymatically dissociated separately with Liberase 0.25 mg/ml in dPBS at 25°C for 15 min followed by manual trituration with increasingly narrower flame polished glass pipette for 3 min at a time for three times. Cells 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 before FACS purification. The flow cytometry experiments were performed on a BD FACSAria II SORP sorter BD Biosciences  San Jose  CA  USA coupled with BD FACSDiva software BD Biosciences for instrument operation  data acquisition  and analysis. A 637 nm and a 488 nm laser were utilized for fluorophore excitation and a 100 μm nozzle was used to generate single droplets under 20PSI sheath pressure. The applied settings were as follows: forward light scatter FSC detector photomultiplier tube PMT gain setting = 80 V with a 1.5 neutral density filter; side light scatter SSC detector PMT gain setting = 90 V; FSC threshold = 10 000; PE Texas Red PE TX Red channel PMT gain setting = 280 V; fluorescein isothiocyanate FITC channel PMT gain setting = 280 V. Sample dilution and flow rate were adjusted to optimal event recordings for 96 well plate single cell sorts below 500 processed events per sec. The population of zebrafish skin iridophores was designated based on their FSC and SSC characteristics and back gating on fluorescence. Control zebrafish skin samples were used to gate out the highly auto fluorescent cells among the members of this population. Fluorescently labeled PNP4 mCherry Eos from either the stripe or interstripe skin samples were sorted separately.  Single cells with high mCherry and Eos expression were collected into 3uL of smart scrb lysis buffer 0.2% Triton X 100 [Sigma]  0.1 U/ul RNAse inhibitor [NEB] using „single cell” indexed sorting mode. Five indexed 96 well plates were collected for each skin band. post sorting  the samples were spun down at 3166 rcf at 4ºC for 2 minutes in an Eppendorf tabletop 5810R centrifuge Eppendorf AG  Hamburg  Germany and stored at  80ºC until further processing. Four plates of each skin band were selected for sequencing.  cDNA was prepared from sorted cells as described previously Cembrowski et al.  2018 with minor modifications to the sequencing configuration.  Reverse transcription  PCR  purification  tagmentation  and library quantification were performed as described.,Zebrafish were housed at 28 °C  14L:10D  fed rotifers  Artemia and flake food,tissue:Flank dermis|stripe pattern:dark|reporter:Adult pnp4a:palmmCherry and pnp4a:nlsEos postive cells,GSM4294468,GSM4294468: Dvir zebrafish Dark 1 010919; Danio rerio; RNA Seq,GSM4294468,,1,Fish were euthanized in MS222 and the stripe and interstiped regions were micro dissected from fish expressing both pnp4a:palmmCherry and pnp4a:nlsEos. Stripe and interstipe regions were enzymatically dissociated separately with Liberase 0.25 mg/ml in dPBS at 25°C for 15 min followed by manual trituration with increasingly narrower flame polished glass pipette for 3 min at a time for three times. Cells 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 before FACS purification. The flow cytometry experiments were performed on a BD FACSAria II SORP sorter BD Biosciences  San Jose  CA  USA coupled with BD FACSDiva software BD Biosciences for instrument operation  data acquisition  and analysis. A 637 nm and a 488 nm laser were utilized for fluorophore excitation and a 100 μm nozzle was used to generate single droplets under 20PSI sheath pressure. The applied settings were as follows: forward light scatter FSC detector photomultiplier tube PMT gain setting = 80 V with a 1.5 neutral density filter; side light scatter SSC detector PMT gain setting = 90 V; FSC threshold = 10 000; PE Texas Red PE TX Red channel PMT gain setting = 280 V; fluorescein isothiocyanate FITC channel PMT gain setting = 280 V. Sample dilution and flow rate were adjusted to optimal event recordings for 96 well plate single cell sorts below 500 processed events per sec. The population of zebrafish skin iridophores was designated based on their FSC and SSC characteristics and back gating on fluorescence. Control zebrafish skin samples were used to gate out the highly auto fluorescent cells among the members of this population. Fluorescently labeled PNP4 mCherry Eos from either the stripe or interstripe skin samples were sorted separately.  Single cells with high mCherry and Eos expression were collected into 3uL of smart scrb lysis buffer 0.2% Triton X 100 [Sigma]  0.1 U/ul RNAse inhibitor [NEB] using „single cell” indexed sorting mode. Five indexed 96 well plates were collected for each skin band. post sorting  the samples were spun down at 3166 rcf at 4ºC for 2 minutes in an Eppendorf tabletop 5810R centrifuge Eppendorf AG  Hamburg  Germany and stored at  80ºC until further processing. Four plates of each skin band were selected for sequencing.  cDNA was prepared from sorted cells as described previously Cembrowski et al.  2018 with minor modifications to the sequencing configuration.  Reverse transcription  PCR  purification  tagmentation  and library quantification were performed as described.,GEO Accession:GSM4294468,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP247126,,,Plate_296_Q7_1.fastq.gz Plate_296_Q7_2.fastq.gz,fastq fastq,2244459740.0,29532365.0,GSM4294468 r1,0:26 1:50,A:624595512;C:431880173;G:469039896;T:718227272;N:716887,26,50,,,624595512,431880173,469039896,718227272,716887,SRX7670819,SRS6098557,SRA1037187,GEO,"JLS, HHMI Janelia Research Campus",2,0.0119,0.7446,0.01114,0.5426,0.99762,0.87253,0.45652,0.56682,26,50,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2020-02-04,Adult,Adult,Skin,Surface Structure
56591,SRR11015119,SRX7670818,SRS6098556,SRP247126,PRJNA604753,IN SITU DIFFERENTIATION OF IRIDOPHORE CRYSTALLOTYPES UNDERLIES ZEBRAFISH STRIPING,GSE144734,Transcriptome Analysis,Skin color patterns are ubiquitous in nature  evolve rapidly  and impact social behavior  predator avoidance  and protection from ultraviolet irradiation. A leading model system for vertebrate skin patterning is the zebrafish; its alternating blue stripes and yellow interstripes depend on guanine crystal containing cells called iridophores that reflect light. It was suggested that the zebrafish's alternating color pattern arises from a single type of iridophore migrating differentially to stripes and interstripes. When we tracked iridophores  however  we found they did not migrate between stripes and interstripes but instead differentiated and proliferated in place based on their micro environment. RNA sequencing analysis further revealed that stripe and interstripe iridophores had different transcriptomic states with many differences in gene expression and pathway enrichment  while cryogenic scanning electron microscopy and micro X ray diffraction identified different guanine crystal organizations and responsiveness to norepinephrine  all indicating that stripe and interstripe iridophores are different cell types. Based on these results  we present a new model of skin patterning in zebrafish in which distinct iridophore crystallotypes containing specialized  physiologically responsive  subcellular organelles arise in stripe and interstripe zones by in situ differentiation. In this model  pattern phenotype depends not only on interactions among pigment cells that affect their arrangements  but also on factors that specify subcellular organization and physiological responsiveness of specialized organelles. Overall design: Unbiased classification of iridophores  based solely on their RNA profiles obtained by single cell RNA sequencing,,pubmed:33319779,,Dvir zebrafish Dark 3 010919,GSM4294467,,source name:Flank dermis|tissue:Flank dermis|stripe pattern:dark|reporter:Adult pnp4a:palmmCherry and pnp4a:nlsEos postive cells,Dvir zebrafish Dark 3 010919,The libraries were pooled and sequenced on an Illumina NextSeq 550 high output flowcell with 26 base pair read1  50 base pair read 2  8 base pair i7 index.  Samples were demultiplexed using bcl2fastq v2.20 software from Illumina with default settings. Barcode and UMI sequences were extracted from read 1 using custom python scripts.  Barcode error correction was done using starcode v1.1 Zorita et al.  2015 with the following additional parameters: “ d 1  q   print clusters”. Read 2 sequences were renamed using the error corrected barcode from starcode and UMI sequences from read 1  and were aligned to the Danio rerio GRCz11.94 genome assembly from Ensembl ensemble.org using STAR Dobin et al.  2013 with the following additional parameters: “  alignIntronMax 200000   outSAMattributes All   outSAMunmapped Within   outSAMtype BAM Unsorted”.  An alignment is considered valid if it aligns to an exon feature on the correct strand and is unique.  Valid alignments that had at least 50% of the read aligned to an exon feature were used to create gene level counts using a custom python script to collapse UMIs by gene.  All custom scripts are available by request. Genome build: Danio rerio GRCz11.94 genome assembly from Ensembl.org Supplementary files format and content: single Microsoft Excel file that includes counts per million CPM and correct p values for each sample and gene,Flank dermis,Untreated fish,Fish were euthanized in MS222 and the stripe and interstiped regions were micro dissected from fish expressing both pnp4a:palmmCherry and pnp4a:nlsEos. Stripe and interstipe regions were enzymatically dissociated separately with Liberase 0.25 mg/ml in dPBS at 25°C for 15 min followed by manual trituration with increasingly narrower flame polished glass pipette for 3 min at a time for three times. Cells 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 before FACS purification. The flow cytometry experiments were performed on a BD FACSAria II SORP sorter BD Biosciences  San Jose  CA  USA coupled with BD FACSDiva software BD Biosciences for instrument operation  data acquisition  and analysis. A 637 nm and a 488 nm laser were utilized for fluorophore excitation and a 100 μm nozzle was used to generate single droplets under 20PSI sheath pressure. The applied settings were as follows: forward light scatter FSC detector photomultiplier tube PMT gain setting = 80 V with a 1.5 neutral density filter; side light scatter SSC detector PMT gain setting = 90 V; FSC threshold = 10 000; PE Texas Red PE TX Red channel PMT gain setting = 280 V; fluorescein isothiocyanate FITC channel PMT gain setting = 280 V. Sample dilution and flow rate were adjusted to optimal event recordings for 96 well plate single cell sorts below 500 processed events per sec. The population of zebrafish skin iridophores was designated based on their FSC and SSC characteristics and back gating on fluorescence. Control zebrafish skin samples were used to gate out the highly auto fluorescent cells among the members of this population. Fluorescently labeled PNP4 mCherry Eos from either the stripe or interstripe skin samples were sorted separately.  Single cells with high mCherry and Eos expression were collected into 3uL of smart scrb lysis buffer 0.2% Triton X 100 [Sigma]  0.1 U/ul RNAse inhibitor [NEB] using „single cell” indexed sorting mode. Five indexed 96 well plates were collected for each skin band. post sorting  the samples were spun down at 3166 rcf at 4ºC for 2 minutes in an Eppendorf tabletop 5810R centrifuge Eppendorf AG  Hamburg  Germany and stored at  80ºC until further processing. Four plates of each skin band were selected for sequencing.  cDNA was prepared from sorted cells as described previously Cembrowski et al.  2018 with minor modifications to the sequencing configuration.  Reverse transcription  PCR  purification  tagmentation  and library quantification were performed as described.,Zebrafish were housed at 28 °C  14L:10D  fed rotifers  Artemia and flake food,tissue:Flank dermis|stripe pattern:dark|reporter:Adult pnp4a:palmmCherry and pnp4a:nlsEos postive cells,GSM4294467,GSM4294467: Dvir zebrafish Dark 3 010919; Danio rerio; RNA Seq,GSM4294467,,1,Fish were euthanized in MS222 and the stripe and interstiped regions were micro dissected from fish expressing both pnp4a:palmmCherry and pnp4a:nlsEos. Stripe and interstipe regions were enzymatically dissociated separately with Liberase 0.25 mg/ml in dPBS at 25°C for 15 min followed by manual trituration with increasingly narrower flame polished glass pipette for 3 min at a time for three times. Cells 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 before FACS purification. The flow cytometry experiments were performed on a BD FACSAria II SORP sorter BD Biosciences  San Jose  CA  USA coupled with BD FACSDiva software BD Biosciences for instrument operation  data acquisition  and analysis. A 637 nm and a 488 nm laser were utilized for fluorophore excitation and a 100 μm nozzle was used to generate single droplets under 20PSI sheath pressure. The applied settings were as follows: forward light scatter FSC detector photomultiplier tube PMT gain setting = 80 V with a 1.5 neutral density filter; side light scatter SSC detector PMT gain setting = 90 V; FSC threshold = 10 000; PE Texas Red PE TX Red channel PMT gain setting = 280 V; fluorescein isothiocyanate FITC channel PMT gain setting = 280 V. Sample dilution and flow rate were adjusted to optimal event recordings for 96 well plate single cell sorts below 500 processed events per sec. The population of zebrafish skin iridophores was designated based on their FSC and SSC characteristics and back gating on fluorescence. Control zebrafish skin samples were used to gate out the highly auto fluorescent cells among the members of this population. Fluorescently labeled PNP4 mCherry Eos from either the stripe or interstripe skin samples were sorted separately.  Single cells with high mCherry and Eos expression were collected into 3uL of smart scrb lysis buffer 0.2% Triton X 100 [Sigma]  0.1 U/ul RNAse inhibitor [NEB] using „single cell” indexed sorting mode. Five indexed 96 well plates were collected for each skin band. post sorting  the samples were spun down at 3166 rcf at 4ºC for 2 minutes in an Eppendorf tabletop 5810R centrifuge Eppendorf AG  Hamburg  Germany and stored at  80ºC until further processing. Four plates of each skin band were selected for sequencing.  cDNA was prepared from sorted cells as described previously Cembrowski et al.  2018 with minor modifications to the sequencing configuration.  Reverse transcription  PCR  purification  tagmentation  and library quantification were performed as described.,GEO Accession:GSM4294467,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP247126,,,Plate_295_Q6_2.fastq.gz Plate_295_Q6_1.fastq.gz,fastq fastq,2427247568.0,31937468.0,GSM4294467 r1,0:26 1:50,A:692706510;C:460103108;G:520860555;T:752816632;N:760763,26,50,,,692706510,460103108,520860555,752816632,760763,SRX7670818,SRS6098556,SRA1037187,GEO,"JLS, HHMI Janelia Research Campus",2,0.01059,0.71366,0.00996,0.51875,0.99825,0.89378,0.5,0.55992,26,50,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2020-02-04,Adult,Adult,Skin,Surface Structure
56592,SRR11015118,SRX7670817,SRS6098553,SRP247126,PRJNA604753,IN SITU DIFFERENTIATION OF IRIDOPHORE CRYSTALLOTYPES UNDERLIES ZEBRAFISH STRIPING,GSE144734,Transcriptome Analysis,Skin color patterns are ubiquitous in nature  evolve rapidly  and impact social behavior  predator avoidance  and protection from ultraviolet irradiation. A leading model system for vertebrate skin patterning is the zebrafish; its alternating blue stripes and yellow interstripes depend on guanine crystal containing cells called iridophores that reflect light. It was suggested that the zebrafish's alternating color pattern arises from a single type of iridophore migrating differentially to stripes and interstripes. When we tracked iridophores  however  we found they did not migrate between stripes and interstripes but instead differentiated and proliferated in place based on their micro environment. RNA sequencing analysis further revealed that stripe and interstripe iridophores had different transcriptomic states with many differences in gene expression and pathway enrichment  while cryogenic scanning electron microscopy and micro X ray diffraction identified different guanine crystal organizations and responsiveness to norepinephrine  all indicating that stripe and interstripe iridophores are different cell types. Based on these results  we present a new model of skin patterning in zebrafish in which distinct iridophore crystallotypes containing specialized  physiologically responsive  subcellular organelles arise in stripe and interstripe zones by in situ differentiation. In this model  pattern phenotype depends not only on interactions among pigment cells that affect their arrangements  but also on factors that specify subcellular organization and physiological responsiveness of specialized organelles. Overall design: Unbiased classification of iridophores  based solely on their RNA profiles obtained by single cell RNA sequencing,,pubmed:33319779,,Dvir zebrafish Light 4 010919,GSM4294466,,source name:Flank dermis|tissue:Flank dermis|stripe pattern:light|reporter:Adult pnp4a:palmmCherry and pnp4a:nlsEos postive cells,Dvir zebrafish Light 4 010919,The libraries were pooled and sequenced on an Illumina NextSeq 550 high output flowcell with 26 base pair read1  50 base pair read 2  8 base pair i7 index.  Samples were demultiplexed using bcl2fastq v2.20 software from Illumina with default settings. Barcode and UMI sequences were extracted from read 1 using custom python scripts.  Barcode error correction was done using starcode v1.1 Zorita et al.  2015 with the following additional parameters: “ d 1  q   print clusters”. Read 2 sequences were renamed using the error corrected barcode from starcode and UMI sequences from read 1  and were aligned to the Danio rerio GRCz11.94 genome assembly from Ensembl ensemble.org using STAR Dobin et al.  2013 with the following additional parameters: “  alignIntronMax 200000   outSAMattributes All   outSAMunmapped Within   outSAMtype BAM Unsorted”.  An alignment is considered valid if it aligns to an exon feature on the correct strand and is unique.  Valid alignments that had at least 50% of the read aligned to an exon feature were used to create gene level counts using a custom python script to collapse UMIs by gene.  All custom scripts are available by request. Genome build: Danio rerio GRCz11.94 genome assembly from Ensembl.org Supplementary files format and content: single Microsoft Excel file that includes counts per million CPM and correct p values for each sample and gene,Flank dermis,Untreated fish,Fish were euthanized in MS222 and the stripe and interstiped regions were micro dissected from fish expressing both pnp4a:palmmCherry and pnp4a:nlsEos. Stripe and interstipe regions were enzymatically dissociated separately with Liberase 0.25 mg/ml in dPBS at 25°C for 15 min followed by manual trituration with increasingly narrower flame polished glass pipette for 3 min at a time for three times. Cells 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 before FACS purification. The flow cytometry experiments were performed on a BD FACSAria II SORP sorter BD Biosciences  San Jose  CA  USA coupled with BD FACSDiva software BD Biosciences for instrument operation  data acquisition  and analysis. A 637 nm and a 488 nm laser were utilized for fluorophore excitation and a 100 μm nozzle was used to generate single droplets under 20PSI sheath pressure. The applied settings were as follows: forward light scatter FSC detector photomultiplier tube PMT gain setting = 80 V with a 1.5 neutral density filter; side light scatter SSC detector PMT gain setting = 90 V; FSC threshold = 10 000; PE Texas Red PE TX Red channel PMT gain setting = 280 V; fluorescein isothiocyanate FITC channel PMT gain setting = 280 V. Sample dilution and flow rate were adjusted to optimal event recordings for 96 well plate single cell sorts below 500 processed events per sec. The population of zebrafish skin iridophores was designated based on their FSC and SSC characteristics and back gating on fluorescence. Control zebrafish skin samples were used to gate out the highly auto fluorescent cells among the members of this population. Fluorescently labeled PNP4 mCherry Eos from either the stripe or interstripe skin samples were sorted separately.  Single cells with high mCherry and Eos expression were collected into 3uL of smart scrb lysis buffer 0.2% Triton X 100 [Sigma]  0.1 U/ul RNAse inhibitor [NEB] using „single cell” indexed sorting mode. Five indexed 96 well plates were collected for each skin band. post sorting  the samples were spun down at 3166 rcf at 4ºC for 2 minutes in an Eppendorf tabletop 5810R centrifuge Eppendorf AG  Hamburg  Germany and stored at  80ºC until further processing. Four plates of each skin band were selected for sequencing.  cDNA was prepared from sorted cells as described previously Cembrowski et al.  2018 with minor modifications to the sequencing configuration.  Reverse transcription  PCR  purification  tagmentation  and library quantification were performed as described.,Zebrafish were housed at 28 °C  14L:10D  fed rotifers  Artemia and flake food,tissue:Flank dermis|stripe pattern:light|reporter:Adult pnp4a:palmmCherry and pnp4a:nlsEos postive cells,GSM4294466,GSM4294466: Dvir zebrafish Light 4 010919; Danio rerio; RNA Seq,GSM4294466,,1,Fish were euthanized in MS222 and the stripe and interstiped regions were micro dissected from fish expressing both pnp4a:palmmCherry and pnp4a:nlsEos. Stripe and interstipe regions were enzymatically dissociated separately with Liberase 0.25 mg/ml in dPBS at 25°C for 15 min followed by manual trituration with increasingly narrower flame polished glass pipette for 3 min at a time for three times. Cells 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 before FACS purification. The flow cytometry experiments were performed on a BD FACSAria II SORP sorter BD Biosciences  San Jose  CA  USA coupled with BD FACSDiva software BD Biosciences for instrument operation  data acquisition  and analysis. A 637 nm and a 488 nm laser were utilized for fluorophore excitation and a 100 μm nozzle was used to generate single droplets under 20PSI sheath pressure. The applied settings were as follows: forward light scatter FSC detector photomultiplier tube PMT gain setting = 80 V with a 1.5 neutral density filter; side light scatter SSC detector PMT gain setting = 90 V; FSC threshold = 10 000; PE Texas Red PE TX Red channel PMT gain setting = 280 V; fluorescein isothiocyanate FITC channel PMT gain setting = 280 V. Sample dilution and flow rate were adjusted to optimal event recordings for 96 well plate single cell sorts below 500 processed events per sec. The population of zebrafish skin iridophores was designated based on their FSC and SSC characteristics and back gating on fluorescence. Control zebrafish skin samples were used to gate out the highly auto fluorescent cells among the members of this population. Fluorescently labeled PNP4 mCherry Eos from either the stripe or interstripe skin samples were sorted separately.  Single cells with high mCherry and Eos expression were collected into 3uL of smart scrb lysis buffer 0.2% Triton X 100 [Sigma]  0.1 U/ul RNAse inhibitor [NEB] using „single cell” indexed sorting mode. Five indexed 96 well plates were collected for each skin band. post sorting  the samples were spun down at 3166 rcf at 4ºC for 2 minutes in an Eppendorf tabletop 5810R centrifuge Eppendorf AG  Hamburg  Germany and stored at  80ºC until further processing. Four plates of each skin band were selected for sequencing.  cDNA was prepared from sorted cells as described previously Cembrowski et al.  2018 with minor modifications to the sequencing configuration.  Reverse transcription  PCR  purification  tagmentation  and library quantification were performed as described.,GEO Accession:GSM4294466,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP247126,,,Plate_294_Q5_1.fastq.gz Plate_294_Q5_2.fastq.gz,fastq fastq,2983254752.0,39253352.0,GSM4294466 r1,0:26 1:50,A:837125645;C:561283018;G:613355402;T:970532483;N:958204,26,50,,,837125645,561283018,613355402,970532483,958204,SRX7670817,SRS6098553,SRA1037187,GEO,"JLS, HHMI Janelia Research Campus",2,0.00956,0.71272,0.00895,0.49972,0.99821,0.87294,0.42857,0.5592,26,50,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2020-02-04,Adult,Adult,Skin,Surface Structure
59125,SRR11684038,SRX8244841,SRS6592476,SRP259990,PRJNA630162,Zebrafish adult skin mpeg+ cells,GSE149788,Transcriptome Analysis,We compared hematopoietic and non hematopoietic mpeg1.1+ cells from the skin of wild type fish with non hematopoietic cells from the skin of zebrafish lacking functional csf1r. We reval that non hematopoietic mpeg1.1 cells from wild type and csf1rDM fish show no major differences and likely represent metaphocytes  a newly characterized ectoderm derived cell population in the skin. Both non hematopoietic mpeg1.1+ cell populations from wild type and csf1r mutatns show a major downregulations in canonical macrophages signature genes as compared to hematopoietic mpeg1.1 cells from wild type fish. Overall design: Two biological replicates were analyzed for each of 6 conditions three genotypes; two treatments per genotype,parent bioproject:PRJNA630158,pubmed:32367800,,GFE6 Csf1r mutant.3,GSM4512730,,tissue:skin mpeg1.1 GFP+ cells|developmental stage:adult 3mo|genotype:csf1raj4e1/j4e1; csf1rbsa1503/csf1rbsa1503 mpeg1 EGFP; Kdrl:Cre; act2b:loxP STOP loxP DsRedexpress|treatment:untreated,GFE6 Csf1r mutant.3,Sequencing and base calling was performed on the IlIllumina Novaseq 6000 Paired end reads were aligned to the GRCz11.94 danio rerio genome using  STAR version 2.5.4b software. Annotations Danio rerio.GRCz11.94.gtf were obtained from ftp.Ensembl.org Gene level counts were obtained using HTSeq count version 0.11.0 Differential gene expression analysis: EdgeR Bioconductor. GSEA: GAGE Bioconductor Genome build: GRCz11.94 Supplementary files format and content: CPM values [.csv] semicolon delimited files,skin mpeg1.1 GFP+ cells,,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,Standard adult zebrafish rearing conditions in multilink system at  26° C  with 12:12 h ligt/dark cycle,developmental stage:adult 3mo|genotype:csf1raj4e1/j4e1; csf1rbsa1503/csf1rbsa1503 mpeg1 EGFP; Kdrl:Cre; act2b:loxP STOP loxP DsRedexpress|treatment:untreated,GSM4512730,GSM4512730: GFE6 Csf1r mutant.3; Danio rerio; RNA Seq,GSM4512730,,1,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,GEO Accession:GSM4512730,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP259990,,,so-zf94_GFE6-Csf1r-mutant_S6_R2_001.fastq.gz so-zf94_GFE6-Csf1r-mutant_S6_R1_001.fastq.gz,fastq fastq,14494840876.0,71756638.0,GSM4512730 r1,0:101 1:101,A:3899647300;C:3479135941;G:3237570754;T:3878261390;N:225491,101,101,,,3899647300,3479135941,3237570754,3878261390,225491,SRX8244841,SRS6592476,SRA1072141,GEO,Erasmus MC,2,0.64161,0.64139,0.26871,0.27571,0.80827,0.80687,0.57871,0.57509,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2020-05-04,Adult,Adult,Skin,Surface Structure
59126,SRR11684037,SRX8244840,SRS6592475,SRP259990,PRJNA630162,Zebrafish adult skin mpeg+ cells,GSE149788,Transcriptome Analysis,We compared hematopoietic and non hematopoietic mpeg1.1+ cells from the skin of wild type fish with non hematopoietic cells from the skin of zebrafish lacking functional csf1r. We reval that non hematopoietic mpeg1.1 cells from wild type and csf1rDM fish show no major differences and likely represent metaphocytes  a newly characterized ectoderm derived cell population in the skin. Both non hematopoietic mpeg1.1+ cell populations from wild type and csf1r mutatns show a major downregulations in canonical macrophages signature genes as compared to hematopoietic mpeg1.1 cells from wild type fish. Overall design: Two biological replicates were analyzed for each of 6 conditions three genotypes; two treatments per genotype,parent bioproject:PRJNA630158,pubmed:32367800,,GFE5 Csf1r mutant.2,GSM4512729,,tissue:skin mpeg1.1 GFP+ cells|developmental stage:adult 3mo|genotype:csf1raj4e1/j4e1; csf1rbsa1503/csf1rbsa1503 tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated,GFE5 Csf1r mutant.2,Sequencing and base calling was performed on the IlIllumina Novaseq 6000 Paired end reads were aligned to the GRCz11.94 danio rerio genome using  STAR version 2.5.4b software. Annotations Danio rerio.GRCz11.94.gtf were obtained from ftp.Ensembl.org Gene level counts were obtained using HTSeq count version 0.11.0 Differential gene expression analysis: EdgeR Bioconductor. GSEA: GAGE Bioconductor Genome build: GRCz11.94 Supplementary files format and content: CPM values [.csv] semicolon delimited files,skin mpeg1.1 GFP+ cells,,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,Standard adult zebrafish rearing conditions in multilink system at  26° C  with 12:12 h ligt/dark cycle,developmental stage:adult 3mo|genotype:csf1raj4e1/j4e1; csf1rbsa1503/csf1rbsa1503 tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated,GSM4512729,GSM4512729: GFE5 Csf1r mutant.2; Danio rerio; RNA Seq,GSM4512729,,1,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,GEO Accession:GSM4512729,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP259990,,,so-zf94_GFE5-Csf1r-mutant_S5_R2_001.fastq.gz so-zf94_GFE5-Csf1r-mutant_S5_R1_001.fastq.gz,fastq fastq,13759568552.0,68116676.0,GSM4512729 r1,0:101 1:101,A:3660704043;C:3344175315;G:3105211222;T:3649262807;N:215165,101,101,,,3660704043,3344175315,3105211222,3649262807,215165,SRX8244840,SRS6592475,SRA1072141,GEO,Erasmus MC,2,0.69777,0.70166,0.28564,0.29683,0.79945,0.80022,0.58707,0.58207,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2020-05-04,Adult,Adult,Skin,Surface Structure
59127,SRR11684036,SRX8244839,SRS6592474,SRP259990,PRJNA630162,Zebrafish adult skin mpeg+ cells,GSE149788,Transcriptome Analysis,We compared hematopoietic and non hematopoietic mpeg1.1+ cells from the skin of wild type fish with non hematopoietic cells from the skin of zebrafish lacking functional csf1r. We reval that non hematopoietic mpeg1.1 cells from wild type and csf1rDM fish show no major differences and likely represent metaphocytes  a newly characterized ectoderm derived cell population in the skin. Both non hematopoietic mpeg1.1+ cell populations from wild type and csf1r mutatns show a major downregulations in canonical macrophages signature genes as compared to hematopoietic mpeg1.1 cells from wild type fish. Overall design: Two biological replicates were analyzed for each of 6 conditions three genotypes; two treatments per genotype,parent bioproject:PRJNA630158,pubmed:32367800,,GFE4 B Switch.1,GSM4512728,,tissue:skin mpeg1.1 GFP+; act2b:loxP STOP loxP DsRedexpress+ cells|developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated,GFE4 B Switch.1,Sequencing and base calling was performed on the IlIllumina Novaseq 6000 Paired end reads were aligned to the GRCz11.94 danio rerio genome using  STAR version 2.5.4b software. Annotations Danio rerio.GRCz11.94.gtf were obtained from ftp.Ensembl.org Gene level counts were obtained using HTSeq count version 0.11.0 Differential gene expression analysis: EdgeR Bioconductor. GSEA: GAGE Bioconductor Genome build: GRCz11.94 Supplementary files format and content: CPM values [.csv] semicolon delimited files,skin mpeg1.1 GFP+;  act2b:loxP STOP loxP DsRedexpress+ cells,,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,Standard adult zebrafish rearing conditions in multilink system at  26° C  with 12:12 h ligt/dark cycle,developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated,GSM4512728,GSM4512728: GFE4 B Switch.1; Danio rerio; RNA Seq,GSM4512728,,1,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,GEO Accession:GSM4512728,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP259990,,,so-zf94_GFE4-B-Switch_WT_S4_R2_001.fastq.gz so-zf94_GFE4-B-Switch_WT_S4_R1_001.fastq.gz,fastq fastq,10963685744.0,54275672.0,GSM4512728 r1,0:101 1:101,A:2843051618;C:2733369632;G:2559200274;T:2827894333;N:169887,101,101,,,2843051618,2733369632,2559200274,2827894333,169887,SRX8244839,SRS6592474,SRA1072141,GEO,Erasmus MC,2,0.81437,0.80007,0.30275,0.3056,0.7933,0.79427,0.60512,0.50903,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2020-05-04,Adult,Adult,Skin,Surface Structure
59128,SRR11684035,SRX8244838,SRS6592477,SRP259990,PRJNA630162,Zebrafish adult skin mpeg+ cells,GSE149788,Transcriptome Analysis,We compared hematopoietic and non hematopoietic mpeg1.1+ cells from the skin of wild type fish with non hematopoietic cells from the skin of zebrafish lacking functional csf1r. We reval that non hematopoietic mpeg1.1 cells from wild type and csf1rDM fish show no major differences and likely represent metaphocytes  a newly characterized ectoderm derived cell population in the skin. Both non hematopoietic mpeg1.1+ cell populations from wild type and csf1r mutatns show a major downregulations in canonical macrophages signature genes as compared to hematopoietic mpeg1.1 cells from wild type fish. Overall design: Two biological replicates were analyzed for each of 6 conditions three genotypes; two treatments per genotype,parent bioproject:PRJNA630158,pubmed:32367800,,GFE3 B Switch.3,GSM4512727,,tissue:skin mpeg1.1 GFP+; act2b:loxP STOP loxP DsRedexpress+ cells|developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated,GFE3 B Switch.3,Sequencing and base calling was performed on the IlIllumina Novaseq 6000 Paired end reads were aligned to the GRCz11.94 danio rerio genome using  STAR version 2.5.4b software. Annotations Danio rerio.GRCz11.94.gtf were obtained from ftp.Ensembl.org Gene level counts were obtained using HTSeq count version 0.11.0 Differential gene expression analysis: EdgeR Bioconductor. GSEA: GAGE Bioconductor Genome build: GRCz11.94 Supplementary files format and content: CPM values [.csv] semicolon delimited files,skin mpeg1.1 GFP+;  act2b:loxP STOP loxP DsRedexpress+ cells,,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,Standard adult zebrafish rearing conditions in multilink system at  26° C  with 12:12 h ligt/dark cycle,developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated,GSM4512727,GSM4512727: GFE3 B Switch.3; Danio rerio; RNA Seq,GSM4512727,,1,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,GEO Accession:GSM4512727,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP259990,,,so-zf94_GFE3-B-Switch_WT_S3_R2_001.fastq.gz so-zf94_GFE3-B-Switch_WT_S3_R1_001.fastq.gz,fastq fastq,12782078634.0,63277617.0,GSM4512727 r1,0:101 1:101,A:3381512327;C:3122362574;G:2918446203;T:3359558840;N:198690,101,101,,,3381512327,3122362574,2918446203,3359558840,198690,SRX8244838,SRS6592477,SRA1072141,GEO,Erasmus MC,2,0.76741,0.76247,0.29132,0.2981,0.78512,0.78561,0.58337,0.57753,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2020-05-04,Adult,Adult,Skin,Surface Structure
59129,SRR11684034,SRX8244837,SRS6595814,SRP259990,PRJNA630162,Zebrafish adult skin mpeg+ cells,GSE149788,Transcriptome Analysis,We compared hematopoietic and non hematopoietic mpeg1.1+ cells from the skin of wild type fish with non hematopoietic cells from the skin of zebrafish lacking functional csf1r. We reval that non hematopoietic mpeg1.1 cells from wild type and csf1rDM fish show no major differences and likely represent metaphocytes  a newly characterized ectoderm derived cell population in the skin. Both non hematopoietic mpeg1.1+ cell populations from wild type and csf1r mutatns show a major downregulations in canonical macrophages signature genes as compared to hematopoietic mpeg1.1 cells from wild type fish. Overall design: Two biological replicates were analyzed for each of 6 conditions three genotypes; two treatments per genotype,parent bioproject:PRJNA630158,pubmed:32367800,,GFE2 WT.2,GSM4512726,,tissue:skin mpeg1.1 GFP+ cells|developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated,GFE2 WT.2,Sequencing and base calling was performed on the IlIllumina Novaseq 6000 Paired end reads were aligned to the GRCz11.94 danio rerio genome using  STAR version 2.5.4b software. Annotations Danio rerio.GRCz11.94.gtf were obtained from ftp.Ensembl.org Gene level counts were obtained using HTSeq count version 0.11.0 Differential gene expression analysis: EdgeR Bioconductor. GSEA: GAGE Bioconductor Genome build: GRCz11.94 Supplementary files format and content: CPM values [.csv] semicolon delimited files,skin mpeg1.1 GFP+ cells,,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,Standard adult zebrafish rearing conditions in multilink system at  26° C  with 12:12 h ligt/dark cycle,developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated,GSM4512726,GSM4512726: GFE2 WT.2; Danio rerio; RNA Seq,GSM4512726,,1,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,GEO Accession:GSM4512726,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP259990,,,so-zf94_GFE2-WT_S2_R1_001.fastq.gz so-zf94_GFE2-WT_S2_R2_001.fastq.gz,fastq fastq,14364066682.0,71109241.0,GSM4512726 r1,0:101 1:101,A:3728039055;C:3584760331;G:3349868256;T:3701175176;N:223864,101,101,,,3728039055,3584760331,3349868256,3701175176,223864,SRX8244837,SRS6595814,SRA1072141,GEO,Erasmus MC,2,0.84099,0.82969,0.32553,0.33066,0.79226,0.79145,0.6061,0.60266,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2020-05-04,Adult,Adult,Skin,Surface Structure
59130,SRR11684033,SRX8244836,SRS6592473,SRP259990,PRJNA630162,Zebrafish adult skin mpeg+ cells,GSE149788,Transcriptome Analysis,We compared hematopoietic and non hematopoietic mpeg1.1+ cells from the skin of wild type fish with non hematopoietic cells from the skin of zebrafish lacking functional csf1r. We reval that non hematopoietic mpeg1.1 cells from wild type and csf1rDM fish show no major differences and likely represent metaphocytes  a newly characterized ectoderm derived cell population in the skin. Both non hematopoietic mpeg1.1+ cell populations from wild type and csf1r mutatns show a major downregulations in canonical macrophages signature genes as compared to hematopoietic mpeg1.1 cells from wild type fish. Overall design: Two biological replicates were analyzed for each of 6 conditions three genotypes; two treatments per genotype,parent bioproject:PRJNA630158,pubmed:32367800,,GFE1 WT.1,GSM4512725,,tissue:skin mpeg1.1 GFP+ cells|developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated,GFE1 WT.1,Sequencing and base calling was performed on the IlIllumina Novaseq 6000 Paired end reads were aligned to the GRCz11.94 danio rerio genome using  STAR version 2.5.4b software. Annotations Danio rerio.GRCz11.94.gtf were obtained from ftp.Ensembl.org Gene level counts were obtained using HTSeq count version 0.11.0 Differential gene expression analysis: EdgeR Bioconductor. GSEA: GAGE Bioconductor Genome build: GRCz11.94 Supplementary files format and content: CPM values [.csv] semicolon delimited files,skin mpeg1.1 GFP+ cells,,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,Standard adult zebrafish rearing conditions in multilink system at  26° C  with 12:12 h ligt/dark cycle,developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated,GSM4512725,GSM4512725: GFE1 WT.1; Danio rerio; RNA Seq,GSM4512725,,1,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,GEO Accession:GSM4512725,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP259990,,,so-zf94_GFE1-WT_S1_R2_001.fastq.gz so-zf94_GFE1-WT_S1_R1_001.fastq.gz,fastq fastq,12446480884.0,61616242.0,GSM4512725 r1,0:101 1:101,A:3368704863;C:2968645301;G:2743627645;T:3365306136;N:196939,101,101,,,3368704863,2968645301,2743627645,3365306136,196939,SRX8244836,SRS6592473,SRA1072141,GEO,Erasmus MC,2,0.79126,0.79765,0.31567,0.32746,0.76893,0.76871,0.55753,0.55755,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2020-05-04,Adult,Adult,Skin,Surface Structure
67321,SRR17117603,SRX13302172,SRS11213397,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs  deciphered transcriptional changes and intermediate cell states during regeneration  and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,KIT Day10,GSM5714340,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:10,KIT Day10,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment  annotation  and counting were performed using CellRanger Downstream QC  Dimenstion Reduction  UMAP generation  and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:kitalf|day:10,GSM5714340,GSM5714340: KIT Day10; Danio rerio; RNA Seq,GSM5714340 r1,GSM5714340,1,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,KITD10_possorted_genome_bam.bam,10X Genomics bam file,13520056900.0,270401138.0,GSM5714340 r1,0:50,A:4003001263;C:2787125304;G:3034885371;T:3692995124;N:2049838,50,,,,4003001263,2787125304,3034885371,3692995124,2049838,SRX13302172,SRS11213397,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.89988,,0.15778,,0.81779,,0.55873,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure
67322,SRR17117604,SRX13302171,SRS11213396,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs  deciphered transcriptional changes and intermediate cell states during regeneration  and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,KIT Day5,GSM5714339,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:5,KIT Day5,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment  annotation  and counting were performed using CellRanger Downstream QC  Dimenstion Reduction  UMAP generation  and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:kitalf|day:5,GSM5714339,GSM5714339: KIT Day5; Danio rerio; RNA Seq,GSM5714339 r1,GSM5714339,1,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,KITD5_possorted_genome_bam.bam,10X Genomics bam file,15339323300.0,306786466.0,GSM5714339 r1,0:50,A:4515134365;C:3259123747;G:3665791919;T:3898089485;N:1183784,50,,,,4515134365,3259123747,3665791919,3898089485,1183784,SRX13302171,SRS11213396,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.90243,,0.15706,,0.80507,,0.59995,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure
67323,SRR17117605,SRX13302170,SRS11213395,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs  deciphered transcriptional changes and intermediate cell states during regeneration  and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,KIT Day3 2,GSM5714338,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:3,KIT Day3 2,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment  annotation  and counting were performed using CellRanger Downstream QC  Dimenstion Reduction  UMAP generation  and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:kitalf|day:3,GSM5714338,GSM5714338: KIT Day3 2; Danio rerio; RNA Seq,GSM5714338 r1,GSM5714338,1,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,KITD3B_possorted_genome_bam.bam,10X Genomics bam file,7025134450.0,140502689.0,GSM5714338 r1,0:50,A:2061820993;C:1482027410;G:1665199726;T:1810366819;N:5719502,50,,,,2061820993,1482027410,1665199726,1810366819,5719502,SRX13302170,SRS11213395,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.90656,,0.17308,,0.80975,,0.61461,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure
67324,SRR17117606,SRX13302169,SRS11213394,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs  deciphered transcriptional changes and intermediate cell states during regeneration  and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,KIT Day3 1,GSM5714337,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:3,KIT Day3 1,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment  annotation  and counting were performed using CellRanger Downstream QC  Dimenstion Reduction  UMAP generation  and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:kitalf|day:3,GSM5714337,GSM5714337: KIT Day3 1; Danio rerio; RNA Seq,GSM5714337 r1,GSM5714337,1,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,KITD3A_possorted_genome_bam.bam,10X Genomics bam file,12309733350.0,246194667.0,GSM5714337 r1,0:50,A:3671780931;C:2604474006;G:3028253002;T:3001177496;N:4047915,50,,,,3671780931,2604474006,3028253002,3001177496,4047915,SRX13302169,SRS11213394,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.8991,,0.14599,,0.82347,,0.59507,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure
67325,SRR17117607,SRX13302168,SRS11213393,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs  deciphered transcriptional changes and intermediate cell states during regeneration  and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,KIT Day2,GSM5714336,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:2,KIT Day2,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment  annotation  and counting were performed using CellRanger Downstream QC  Dimenstion Reduction  UMAP generation  and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:kitalf|day:2,GSM5714336,GSM5714336: KIT Day2; Danio rerio; RNA Seq,GSM5714336 r1,GSM5714336,1,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,KITD2_possorted_genome_bam.bam,10X Genomics bam file,12734582200.0,254691644.0,GSM5714336 r1,0:50,A:3752064713;C:2645000864;G:2866879156;T:3468673547;N:1963920,50,,,,3752064713,2645000864,2866879156,3468673547,1963920,SRX13302168,SRS11213393,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.9007,,0.15094,,0.82601,,0.58222,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure
67326,SRR17117608,SRX13302167,SRS11213392,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs  deciphered transcriptional changes and intermediate cell states during regeneration  and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,KIT Day1,GSM5714335,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:1,KIT Day1,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment  annotation  and counting were performed using CellRanger Downstream QC  Dimenstion Reduction  UMAP generation  and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:kitalf|day:1,GSM5714335,GSM5714335: KIT Day1; Danio rerio; RNA Seq,GSM5714335 r1,GSM5714335,1,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,KITD1_possorted_genome_bam.bam,10X Genomics bam file,11105860850.0,222117217.0,GSM5714335 r1,0:50,A:3280343742;C:2367594246;G:2631026655;T:2823244720;N:3651487,50,,,,3280343742,2367594246,2631026655,2823244720,3651487,SRX13302167,SRS11213392,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.91294,,0.1651,,0.81592,,0.60997,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure
67327,SRR17117609,SRX13302166,SRS11213391,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs  deciphered transcriptional changes and intermediate cell states during regeneration  and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,KIT day x,GSM5714334,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:kitalf|day:0,KIT day x,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment  annotation  and counting were performed using CellRanger Downstream QC  Dimenstion Reduction  UMAP generation  and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:kitalf|day:0,GSM5714334,GSM5714334: KIT day x; Danio rerio; RNA Seq,GSM5714334 r1,GSM5714334,1,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,KITD0_possorted_genome_bam.bam,10X Genomics bam file,8896963450.0,177939269.0,GSM5714334 r1,0:50,A:2644408729;C:1877280130;G:2120951498;T:2253636691;N:686402,50,,,,2644408729,1877280130,2120951498,2253636691,686402,SRX13302166,SRS11213391,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.90601,,0.17428,,0.8144,,0.6019,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure
67328,SRR17117610,SRX13302165,SRS11213390,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs  deciphered transcriptional changes and intermediate cell states during regeneration  and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,WT Day10,GSM5714333,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:10,WT Day10,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment  annotation  and counting were performed using CellRanger Downstream QC  Dimenstion Reduction  UMAP generation  and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:WT|day:10,GSM5714333,GSM5714333: WT Day10; Danio rerio; RNA Seq,GSM5714333 r1,GSM5714333,1,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,WTD10_possorted_genome_bam.bam,10X Genomics bam file,12279427400.0,245588548.0,GSM5714333 r1,0:50,A:3639861301;C:2609067706;G:2996068551;T:3030567477;N:3862365,50,,,,3639861301,2609067706,2996068551,3030567477,3862365,SRX13302165,SRS11213390,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.90407,,0.15949,,0.83019,,0.59401,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure
67329,SRR17117611,SRX13302164,SRS11213389,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs  deciphered transcriptional changes and intermediate cell states during regeneration  and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,WT Day5,GSM5714332,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:5,WT Day5,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment  annotation  and counting were performed using CellRanger Downstream QC  Dimenstion Reduction  UMAP generation  and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:WT|day:5,GSM5714332,GSM5714332: WT Day5; Danio rerio; RNA Seq,GSM5714332 r1,GSM5714332,1,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,WTD5_possorted_genome_bam.bam,10X Genomics bam file,8474510800.0,169490216.0,GSM5714332 r1,0:50,A:2564658874;C:1701773199;G:1897587120;T:2308201539;N:2290068,50,,,,2564658874,1701773199,1897587120,2308201539,2290068,SRX13302164,SRS11213389,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.89752,,0.17262,,0.8115,,0.6036,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure
67330,SRR17117612,SRX13302163,SRS11213388,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs  deciphered transcriptional changes and intermediate cell states during regeneration  and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,WT Day3,GSM5714331,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:3,WT Day3,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment  annotation  and counting were performed using CellRanger Downstream QC  Dimenstion Reduction  UMAP generation  and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:WT|day:3,GSM5714331,GSM5714331: WT Day3; Danio rerio; RNA Seq,GSM5714331 r1,GSM5714331,1,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,WTD3_possorted_genome_bam.bam,10X Genomics bam file,9051704300.0,181034086.0,GSM5714331 r1,0:50,A:2665138947;C:1946161834;G:2211744115;T:2225805018;N:2854386,50,,,,2665138947,1946161834,2211744115,2225805018,2854386,SRX13302163,SRS11213388,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.90675,,0.14473,,0.81884,,0.58208,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure
67331,SRR17117613,SRX13302162,SRS11213387,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs  deciphered transcriptional changes and intermediate cell states during regeneration  and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,WT Day2,GSM5714330,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:2,WT Day2,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment  annotation  and counting were performed using CellRanger Downstream QC  Dimenstion Reduction  UMAP generation  and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:WT|day:2,GSM5714330,GSM5714330: WT Day2; Danio rerio; RNA Seq,GSM5714330 r1,GSM5714330,1,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,WTD2_possorted_genome_bam.bam,10X Genomics bam file,14707462000.0,294149240.0,GSM5714330 r1,0:50,A:4299212743;C:3141543121;G:3608335320;T:3651134459;N:7236357,50,,,,4299212743,3141543121,3608335320,3651134459,7236357,SRX13302162,SRS11213387,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.90948,,0.15,,0.81986,,0.58797,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure
67332,SRR17117614,SRX13302161,SRS11213386,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs  deciphered transcriptional changes and intermediate cell states during regeneration  and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,WT Day1,GSM5714329,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:1,WT Day1,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment  annotation  and counting were performed using CellRanger Downstream QC  Dimenstion Reduction  UMAP generation  and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:WT|day:1,GSM5714329,GSM5714329: WT Day1; Danio rerio; RNA Seq,GSM5714329 r1,GSM5714329,1,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,WTD1_possorted_genome_bam.bam,10X Genomics bam file,11285903150.0,225718063.0,GSM5714329 r1,0:50,A:3319310923;C:2416106902;G:2709775130;T:2835193792;N:5516403,50,,,,3319310923,2416106902,2709775130,2835193792,5516403,SRX13302161,SRS11213386,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.90815,,0.15237,,0.82181,,0.57459,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure
67333,SRR17117615,SRX13302160,SRS11213385,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs  deciphered transcriptional changes and intermediate cell states during regeneration  and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,WT day x 2,GSM5714328,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:0,WT day x 2,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment  annotation  and counting were performed using CellRanger Downstream QC  Dimenstion Reduction  UMAP generation  and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:WT|day:0,GSM5714328,GSM5714328: WT day x 2; Danio rerio; RNA Seq,GSM5714328 r1,GSM5714328,1,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,WTD0B_possorted_genome_bam.bam,10X Genomics bam file,6680383400.0,133607668.0,GSM5714328 r1,0:50,A:2032360836;C:1342388936;G:1478261391;T:1825537806;N:1834431,50,,,,2032360836,1342388936,1478261391,1825537806,1834431,SRX13302160,SRS11213385,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.90381,,0.1609,,0.81813,,0.61231,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure
67334,SRR17117616,SRX13302159,SRS11213384,SRP349128,PRJNA785890,Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish,GSE190115,Transcriptome Analysis,To elucidate mechanisms governing McSC self renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs  deciphered transcriptional changes and intermediate cell states during regeneration  and analyzed cell cell signaling changes to discover mechanisms governing melanocyte regeneration. Overall design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration,,pubmed:37021774,,WT day x 1,GSM5714327,,tissue:Tgmitfa:nlsEGFP FACS enriched cells|genotype:WT|day:0,WT day x 1,Base call files were generated from the Illumina NextSeq 500 Fastq files for each sample were generated from base call files using CellRanger's MkFastQ Alignment  annotation  and counting were performed using CellRanger Downstream QC  Dimenstion Reduction  UMAP generation  and DEG analysis were performed in Seuratv3 Genome build: Lawson lab zebrafish annotation V4.3.2 Supplementary files format and content: txt.gz fiiles saved from Seurat Objects,Tgmitfa:nlsEGFP FACS enriched cells,750nM Neocuproine applied for 24 hours between day x and Day 1 to ablate mature melanocytes,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,Tgmitfa:nlsEGFP animals in either a WT or kitalf background were raised to 3 month 6 month of age,genotype:WT|day:0,GSM5714327,GSM5714327: WT day x 1; Danio rerio; RNA Seq,GSM5714327 r1,GSM5714327,1,Scales were removed  zebrafish skin cut and peeled off underlying musce  enzymatic and mechanical dissociation  and mitfa:nlsEGFP cells were enriched for during FACS  single cell barcoding using the 10X controller 10X three prime v3.1 scRNAseq library prep steps were followed Samples were sequenced on an Illumina NextSeq 500 using a 75 cycle PE kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP349128,,assembly:Lawson lab zebrafish annotation V4.3.2|intentional duplicate,WTD0A_possorted_genome_bam.bam,10X Genomics bam file,7628491300.0,152569826.0,GSM5714327 r1,0:50,A:2377995758;C:1521202402;G:1696947530;T:2030231260;N:2114350,50,,,,2377995758,1521202402,1696947530,2030231260,2114350,SRX13302159,SRS11213384,SRA1620868,"Craig Ceol, Molecular Medicine, UMass Medical School","Craig Ceol, Molecular Medicine, UMass Medical School",1,0.90188,,0.1668,,0.82154,,0.599,,50,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-03,Adult,Adult,Skin,Surface Structure
69552,SRR18901596,SRX14979865,SRS12729755,SRP371883,PRJNA831276,Lipid droplets are a metabolic vulnerability in melanoma,GSE201378,Transcriptome Analysis,Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma,,pubmed:37268606,,sgDGAT1a 3 bulk RNAseq,GSM6062270,,source name:Skin|tissue:Skin|cell type:melanoma|genotype:DGAT1a knockout,sgDGAT1a 3 bulk RNAseq,Sequencing reads underwent quality control with FASTQC 0.11.9  trimming with TRIMMOMATIC 14.0.1 and aligned using Salmon 1.4.0 to the danio rerio GRCz11. Data analysis was conducted in R version 4.0.5. Differential expression and normalized counts were calculated using DESeq2 1.30.1 using default parameters. Normalized counts derived from DESeq2 processing. Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11,Skin,,Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.,,tissue:Skin|cell type:melanoma|genotype:DGAT1a knockout,GSM6062270,GSM6062270: sgDGAT1a 3 bulk RNAseq; Danio rerio; RNA Seq,GSM6062270 r1,GSM6062270,1,Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,loader:fastq load.py,DGAT1a_3_R1.fastq.gz DGAT1a_3_R2.fastq.gz,fastq fastq,6999632088.0,34651644.0,GSM6062270 r1,0:101 1:101,A:1966677410;C:1379731640;G:1488012081;T:2165132052;N:78905,101,101,,,1966677410,1379731640,1488012081,2165132052,78905,SRX14979865,SRS12729755,SRA1408865,"Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center","Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.92364,0.83987,0.12298,0.10958,0.7289,0.75205,0.55329,0.53686,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,sc_generic,bulk,bulk,,United States,2022-04-23,Undetermined,Undetermined,Skin,Surface Structure
69553,SRR18901597,SRX14979864,SRS12729754,SRP371883,PRJNA831276,Lipid droplets are a metabolic vulnerability in melanoma,GSE201378,Transcriptome Analysis,Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma,,pubmed:37268606,,sgDGAT1a 2 bulk RNAseq,GSM6062269,,source name:Skin|tissue:Skin|cell type:melanoma|genotype:DGAT1a knockout,sgDGAT1a 2 bulk RNAseq,Sequencing reads underwent quality control with FASTQC 0.11.9  trimming with TRIMMOMATIC 14.0.1 and aligned using Salmon 1.4.0 to the danio rerio GRCz11. Data analysis was conducted in R version 4.0.5. Differential expression and normalized counts were calculated using DESeq2 1.30.1 using default parameters. Normalized counts derived from DESeq2 processing. Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11,Skin,,Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.,,tissue:Skin|cell type:melanoma|genotype:DGAT1a knockout,GSM6062269,GSM6062269: sgDGAT1a 2 bulk RNAseq; Danio rerio; RNA Seq,GSM6062269 r1,GSM6062269,1,Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,loader:fastq load.py,DGAT1a_2_R1.fastq.gz DGAT1a_2_R2.fastq.gz,fastq fastq,8251144500.0,40847250.0,GSM6062269 r1,0:101 1:101,A:2347333328;C:1614724681;G:1750159235;T:2538833381;N:93875,101,101,,,2347333328,1614724681,1750159235,2538833381,93875,SRX14979864,SRS12729754,SRA1408865,"Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center","Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.91689,0.85062,0.17154,0.15832,0.7135,0.73357,0.55242,0.53573,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,sc_generic,bulk,bulk,,United States,2022-04-23,Undetermined,Undetermined,Skin,Surface Structure
69554,SRR18901598,SRX14979863,SRS12729783,SRP371883,PRJNA831276,Lipid droplets are a metabolic vulnerability in melanoma,GSE201378,Transcriptome Analysis,Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma,,pubmed:37268606,,sgDGAT1a 1 bulk RNAseq,GSM6062268,,source name:Skin|tissue:Skin|cell type:melanoma|genotype:DGAT1a knockout,sgDGAT1a 1 bulk RNAseq,Sequencing reads underwent quality control with FASTQC 0.11.9  trimming with TRIMMOMATIC 14.0.1 and aligned using Salmon 1.4.0 to the danio rerio GRCz11. Data analysis was conducted in R version 4.0.5. Differential expression and normalized counts were calculated using DESeq2 1.30.1 using default parameters. Normalized counts derived from DESeq2 processing. Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11,Skin,,Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.,,tissue:Skin|cell type:melanoma|genotype:DGAT1a knockout,GSM6062268,GSM6062268: sgDGAT1a 1 bulk RNAseq; Danio rerio; RNA Seq,GSM6062268 r1,GSM6062268,1,Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,loader:fastq load.py,DGAT1a_1_R1.fastq.gz DGAT1a_1_R2.fastq.gz,fastq fastq,18660768484.0,92380042.0,GSM6062268 r1,0:101 1:101,A:5305116678;C:3630125100;G:3862694653;T:5862619976;N:212077,101,101,,,5305116678,3630125100,3862694653,5862619976,212077,SRX14979863,SRS12729783,SRA1408865,"Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center","Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.91727,0.83321,0.16534,0.14775,0.71037,0.73594,0.53932,0.52443,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,sc_generic,bulk,bulk,,United States,2022-04-23,Undetermined,Undetermined,Skin,Surface Structure
69555,SRR18901599,SRX14979862,SRS12729753,SRP371883,PRJNA831276,Lipid droplets are a metabolic vulnerability in melanoma,GSE201378,Transcriptome Analysis,Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma,,pubmed:37268606,,sgNT 3 bulk RNAseq,GSM6062267,,source name:Skin|tissue:Skin|cell type:melanoma|genotype:WT,sgNT 3 bulk RNAseq,Sequencing reads underwent quality control with FASTQC 0.11.9  trimming with TRIMMOMATIC 14.0.1 and aligned using Salmon 1.4.0 to the danio rerio GRCz11. Data analysis was conducted in R version 4.0.5. Differential expression and normalized counts were calculated using DESeq2 1.30.1 using default parameters. Normalized counts derived from DESeq2 processing. Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11,Skin,,Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.,,tissue:Skin|cell type:melanoma|genotype:WT,GSM6062267,GSM6062267: sgNT 3 bulk RNAseq; Danio rerio; RNA Seq,GSM6062267 r1,GSM6062267,1,Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,loader:fastq load.py,NT_3_R1.fastq.gz NT_3_R2.fastq.gz,fastq fastq,11541383120.0,57135560.0,GSM6062267 r1,0:101 1:101,A:3251133156;C:2311327780;G:2454133526;T:3524658644;N:130014,101,101,,,3251133156,2311327780,2454133526,3524658644,130014,SRX14979862,SRS12729753,SRA1408865,"Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center","Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.91632,0.84851,0.15351,0.14147,0.71366,0.73294,0.51256,0.49995,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,sc_generic,bulk,bulk,,United States,2022-04-23,Undetermined,Undetermined,Skin,Surface Structure
69556,SRR18901600,SRX14979861,SRS12729752,SRP371883,PRJNA831276,Lipid droplets are a metabolic vulnerability in melanoma,GSE201378,Transcriptome Analysis,Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma,,pubmed:37268606,,sgNT 2 bulk RNAseq,GSM6062266,,source name:Skin|tissue:Skin|cell type:melanoma|genotype:WT,sgNT 2 bulk RNAseq,Sequencing reads underwent quality control with FASTQC 0.11.9  trimming with TRIMMOMATIC 14.0.1 and aligned using Salmon 1.4.0 to the danio rerio GRCz11. Data analysis was conducted in R version 4.0.5. Differential expression and normalized counts were calculated using DESeq2 1.30.1 using default parameters. Normalized counts derived from DESeq2 processing. Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11,Skin,,Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.,,tissue:Skin|cell type:melanoma|genotype:WT,GSM6062266,GSM6062266: sgNT 2 bulk RNAseq; Danio rerio; RNA Seq,GSM6062266 r1,GSM6062266,1,Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,loader:fastq load.py,NT_2_R1.fastq.gz NT_2_R2.fastq.gz,fastq fastq,12944530468.0,64081834.0,GSM6062266 r1,0:101 1:101,A:3642085778;C:2657512300;G:2804491849;T:3840293107;N:147434,101,101,,,3642085778,2657512300,2804491849,3840293107,147434,SRX14979861,SRS12729752,SRA1408865,"Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center","Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.91453,0.86557,0.10035,0.0905,0.73261,0.7428,0.52684,0.51769,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,sc_generic,bulk,bulk,,United States,2022-04-23,Undetermined,Undetermined,Skin,Surface Structure
69557,SRR18901601,SRX14979860,SRS12729751,SRP371883,PRJNA831276,Lipid droplets are a metabolic vulnerability in melanoma,GSE201378,Transcriptome Analysis,Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma,,pubmed:37268606,,sgNT 1 bulk RNAseq,GSM6062265,,source name:Skin|tissue:Skin|cell type:melanoma|genotype:WT,sgNT 1 bulk RNAseq,Sequencing reads underwent quality control with FASTQC 0.11.9  trimming with TRIMMOMATIC 14.0.1 and aligned using Salmon 1.4.0 to the danio rerio GRCz11. Data analysis was conducted in R version 4.0.5. Differential expression and normalized counts were calculated using DESeq2 1.30.1 using default parameters. Normalized counts derived from DESeq2 processing. Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11,Skin,,Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.,,tissue:Skin|cell type:melanoma|genotype:WT,GSM6062265,GSM6062265: sgNT 1 bulk RNAseq; Danio rerio; RNA Seq,GSM6062265 r1,GSM6062265,1,Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,loader:fastq load.py,NT_1_R1.fastq.gz NT_1_R2.fastq.gz,fastq fastq,4065801864.0,20127732.0,GSM6062265 r1,0:101 1:101,A:1126164942;C:831186106;G:895618283;T:1212785857;N:46676,101,101,,,1126164942,831186106,895618283,1212785857,46676,SRX14979860,SRS12729751,SRA1408865,"Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center","Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.92125,0.86236,0.09794,0.08896,0.73148,0.7457,0.52439,0.51074,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,sc_generic,bulk,bulk,,United States,2022-04-23,Undetermined,Undetermined,Skin,Surface Structure
69558,SRR18901602,SRX14979859,SRS12729750,SRP371883,PRJNA831276,Lipid droplets are a metabolic vulnerability in melanoma,GSE201378,Transcriptome Analysis,Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma,,pubmed:37268606,,TEAZ scRNAseq,GSM6062264,,source name:Skin|tissue:Skin|cell type:melanoma,TEAZ scRNAseq,Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Counts matrix derived from Seurat Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11,Skin,,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,tissue:Skin|cell type:melanoma,GSM6062264,GSM6062264: TEAZ scRNAseq; Danio rerio; RNA Seq,GSM6062264 r1,GSM6062264,1,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell three prime Library and Gel Bead Kit v3 and Chromium Single Cell three prime Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,loader:fastq load.py,2544_PTEN_combined_IGO_11963_4_S2_L001_R1_001.fastq.gz 2544_PTEN_combined_IGO_11963_4_S2_L001_R2_001.fastq.gz,fastq fastq,9314576760.0,77621473.0,GSM6062264 r1,0:29 1:91,A:2571624849;C:2103171866;G:2248508025;T:2390911966;N:360054,29,91,,,2571624849,2103171866,2248508025,2390911966,360054,SRX14979859,SRS12729750,SRA1408865,"Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center","Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.00434,0.8777,0.00177,0.14429,0.99253,0.78492,0.35282,0.53036,29,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-04-23,Undetermined,Undetermined,Skin,Surface Structure
69559,SRR18901603,SRX14979859,SRS12729750,SRP371883,PRJNA831276,Lipid droplets are a metabolic vulnerability in melanoma,GSE201378,Transcriptome Analysis,Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma,,pubmed:37268606,,TEAZ scRNAseq,GSM6062264,,source name:Skin|tissue:Skin|cell type:melanoma,TEAZ scRNAseq,Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Counts matrix derived from Seurat Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11,Skin,,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,tissue:Skin|cell type:melanoma,GSM6062264,GSM6062264: TEAZ scRNAseq; Danio rerio; RNA Seq,GSM6062264 r1,GSM6062264,1,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell three prime Library and Gel Bead Kit v3 and Chromium Single Cell three prime Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,loader:fastq load.py,2544_PTEN_combined_IGO_11963_4_S2_L002_R1_001.fastq.gz 2544_PTEN_combined_IGO_11963_4_S2_L002_R2_001.fastq.gz,fastq fastq,9122357880.0,76019649.0,GSM6062264 r2,0:29 1:91,A:2521047948;C:2056950129;G:2200048731;T:2343919901;N:391171,29,91,,,2521047948,2056950129,2200048731,2343919901,391171,SRX14979859,SRS12729750,SRA1408865,"Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center","Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.00471,0.87992,0.00196,0.14374,0.99255,0.78476,0.35593,0.54484,29,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-04-23,Undetermined,Undetermined,Skin,Surface Structure
69560,SRR18901604,SRX14979859,SRS12729750,SRP371883,PRJNA831276,Lipid droplets are a metabolic vulnerability in melanoma,GSE201378,Transcriptome Analysis,Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma,,pubmed:37268606,,TEAZ scRNAseq,GSM6062264,,source name:Skin|tissue:Skin|cell type:melanoma,TEAZ scRNAseq,Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Counts matrix derived from Seurat Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11,Skin,,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,tissue:Skin|cell type:melanoma,GSM6062264,GSM6062264: TEAZ scRNAseq; Danio rerio; RNA Seq,GSM6062264 r1,GSM6062264,1,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell three prime Library and Gel Bead Kit v3 and Chromium Single Cell three prime Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,loader:fastq load.py,2544_PTEN_combined_IGO_11963_4_S2_L003_R1_001.fastq.gz 2544_PTEN_combined_IGO_11963_4_S2_L003_R2_001.fastq.gz,fastq fastq,9307586160.0,77563218.0,GSM6062264 r3,0:29 1:91,A:2569072609;C:2102732051;G:2247036264;T:2388393636;N:351600,29,91,,,2569072609,2102732051,2247036264,2388393636,351600,SRX14979859,SRS12729750,SRA1408865,"Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center","Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.00429,0.87889,0.00178,0.1429,0.99271,0.78589,0.35728,0.54587,29,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-04-23,Undetermined,Undetermined,Skin,Surface Structure
69561,SRR18901605,SRX14979859,SRS12729750,SRP371883,PRJNA831276,Lipid droplets are a metabolic vulnerability in melanoma,GSE201378,Transcriptome Analysis,Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma,,pubmed:37268606,,TEAZ scRNAseq,GSM6062264,,source name:Skin|tissue:Skin|cell type:melanoma,TEAZ scRNAseq,Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Counts matrix derived from Seurat Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11,Skin,,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,tissue:Skin|cell type:melanoma,GSM6062264,GSM6062264: TEAZ scRNAseq; Danio rerio; RNA Seq,GSM6062264 r1,GSM6062264,1,Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell three prime Library and Gel Bead Kit v3 and Chromium Single Cell three prime Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,loader:fastq load.py,2544_PTEN_combined_IGO_11963_4_S2_L004_R1_001.fastq.gz 2544_PTEN_combined_IGO_11963_4_S2_L004_R2_001.fastq.gz,fastq fastq,9382270920.0,78185591.0,GSM6062264 r4,0:29 1:91,A:2591803792;C:2116313097;G:2264892157;T:2408930364;N:331510,29,91,,,2591803792,2116313097,2264892157,2408930364,331510,SRX14979859,SRS12729750,SRA1408865,"Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center","Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.00445,0.87912,0.00184,0.14625,0.99287,0.78573,0.37029,0.5207,29,91,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-04-23,Undetermined,Undetermined,Skin,Surface Structure
74043,SRR23360139,SRX19301395,SRS16701439,SRP421311,PRJNA932229,Transcriptomic profiling of tissue environments critical for post embryonic patterning and morphogenesis of zebrafish skin,GSE224695,Other,Pigment patterns and skin appendages are prominent features of vertebrate skin. In zebrafish  regularly patterned pigment stripes and an array of calcified scales form simultaneously in the skin during post embryonic development. Understanding mechanisms that regulate stripe patterning and scale morphogenesis may lead to discovery of fundamental mechanisms that govern development of animal form. To learn about cell types and potential signaling interactions that govern skin patterning and morphogenesis we generated and analyzed single cell transcriptomes of skin with genetic or induced defects in pigmentation and squamation. These data reveal a previously undescribed population of epidermal cells that express transcripts encoding enamel matrix proteins  suggest hormonal control of epithelial mesenchymal signaling  clarify the signaling network that governs scale papillae development  and identify a critical role for the hypodermis in supporting pigment cell development. Additionally  this comprehensive single cell transcriptome data from biomedically relevant skin conditions provide a useful resource to accelerate discovery of mechanisms governing skin development. Overall design: Dissected skin tissue from post embryonic zebrafish 9.6 SSL from four genetic backgrounds wild type  eda mutant  bnc2 mutant  and hypothyroid were profiled with with sci RNA seq2.,,pubmed:37695017,,Multi genotype zebrafish skin snRNAseq,GSM7029635,,tissue:Whole skin tissue|cell type:Whole skin tissue|developmental stage:9.6 SSL SP  squamation onset posterior|strain:Tgsp7:EGFPb1212|genotype:wild type  eda mutant homozygous  bnc2 mutant homozygous  hypothryoid|geo loc name:missing|collection date:missing,Multi genotype zebrafish skin snRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the processing pipeline from Cao et al.  2017 doi: 10.1126/science.aam8940. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zskin wildtype cds.RDS: monocle3 cell data set object Supplementary files format and content: zskin wildtype raw counts.RDS: dgCMatrix with raw counts Supplementary files format and content: zskin wildtype cell metadata.csv: cell metadata table comma separated Supplementary files format and content: zskin wildtype gene metadata.csv: gene metadata table comma separated Supplementary files format and content: zskin all genotypes cds.RDS: monocle3 cell data set object Supplementary files format and content: zskin all genotypes raw counts.RDS: dgCMatrix with raw counts Supplementary files format and content: zskin all genotypes cell metadata.csv: cell metadata table comma separated Supplementary files format and content: zskin all genotypes gene metadata.csv: gene metadata table comma separated,Whole skin tissue,Hypothyroid zebrafish  Tgtg:nVenus v2a nfnBwprt8Tg  underwent a metronidazole treatment to ablate the thyroid gland at 5 dpf.,Fish were staged and selected for dissection  euthanized with MS 222 and processed immediately. Following removal of the head and fins  skins were removed with forceps and immediately flash frozen in liquid nitrogen then stored at  80°C prior to isolation of nuclei. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish were raised at 28.5℃ and selected for dissection based on staging landmarks Parichy et al.  2009.,cell type:Whole skin tissue|developmental stage:9.6 SSL SP  squamation onset posterior|strain:Tgsp7:EGFPb1212|genotype:wild type  eda mutant homozygous  bnc2 mutant homozygous  hypothryoid,GSM7029635,GSM7029635: Multi genotype zebrafish skin snRNAseq; Danio rerio; RNA Seq,GSM7029635 r1,GSM7029635,1,Fish were staged and selected for dissection  euthanized with MS 222 and processed immediately. Following removal of the head and fins  skins were removed with forceps and immediately flash frozen in liquid nitrogen then stored at  80°C prior to isolation of nuclei. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP421311,,loader:fastq load.py,zskin_sciRNA_seq1_R2_merge.fastq.gz zskin_sciRNA_seq1_R1_merge.fastq.gz,fastq fastq,11447467220.0,163535246.0,GSM7029635 r1,0:18 1:52,A:3502484926;C:2381891741;G:2327139583;T:3234563798;N:1387172,18,52,,,3502484926,2381891741,2327139583,3234563798,1387172,SRX19301395,SRS16701439,SRA1657186,"Genome Sciences, University of Washington","Genome Sciences, University of Washington",2,0.0,0.82847,0.0,0.51633,1.0,0.82692,,0.58473,18,52,T,B,sc-like readlen,illumina,nextseq,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2023-02-07,Larval,Larval,Skin,Surface Structure
74044,SRR23360140,SRX19301395,SRS16701439,SRP421311,PRJNA932229,Transcriptomic profiling of tissue environments critical for post embryonic patterning and morphogenesis of zebrafish skin,GSE224695,Other,Pigment patterns and skin appendages are prominent features of vertebrate skin. In zebrafish  regularly patterned pigment stripes and an array of calcified scales form simultaneously in the skin during post embryonic development. Understanding mechanisms that regulate stripe patterning and scale morphogenesis may lead to discovery of fundamental mechanisms that govern development of animal form. To learn about cell types and potential signaling interactions that govern skin patterning and morphogenesis we generated and analyzed single cell transcriptomes of skin with genetic or induced defects in pigmentation and squamation. These data reveal a previously undescribed population of epidermal cells that express transcripts encoding enamel matrix proteins  suggest hormonal control of epithelial mesenchymal signaling  clarify the signaling network that governs scale papillae development  and identify a critical role for the hypodermis in supporting pigment cell development. Additionally  this comprehensive single cell transcriptome data from biomedically relevant skin conditions provide a useful resource to accelerate discovery of mechanisms governing skin development. Overall design: Dissected skin tissue from post embryonic zebrafish 9.6 SSL from four genetic backgrounds wild type  eda mutant  bnc2 mutant  and hypothyroid were profiled with with sci RNA seq2.,,pubmed:37695017,,Multi genotype zebrafish skin snRNAseq,GSM7029635,,tissue:Whole skin tissue|cell type:Whole skin tissue|developmental stage:9.6 SSL SP  squamation onset posterior|strain:Tgsp7:EGFPb1212|genotype:wild type  eda mutant homozygous  bnc2 mutant homozygous  hypothryoid|geo loc name:missing|collection date:missing,Multi genotype zebrafish skin snRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the processing pipeline from Cao et al.  2017 doi: 10.1126/science.aam8940. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zskin wildtype cds.RDS: monocle3 cell data set object Supplementary files format and content: zskin wildtype raw counts.RDS: dgCMatrix with raw counts Supplementary files format and content: zskin wildtype cell metadata.csv: cell metadata table comma separated Supplementary files format and content: zskin wildtype gene metadata.csv: gene metadata table comma separated Supplementary files format and content: zskin all genotypes cds.RDS: monocle3 cell data set object Supplementary files format and content: zskin all genotypes raw counts.RDS: dgCMatrix with raw counts Supplementary files format and content: zskin all genotypes cell metadata.csv: cell metadata table comma separated Supplementary files format and content: zskin all genotypes gene metadata.csv: gene metadata table comma separated,Whole skin tissue,Hypothyroid zebrafish  Tgtg:nVenus v2a nfnBwprt8Tg  underwent a metronidazole treatment to ablate the thyroid gland at 5 dpf.,Fish were staged and selected for dissection  euthanized with MS 222 and processed immediately. Following removal of the head and fins  skins were removed with forceps and immediately flash frozen in liquid nitrogen then stored at  80°C prior to isolation of nuclei. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish were raised at 28.5℃ and selected for dissection based on staging landmarks Parichy et al.  2009.,cell type:Whole skin tissue|developmental stage:9.6 SSL SP  squamation onset posterior|strain:Tgsp7:EGFPb1212|genotype:wild type  eda mutant homozygous  bnc2 mutant homozygous  hypothryoid,GSM7029635,GSM7029635: Multi genotype zebrafish skin snRNAseq; Danio rerio; RNA Seq,GSM7029635 r1,GSM7029635,1,Fish were staged and selected for dissection  euthanized with MS 222 and processed immediately. Following removal of the head and fins  skins were removed with forceps and immediately flash frozen in liquid nitrogen then stored at  80°C prior to isolation of nuclei. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP421311,,loader:fastq load.py,zskin_sciRNA_seq2_R1_merge.fastq.gz zskin_sciRNA_seq2_R2_merge.fastq.gz,fastq fastq,36112843060.0,515897758.0,GSM7029635 r2,0:18 1:52,A:10807852102;C:7597254398;G:7380368668;T:10325233398;N:2134494,18,52,,,10807852102,7597254398,7380368668,10325233398,2134494,SRX19301395,SRS16701439,SRA1657186,"Genome Sciences, University of Washington","Genome Sciences, University of Washington",2,0.0,0.84202,0.0,0.54094,1.0,0.8411,,0.58834,18,52,T,B,sc-like readlen,illumina,nextseq,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2023-02-07,Larval,Larval,Skin,Surface Structure
74045,SRR23360141,SRX19301395,SRS16701439,SRP421311,PRJNA932229,Transcriptomic profiling of tissue environments critical for post embryonic patterning and morphogenesis of zebrafish skin,GSE224695,Other,Pigment patterns and skin appendages are prominent features of vertebrate skin. In zebrafish  regularly patterned pigment stripes and an array of calcified scales form simultaneously in the skin during post embryonic development. Understanding mechanisms that regulate stripe patterning and scale morphogenesis may lead to discovery of fundamental mechanisms that govern development of animal form. To learn about cell types and potential signaling interactions that govern skin patterning and morphogenesis we generated and analyzed single cell transcriptomes of skin with genetic or induced defects in pigmentation and squamation. These data reveal a previously undescribed population of epidermal cells that express transcripts encoding enamel matrix proteins  suggest hormonal control of epithelial mesenchymal signaling  clarify the signaling network that governs scale papillae development  and identify a critical role for the hypodermis in supporting pigment cell development. Additionally  this comprehensive single cell transcriptome data from biomedically relevant skin conditions provide a useful resource to accelerate discovery of mechanisms governing skin development. Overall design: Dissected skin tissue from post embryonic zebrafish 9.6 SSL from four genetic backgrounds wild type  eda mutant  bnc2 mutant  and hypothyroid were profiled with with sci RNA seq2.,,pubmed:37695017,,Multi genotype zebrafish skin snRNAseq,GSM7029635,,tissue:Whole skin tissue|cell type:Whole skin tissue|developmental stage:9.6 SSL SP  squamation onset posterior|strain:Tgsp7:EGFPb1212|genotype:wild type  eda mutant homozygous  bnc2 mutant homozygous  hypothryoid|geo loc name:missing|collection date:missing,Multi genotype zebrafish skin snRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the processing pipeline from Cao et al.  2017 doi: 10.1126/science.aam8940. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zskin wildtype cds.RDS: monocle3 cell data set object Supplementary files format and content: zskin wildtype raw counts.RDS: dgCMatrix with raw counts Supplementary files format and content: zskin wildtype cell metadata.csv: cell metadata table comma separated Supplementary files format and content: zskin wildtype gene metadata.csv: gene metadata table comma separated Supplementary files format and content: zskin all genotypes cds.RDS: monocle3 cell data set object Supplementary files format and content: zskin all genotypes raw counts.RDS: dgCMatrix with raw counts Supplementary files format and content: zskin all genotypes cell metadata.csv: cell metadata table comma separated Supplementary files format and content: zskin all genotypes gene metadata.csv: gene metadata table comma separated,Whole skin tissue,Hypothyroid zebrafish  Tgtg:nVenus v2a nfnBwprt8Tg  underwent a metronidazole treatment to ablate the thyroid gland at 5 dpf.,Fish were staged and selected for dissection  euthanized with MS 222 and processed immediately. Following removal of the head and fins  skins were removed with forceps and immediately flash frozen in liquid nitrogen then stored at  80°C prior to isolation of nuclei. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish were raised at 28.5℃ and selected for dissection based on staging landmarks Parichy et al.  2009.,cell type:Whole skin tissue|developmental stage:9.6 SSL SP  squamation onset posterior|strain:Tgsp7:EGFPb1212|genotype:wild type  eda mutant homozygous  bnc2 mutant homozygous  hypothryoid,GSM7029635,GSM7029635: Multi genotype zebrafish skin snRNAseq; Danio rerio; RNA Seq,GSM7029635 r1,GSM7029635,1,Fish were staged and selected for dissection  euthanized with MS 222 and processed immediately. Following removal of the head and fins  skins were removed with forceps and immediately flash frozen in liquid nitrogen then stored at  80°C prior to isolation of nuclei. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP421311,,loader:fastq load.py,zskin_sciRNA_seq3_R2_merge.fastq.gz zskin_sciRNA_seq3_R1_merge.fastq.gz,fastq fastq,23819946500.0,340284950.0,GSM7029635 r3,0:18 1:52,A:7652488300;C:4862634258;G:4789709798;T:6501533014;N:13581130,18,52,,,7652488300,4862634258,4789709798,6501533014,13581130,SRX19301395,SRS16701439,SRA1657186,"Genome Sciences, University of Washington","Genome Sciences, University of Washington",2,0.0,0.83093,0.0,0.53155,1.0,0.82986,,0.59518,18,52,T,B,sc-like readlen,illumina,nextseq,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2023-02-07,Larval,Larval,Skin,Surface Structure
74046,SRR23360142,SRX19301395,SRS16701439,SRP421311,PRJNA932229,Transcriptomic profiling of tissue environments critical for post embryonic patterning and morphogenesis of zebrafish skin,GSE224695,Other,Pigment patterns and skin appendages are prominent features of vertebrate skin. In zebrafish  regularly patterned pigment stripes and an array of calcified scales form simultaneously in the skin during post embryonic development. Understanding mechanisms that regulate stripe patterning and scale morphogenesis may lead to discovery of fundamental mechanisms that govern development of animal form. To learn about cell types and potential signaling interactions that govern skin patterning and morphogenesis we generated and analyzed single cell transcriptomes of skin with genetic or induced defects in pigmentation and squamation. These data reveal a previously undescribed population of epidermal cells that express transcripts encoding enamel matrix proteins  suggest hormonal control of epithelial mesenchymal signaling  clarify the signaling network that governs scale papillae development  and identify a critical role for the hypodermis in supporting pigment cell development. Additionally  this comprehensive single cell transcriptome data from biomedically relevant skin conditions provide a useful resource to accelerate discovery of mechanisms governing skin development. Overall design: Dissected skin tissue from post embryonic zebrafish 9.6 SSL from four genetic backgrounds wild type  eda mutant  bnc2 mutant  and hypothyroid were profiled with with sci RNA seq2.,,pubmed:37695017,,Multi genotype zebrafish skin snRNAseq,GSM7029635,,tissue:Whole skin tissue|cell type:Whole skin tissue|developmental stage:9.6 SSL SP  squamation onset posterior|strain:Tgsp7:EGFPb1212|genotype:wild type  eda mutant homozygous  bnc2 mutant homozygous  hypothryoid|geo loc name:missing|collection date:missing,Multi genotype zebrafish skin snRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the processing pipeline from Cao et al.  2017 doi: 10.1126/science.aam8940. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file  Cell Metadata comma separated values  .csv  Gene Metadata comma separated values  .csv Supplementary files format and content: zskin wildtype cds.RDS: monocle3 cell data set object Supplementary files format and content: zskin wildtype raw counts.RDS: dgCMatrix with raw counts Supplementary files format and content: zskin wildtype cell metadata.csv: cell metadata table comma separated Supplementary files format and content: zskin wildtype gene metadata.csv: gene metadata table comma separated Supplementary files format and content: zskin all genotypes cds.RDS: monocle3 cell data set object Supplementary files format and content: zskin all genotypes raw counts.RDS: dgCMatrix with raw counts Supplementary files format and content: zskin all genotypes cell metadata.csv: cell metadata table comma separated Supplementary files format and content: zskin all genotypes gene metadata.csv: gene metadata table comma separated,Whole skin tissue,Hypothyroid zebrafish  Tgtg:nVenus v2a nfnBwprt8Tg  underwent a metronidazole treatment to ablate the thyroid gland at 5 dpf.,Fish were staged and selected for dissection  euthanized with MS 222 and processed immediately. Following removal of the head and fins  skins were removed with forceps and immediately flash frozen in liquid nitrogen then stored at  80°C prior to isolation of nuclei. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,Zebrafish were raised at 28.5℃ and selected for dissection based on staging landmarks Parichy et al.  2009.,cell type:Whole skin tissue|developmental stage:9.6 SSL SP  squamation onset posterior|strain:Tgsp7:EGFPb1212|genotype:wild type  eda mutant homozygous  bnc2 mutant homozygous  hypothryoid,GSM7029635,GSM7029635: Multi genotype zebrafish skin snRNAseq; Danio rerio; RNA Seq,GSM7029635 r1,GSM7029635,1,Fish were staged and selected for dissection  euthanized with MS 222 and processed immediately. Following removal of the head and fins  skins were removed with forceps and immediately flash frozen in liquid nitrogen then stored at  80°C prior to isolation of nuclei. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP421311,,loader:fastq load.py,zskin_sciRNA_seq4_R1_merge.fastq.gz zskin_sciRNA_seq4_R2_merge.fastq.gz,fastq fastq,33417347600.0,477390680.0,GSM7029635 r4,0:18 1:52,A:10992313767;C:6719060839;G:6813342549;T:8874815927;N:17814518,18,52,,,10992313767,6719060839,6813342549,8874815927,17814518,SRX19301395,SRS16701439,SRA1657186,"Genome Sciences, University of Washington","Genome Sciences, University of Washington",2,0.0,0.7972,0.0,0.51142,1.0,0.84435,,0.56962,18,52,T,B,sc-like readlen,illumina,nextseq,3prime,random_priming,unknown,sc,single_cell_plate,scirnaseq,,United States,2023-02-07,Larval,Larval,Skin,Surface Structure
74790,SRR24042941,SRX19844898,SRS17203996,SRP430475,PRJNA951376,Spic is required for the differentiation of metaphocyte progenitor cells,GSE228732,Transcriptome Analysis,Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic.  Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors  it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants  we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes  either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings,parent bioproject:PRJNA951389,pubmed:37148242,,mutant epidermis 7,GSM7135698,,source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult,mutant epidermis 7,Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package  and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample,epidermis,,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult,GSM7135698,GSM7135698: mutant epidermis 7; Danio rerio; RNA Seq,GSM7135698 r1,GSM7135698,1,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP430475,,loader:fastq load.py,mut_epi_7_R1.fq.gz mut_epi_7_R2.fq.gz,fastq fastq,5000082600.0,16666942.0,GSM7135698 r1,0:150 1:150,A:1356614389;C:1145976228;G:1015865485;T:1481123817;N:502681,150,150,,,1356614389,1145976228,1015865485,1481123817,502681,SRX19844898,SRS17203996,SRA1614434,"WEN lab, Life Science, Hong Kong University of Science and Technology","WEN lab, Life Science, Hong Kong University of Science and Technology",2,0.8389,0.84116,0.1854,0.18546,0.85543,0.85571,0.60232,0.62058,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,China,2023-04-02,Adult,Adult,Skin,Surface Structure
74791,SRR24042942,SRX19844897,SRS17203995,SRP430475,PRJNA951376,Spic is required for the differentiation of metaphocyte progenitor cells,GSE228732,Transcriptome Analysis,Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic.  Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors  it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants  we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes  either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings,parent bioproject:PRJNA951389,pubmed:37148242,,mutant epidermis 6,GSM7135697,,source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult,mutant epidermis 6,Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package  and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample,epidermis,,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult,GSM7135697,GSM7135697: mutant epidermis 6; Danio rerio; RNA Seq,GSM7135697 r1,GSM7135697,1,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP430475,,loader:fastq load.py,mut_epi_6_R1.fq.gz mut_epi_6_R2.fq.gz,fastq fastq,5150526900.0,17168423.0,GSM7135697 r1,0:150 1:150,A:1413867032;C:1148708171;G:1068645696;T:1518782074;N:523927,150,150,,,1413867032,1148708171,1068645696,1518782074,523927,SRX19844897,SRS17203995,SRA1614434,"WEN lab, Life Science, Hong Kong University of Science and Technology","WEN lab, Life Science, Hong Kong University of Science and Technology",2,0.85431,0.85836,0.20685,0.20717,0.86746,0.86645,0.546,0.5461,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,China,2023-04-02,Adult,Adult,Skin,Surface Structure
74792,SRR24042943,SRX19844896,SRS17203994,SRP430475,PRJNA951376,Spic is required for the differentiation of metaphocyte progenitor cells,GSE228732,Transcriptome Analysis,Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic.  Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors  it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants  we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes  either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings,parent bioproject:PRJNA951389,pubmed:37148242,,mutant epidermis 5,GSM7135696,,source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult,mutant epidermis 5,Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package  and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample,epidermis,,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult,GSM7135696,GSM7135696: mutant epidermis 5; Danio rerio; RNA Seq,GSM7135696 r1,GSM7135696,1,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP430475,,loader:fastq load.py,mut_epi_5_R1.fq.gz mut_epi_5_R2.fq.gz,fastq fastq,5444193600.0,18147312.0,GSM7135696 r1,0:150 1:150,A:1506955248;C:1203830842;G:1100776758;T:1632090095;N:540657,150,150,,,1506955248,1203830842,1100776758,1632090095,540657,SRX19844896,SRS17203994,SRA1614434,"WEN lab, Life Science, Hong Kong University of Science and Technology","WEN lab, Life Science, Hong Kong University of Science and Technology",2,0.84926,0.85327,0.24961,0.24986,0.86665,0.8658,0.59696,0.59563,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,China,2023-04-02,Adult,Adult,Skin,Surface Structure
74793,SRR24042944,SRX19844895,SRS17203993,SRP430475,PRJNA951376,Spic is required for the differentiation of metaphocyte progenitor cells,GSE228732,Transcriptome Analysis,Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic.  Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors  it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants  we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes  either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings,parent bioproject:PRJNA951389,pubmed:37148242,,mutant epidermis 4,GSM7135695,,source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult,mutant epidermis 4,Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package  and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample,epidermis,,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult,GSM7135695,GSM7135695: mutant epidermis 4; Danio rerio; RNA Seq,GSM7135695 r1,GSM7135695,1,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP430475,,loader:fastq load.py,mut_epi_4_R1.fq.gz mut_epi_4_R2.fq.gz,fastq fastq,5002087200.0,16673624.0,GSM7135695 r1,0:150 1:150,A:1390303577;C:1103953823;G:1001952998;T:1505374747;N:502055,150,150,,,1390303577,1103953823,1001952998,1505374747,502055,SRX19844895,SRS17203993,SRA1614434,"WEN lab, Life Science, Hong Kong University of Science and Technology","WEN lab, Life Science, Hong Kong University of Science and Technology",2,0.84071,0.84398,0.25782,0.25789,0.89045,0.89027,0.594,0.59396,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,China,2023-04-02,Adult,Adult,Skin,Surface Structure
74794,SRR24042945,SRX19844894,SRS17203992,SRP430475,PRJNA951376,Spic is required for the differentiation of metaphocyte progenitor cells,GSE228732,Transcriptome Analysis,Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic.  Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors  it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants  we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes  either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings,parent bioproject:PRJNA951389,pubmed:37148242,,mutant epidermis 3,GSM7135694,,source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult,mutant epidermis 3,Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package  and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample,epidermis,,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult,GSM7135694,GSM7135694: mutant epidermis 3; Danio rerio; RNA Seq,GSM7135694 r1,GSM7135694,1,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP430475,,loader:fastq load.py,mut_epi_3_R1.fq.gz mut_epi_3_R2.fq.gz,fastq fastq,5088778800.0,16962596.0,GSM7135694 r1,0:150 1:150,A:1423520633;C:1124312893;G:1051927427;T:1488506070;N:511777,150,150,,,1423520633,1124312893,1051927427,1488506070,511777,SRX19844894,SRS17203992,SRA1614434,"WEN lab, Life Science, Hong Kong University of Science and Technology","WEN lab, Life Science, Hong Kong University of Science and Technology",2,0.87032,0.87262,0.21802,0.21697,0.84478,0.84516,0.57085,0.56848,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,China,2023-04-02,Adult,Adult,Skin,Surface Structure
74795,SRR24042946,SRX19844893,SRS17203991,SRP430475,PRJNA951376,Spic is required for the differentiation of metaphocyte progenitor cells,GSE228732,Transcriptome Analysis,Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic.  Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors  it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants  we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes  either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings,parent bioproject:PRJNA951389,pubmed:37148242,,mutant epidermis 2,GSM7135693,,source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult,mutant epidermis 2,Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package  and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample,epidermis,,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult,GSM7135693,GSM7135693: mutant epidermis 2; Danio rerio; RNA Seq,GSM7135693 r1,GSM7135693,1,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP430475,,loader:fastq load.py,mut_epi_2_R1.fq.gz mut_epi_2_R2.fq.gz,fastq fastq,4328463900.0,14428213.0,GSM7135693 r1,0:150 1:150,A:1188821495;C:969906063;G:882155508;T:1287158594;N:422240,150,150,,,1188821495,969906063,882155508,1287158594,422240,SRX19844893,SRS17203991,SRA1614434,"WEN lab, Life Science, Hong Kong University of Science and Technology","WEN lab, Life Science, Hong Kong University of Science and Technology",2,0.85046,0.85261,0.24989,0.25021,0.89025,0.8897,0.55974,0.55601,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,China,2023-04-02,Adult,Adult,Skin,Surface Structure
74796,SRR24042947,SRX19844892,SRS17203990,SRP430475,PRJNA951376,Spic is required for the differentiation of metaphocyte progenitor cells,GSE228732,Transcriptome Analysis,Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic.  Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors  it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants  we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes  either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings,parent bioproject:PRJNA951389,pubmed:37148242,,mutant epidermis 1,GSM7135692,,source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult,mutant epidermis 1,Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package  and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample,epidermis,,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:mutant|Stage:adult,GSM7135692,GSM7135692: mutant epidermis 1; Danio rerio; RNA Seq,GSM7135692 r1,GSM7135692,1,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP430475,,loader:fastq load.py,mut_epi_1_R1.fq.gz mut_epi_1_R2.fq.gz,fastq fastq,4852088400.0,16173628.0,GSM7135692 r1,0:150 1:150,A:1355547120;C:1052947209;G:998601349;T:1444516092;N:476630,150,150,,,1355547120,1052947209,998601349,1444516092,476630,SRX19844892,SRS17203990,SRA1614434,"WEN lab, Life Science, Hong Kong University of Science and Technology","WEN lab, Life Science, Hong Kong University of Science and Technology",2,0.82126,0.82514,0.19738,0.19774,0.8521,0.85171,0.56371,0.58039,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,China,2023-04-02,Adult,Adult,Skin,Surface Structure
74797,SRR24042948,SRX19844891,SRS17203989,SRP430475,PRJNA951376,Spic is required for the differentiation of metaphocyte progenitor cells,GSE228732,Transcriptome Analysis,Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic.  Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors  it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants  we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes  either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings,parent bioproject:PRJNA951389,pubmed:37148242,,sibling epidermis 7,GSM7135691,,source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult,sibling epidermis 7,Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package  and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample,epidermis,,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult,GSM7135691,GSM7135691: sibling epidermis 7; Danio rerio; RNA Seq,GSM7135691 r1,GSM7135691,1,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP430475,,loader:fastq load.py,sib_epi_7_R1.fq.gz sib_epi_7_R2.fq.gz,fastq fastq,5331845400.0,17772818.0,GSM7135691 r1,0:150 1:150,A:1430690183;C:1254783660;G:1084303117;T:1561520361;N:548079,150,150,,,1430690183,1254783660,1084303117,1561520361,548079,SRX19844891,SRS17203989,SRA1614434,"WEN lab, Life Science, Hong Kong University of Science and Technology","WEN lab, Life Science, Hong Kong University of Science and Technology",2,0.85507,0.85819,0.17442,0.17439,0.8495,0.84991,0.59457,0.59698,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,China,2023-04-02,Adult,Adult,Skin,Surface Structure
74798,SRR24042949,SRX19844890,SRS17203987,SRP430475,PRJNA951376,Spic is required for the differentiation of metaphocyte progenitor cells,GSE228732,Transcriptome Analysis,Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic.  Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors  it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants  we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes  either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings,parent bioproject:PRJNA951389,pubmed:37148242,,sibling epidermis 6,GSM7135690,,source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult,sibling epidermis 6,Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package  and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample,epidermis,,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult,GSM7135690,GSM7135690: sibling epidermis 6; Danio rerio; RNA Seq,GSM7135690 r1,GSM7135690,1,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP430475,,loader:fastq load.py,sib_epi_6_R1.fq.gz sib_epi_6_R2.fq.gz,fastq fastq,5250903600.0,17503012.0,GSM7135690 r1,0:150 1:150,A:1422246673;C:1203178539;G:1084296067;T:1540644470;N:537851,150,150,,,1422246673,1203178539,1084296067,1540644470,537851,SRX19844890,SRS17203987,SRA1614434,"WEN lab, Life Science, Hong Kong University of Science and Technology","WEN lab, Life Science, Hong Kong University of Science and Technology",2,0.86662,0.86998,0.17496,0.17481,0.85697,0.85669,0.60671,0.60577,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,China,2023-04-02,Adult,Adult,Skin,Surface Structure
74799,SRR24042950,SRX19844889,SRS17203988,SRP430475,PRJNA951376,Spic is required for the differentiation of metaphocyte progenitor cells,GSE228732,Transcriptome Analysis,Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic.  Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors  it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants  we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes  either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings,parent bioproject:PRJNA951389,pubmed:37148242,,sibling epidermis 5,GSM7135689,,source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult,sibling epidermis 5,Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package  and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample,epidermis,,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult,GSM7135689,GSM7135689: sibling epidermis 5; Danio rerio; RNA Seq,GSM7135689 r1,GSM7135689,1,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP430475,,loader:fastq load.py,sib_epi_5_R1.fq.gz sib_epi_5_R2.fq.gz,fastq fastq,5357108100.0,17857027.0,GSM7135689 r1,0:150 1:150,A:1442683833;C:1246002420;G:1107335060;T:1560544984;N:541803,150,150,,,1442683833,1246002420,1107335060,1560544984,541803,SRX19844889,SRS17203988,SRA1614434,"WEN lab, Life Science, Hong Kong University of Science and Technology","WEN lab, Life Science, Hong Kong University of Science and Technology",2,0.88017,0.88379,0.15935,0.1591,0.83822,0.83784,0.5992,0.59047,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,China,2023-04-02,Adult,Adult,Skin,Surface Structure
74800,SRR24042951,SRX19844888,SRS17203986,SRP430475,PRJNA951376,Spic is required for the differentiation of metaphocyte progenitor cells,GSE228732,Transcriptome Analysis,Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic.  Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors  it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants  we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes  either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings,parent bioproject:PRJNA951389,pubmed:37148242,,sibling epidermis 4,GSM7135688,,source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult,sibling epidermis 4,Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package  and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample,epidermis,,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult,GSM7135688,GSM7135688: sibling epidermis 4; Danio rerio; RNA Seq,GSM7135688 r1,GSM7135688,1,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP430475,,loader:fastq load.py,sib_epi_4_R1.fq.gz sib_epi_4_R2.fq.gz,fastq fastq,4729031400.0,15763438.0,GSM7135688 r1,0:150 1:150,A:1269897945;C:1106204392;G:980800578;T:1371651398;N:477087,150,150,,,1269897945,1106204392,980800578,1371651398,477087,SRX19844888,SRS17203986,SRA1614434,"WEN lab, Life Science, Hong Kong University of Science and Technology","WEN lab, Life Science, Hong Kong University of Science and Technology",2,0.89554,0.89737,0.15933,0.1589,0.84173,0.84181,0.57695,0.58999,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,China,2023-04-02,Adult,Adult,Skin,Surface Structure
74801,SRR24042952,SRX19844887,SRS17203985,SRP430475,PRJNA951376,Spic is required for the differentiation of metaphocyte progenitor cells,GSE228732,Transcriptome Analysis,Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic.  Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors  it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants  we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes  either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings,parent bioproject:PRJNA951389,pubmed:37148242,,sibling epidermis 3,GSM7135687,,source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult,sibling epidermis 3,Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package  and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample,epidermis,,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult,GSM7135687,GSM7135687: sibling epidermis 3; Danio rerio; RNA Seq,GSM7135687 r1,GSM7135687,1,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP430475,,loader:fastq load.py,sib_epi_3_R1.fq.gz sib_epi_3_R2.fq.gz,fastq fastq,5540201400.0,18467338.0,GSM7135687 r1,0:150 1:150,A:1505221042;C:1289954851;G:1159697425;T:1584759074;N:569008,150,150,,,1505221042,1289954851,1159697425,1584759074,569008,SRX19844887,SRS17203985,SRA1614434,"WEN lab, Life Science, Hong Kong University of Science and Technology","WEN lab, Life Science, Hong Kong University of Science and Technology",2,0.88805,0.89059,0.13525,0.1353,0.84084,0.84155,0.58614,0.58632,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,China,2023-04-02,Adult,Adult,Skin,Surface Structure
74802,SRR24042953,SRX19844886,SRS17203984,SRP430475,PRJNA951376,Spic is required for the differentiation of metaphocyte progenitor cells,GSE228732,Transcriptome Analysis,Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic.  Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors  it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants  we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes  either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings,parent bioproject:PRJNA951389,pubmed:37148242,,sibling epidermis 2,GSM7135686,,source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult,sibling epidermis 2,Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package  and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample,epidermis,,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult,GSM7135686,GSM7135686: sibling epidermis 2; Danio rerio; RNA Seq,GSM7135686 r1,GSM7135686,1,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP430475,,loader:fastq load.py,sib_epi_2_R1.fq.gz sib_epi_2_R2.fq.gz,fastq fastq,3922961700.0,13076539.0,GSM7135686 r1,0:150 1:150,A:1059915956;C:914101921;G:808452034;T:1140105054;N:386735,150,150,,,1059915956,914101921,808452034,1140105054,386735,SRX19844886,SRS17203984,SRA1614434,"WEN lab, Life Science, Hong Kong University of Science and Technology","WEN lab, Life Science, Hong Kong University of Science and Technology",2,0.88232,0.88475,0.19744,0.1966,0.83489,0.8342,0.45587,0.45386,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,China,2023-04-02,Adult,Adult,Skin,Surface Structure
74803,SRR24042954,SRX19844885,SRS17203983,SRP430475,PRJNA951376,Spic is required for the differentiation of metaphocyte progenitor cells,GSE228732,Transcriptome Analysis,Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic.  Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors  it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants  we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid associated genes  either directly or indirectly through downstream transcription factors. Overall design: Gene expression profiling analysis of bulk RNA seq data for metaphocyte progenitor cells from the epidermis and gill of spic mutant fish and siblings,parent bioproject:PRJNA951389,pubmed:37148242,,sibling epidermis 1,GSM7135685,,source name:epidermis|tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult,sibling epidermis 1,Reads were aligned to the GRCz11.94 danRer11 zebrafish reference genome using the STAR package  and gene counts were calculated using feature Counts. The count tables were normalized to produce transcripts per million TPM tables. Principal component analysis PCA was carried out using the R Stats package. Differential expression genes DEGs were assessed with the R DESeq2 package. Assembly: danRer11 Supplementary files format and content: comma separated values file of TPM values for each sample,epidermis,,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,tissue:epidermis|strain:Tgspic:EGFP; mpeg1:DsRedx|cell type:spic:EGFP+mpeg1:DsRedx  cells|genotype:sibling|Stage:adult,GSM7135685,GSM7135685: sibling epidermis 1; Danio rerio; RNA Seq,GSM7135685 r1,GSM7135685,1,The EGFP+DsRedx  progenitor cells for RNA seq were sorted by BD FACSAria™ IIIu cell sorter. 30 cells per sample were sorted. cDNA library was prepared according to the standard Smart seq2 protocol with minor modifications. Briefly  30 cells per sample were sorted into the lysis buffer premixed with dNTP and oligo dT primer. The whole lysate was proceeded to reverse transcription by SuperScript™ II Reverse Transcriptase 18064071  Invitrogen. The cDNA was then amplified with KAPA HiFi HotStart ReadyMix PCR Kit 50 196 5217  Roche for 23 cycles and purified with the Ampure XP beads A63881  Beckman. The cDNA library was prepared with TruePrep DNA Library Prep Kit V2 for Illumina TD501  Vazyme.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP430475,,loader:fastq load.py,sib_epi_1_R1.fq.gz sib_epi_1_R2.fq.gz,fastq fastq,4876464000.0,16254880.0,GSM7135685 r1,0:150 1:150,A:1349569338;C:1090614080;G:1014099843;T:1421695200;N:485539,150,150,,,1349569338,1090614080,1014099843,1421695200,485539,SRX19844885,SRS17203983,SRA1614434,"WEN lab, Life Science, Hong Kong University of Science and Technology","WEN lab, Life Science, Hong Kong University of Science and Technology",2,0.88374,0.88675,0.17619,0.17572,0.83889,0.83883,0.42946,0.57922,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,China,2023-04-02,Adult,Adult,Skin,Surface Structure
74804,SRR24043073,SRX19845029,SRS17204126,SRP430482,PRJNA951388,single cell RNA sequencing analysis of metaphocytes and epidermal cells,GSE228737,Transcriptome Analysis,Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. To reveal the genetic programs underlying the development of metaphocytes  we performed single cell RNA sequencing analysis of spic:GFP+ cells in the  epidermis of adult Tgspic:EGFP fish. The result further supports that mature metaphocytes are generated from spic+ progenitors via an intermediate immature state and gradually obtain their myeloid characteristics during this process. Overall design: scRNA seq 10X genomics three prime V3.1 analysis of FACS sorted spic:EGFP+ and singlet cells  from the epidemris of 6 mpf Tgspic:EGFP fish,parent bioproject:PRJNA951389,pubmed:37148242,,epi2,GSM7135751,,source name:epidermis|tissue:epidermis|development stage:6 mpf|cell type:spic:EGFP+ and singlet cells|strain:Tgspic:EGFP|genotype:WT,epi2,Raw reads were aligned to zebrafish reference genome genome reference: GRCz11; annotation reference: GRCz11.103 combined with the sequences for DsRedx using the Cell Ranger pipelines v6.0. Downstream analysis of unique molecular identifiers UMI count matrix was conducted in R using the Seurat pipeline v4.0.5. Pseudotime analysis was performed with the Monocle3 package in R. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,epidermis,,Six adult Tgspic:EGFP fish were sacrificed  8 000 EGFP+ cells  and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. In brief  post the cell sorting  single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System  followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.,,tissue:epidermis|development stage:6 mpf|cell type:spic:EGFP+ and singlet cells|strain:Tgspic:EGFP|genotype:WT,GSM7135751,GSM7135751: epi2; Danio rerio; RNA Seq,GSM7135751 r1,GSM7135751,1,Six adult Tgspic:EGFP fish were sacrificed  8 000 EGFP+ cells  and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. In brief  post the cell sorting  single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System  followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP430482,,,epi2_S1_L001_R1_001.fastq.gz epi2_S1_L001_R2_001.fastq.gz,fastq fastq,53272554600.0,177575182.0,GSM7135751 r1,0:150 1:150,A:22273594251;C:9171565164;G:8634752690;T:13192111379;N:531116,150,150,,,22273594251,9171565164,8634752690,13192111379,531116,SRX19845029,SRS17204126,SRA1614473,"WEN lab, Life Science, Hong Kong University of Science and Technology","WEN lab, Life Science, Hong Kong University of Science and Technology",2,0.0,0.87992,0.0,0.19142,1.0,0.8143,,0.56327,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-04-02,Adult,Adult,Skin,Surface Structure
74805,SRR24043074,SRX19845029,SRS17204126,SRP430482,PRJNA951388,single cell RNA sequencing analysis of metaphocytes and epidermal cells,GSE228737,Transcriptome Analysis,Metaphocytes are tissue resident myeloid like cells of non hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tgspic:EGFP transgenic fish were found to label both metaphocytes and their progenitor cells. To reveal the genetic programs underlying the development of metaphocytes  we performed single cell RNA sequencing analysis of spic:GFP+ cells in the  epidermis of adult Tgspic:EGFP fish. The result further supports that mature metaphocytes are generated from spic+ progenitors via an intermediate immature state and gradually obtain their myeloid characteristics during this process. Overall design: scRNA seq 10X genomics three prime V3.1 analysis of FACS sorted spic:EGFP+ and singlet cells  from the epidemris of 6 mpf Tgspic:EGFP fish,parent bioproject:PRJNA951389,pubmed:37148242,,epi2,GSM7135751,,source name:epidermis|tissue:epidermis|development stage:6 mpf|cell type:spic:EGFP+ and singlet cells|strain:Tgspic:EGFP|genotype:WT,epi2,Raw reads were aligned to zebrafish reference genome genome reference: GRCz11; annotation reference: GRCz11.103 combined with the sequences for DsRedx using the Cell Ranger pipelines v6.0. Downstream analysis of unique molecular identifiers UMI count matrix was conducted in R using the Seurat pipeline v4.0.5. Pseudotime analysis was performed with the Monocle3 package in R. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,epidermis,,Six adult Tgspic:EGFP fish were sacrificed  8 000 EGFP+ cells  and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. In brief  post the cell sorting  single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System  followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.,,tissue:epidermis|development stage:6 mpf|cell type:spic:EGFP+ and singlet cells|strain:Tgspic:EGFP|genotype:WT,GSM7135751,GSM7135751: epi2; Danio rerio; RNA Seq,GSM7135751 r1,GSM7135751,1,Six adult Tgspic:EGFP fish were sacrificed  8 000 EGFP+ cells  and 50 000 singlet cells from the single cell suspension of epidermis were sorted into 5 μl 1% BSA/PBS with 0.5 μl RNase inhibitor by the BD Influx™ Cell Sorter. The concentration of sorted cells was measured with the Countess™ II FL Automated Cell Counter Invitrogen. 10x scRNA seq library was carried out with a 10X Chromium single cell platform. In brief  post the cell sorting  single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System  followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP430482,,,epi2_S1_L002_R1_001.fastq.gz epi2_S1_L002_R2_001.fastq.gz,fastq fastq,48364190400.0,161213968.0,GSM7135751 r2,0:150 1:150,A:20333401181;C:8352480913;G:7827379016;T:11850446550;N:482740,150,150,,,20333401181,8352480913,7827379016,11850446550,482740,SRX19845029,SRS17204126,SRA1614473,"WEN lab, Life Science, Hong Kong University of Science and Technology","WEN lab, Life Science, Hong Kong University of Science and Technology",2,0.0,0.87888,0.0,0.19128,1.0,0.81306,,0.55856,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-04-02,Adult,Adult,Skin,Surface Structure