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159 rows where experiment.library_layout = "PAIRED", tissue_curation = "Skin" and tissue_curation_coarse = "Surface Structure"

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devstage_curation 7

devstage_curation_coarse 6

experiment.library_selection 5

experiment.platform 3

experiment.library_strategy 2

experiment.library_source 2

tissue_curation_coarse 1

  • Surface Structure · 159 ✖

tissue_curation 1

  • Skin · 159 ✖

experiment.library_layout 1

  • PAIRED · 159 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
9770 9770 ERR5838122 ERX5487778 ERS6337138 ERP119543 PRJEB36360 Transcriptomic analysis of adult skin from 9 Danio species ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27 Other Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21 PUBMED:33277491 Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. Transcriptomic analysis of adult skin from 9 Danio species SAMEA8652584 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652584|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:05 Danio rerio adult skin 5|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:05 Danio rerio adult skin 5|sex:male|tissue type:skin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 5 unspecified 1 TruSeq stranded mRNA Illumina   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP119543 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29 S1385Nr5.1.fastq.gz S1385Nr5.2.fastq.gz fastq fastq 6912206316.0 34306523.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 5 0:100.74 1:100.74 A:1853779551;C:1607929988;G:1658402611;T:1792045990;N:48176 100 100     1853779551 1607929988 1658402611 1792045990 48176 ERX5487778 ERS6337138 ERA4129786 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 2 0.96095 0.962 0.08049 0.07821 0.70654 0.70926 0.51398 0.51064 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-03-21 Adult Adult Skin Surface Structure
9771 9771 ERR5838121 ERX5487777 ERS6337136 ERP119543 PRJEB36360 Transcriptomic analysis of adult skin from 9 Danio species ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27 Other Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21 PUBMED:33277491 Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. Transcriptomic analysis of adult skin from 9 Danio species SAMEA8652582 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652582|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:04 Danio rerio adult skin 4|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:04 Danio rerio adult skin 4|sex:male|tissue type:skin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 4 unspecified 1 TruSeq stranded mRNA Illumina   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP119543 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29 S1385Nr4.1.fastq.gz S1385Nr4.2.fastq.gz fastq fastq 6161942050.0 30595009.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 4 0:100.70 1:100.70 A:1642716052;C:1446485458;G:1490121106;T:1582576605;N:42829 100 100     1642716052 1446485458 1490121106 1582576605 42829 ERX5487777 ERS6337136 ERA4129786 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 2 0.96544 0.96564 0.07368 0.07303 0.70822 0.71092 0.50154 0.50781 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-03-21 Adult Adult Skin Surface Structure
9772 9772 ERR5838120 ERX5487776 ERS6337133 ERP119543 PRJEB36360 Transcriptomic analysis of adult skin from 9 Danio species ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27 Other Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21 PUBMED:33277491 Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. Transcriptomic analysis of adult skin from 9 Danio species SAMEA8652579 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652579|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:03 Danio rerio adult skin 3|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:03 Danio rerio adult skin 3|sex:female|tissue type:skin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 3 unspecified 1 TruSeq stranded mRNA Illumina   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP119543 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29 S1385Nr3.1.fastq.gz S1385Nr3.2.fastq.gz fastq fastq 7422881394.0 36866805.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 3 0:100.67 1:100.67 A:1950275527;C:1768648993;G:1827362519;T:1876542858;N:51497 100 100     1950275527 1768648993 1827362519 1876542858 51497 ERX5487776 ERS6337133 ERA4129786 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 2 0.97031 0.97047 0.04915 0.04817 0.71459 0.71894 0.51089 0.5097 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-03-21 Adult Adult Skin Surface Structure
9773 9773 ERR5838119 ERX5487775 ERS6337132 ERP119543 PRJEB36360 Transcriptomic analysis of adult skin from 9 Danio species ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27 Other Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21 PUBMED:33277491 Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. Transcriptomic analysis of adult skin from 9 Danio species SAMEA8652578 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652578|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:02 Danio rerio adult skin 2|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:02 Danio rerio adult skin 2|sex:female|tissue type:skin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 2 unspecified 1 TruSeq stranded mRNA Illumina   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP119543 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29 S1385Nr2.1.fastq.gz S1385Nr2.2.fastq.gz fastq fastq 7006718028.0 34786110.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 2 0:100.71 1:100.71 A:1847371523;C:1665346769;G:1712373266;T:1781565768;N:60702 100 100     1847371523 1665346769 1712373266 1781565768 60702 ERX5487775 ERS6337132 ERA4129786 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 2 0.96136 0.96039 0.05872 0.05752 0.70325 0.70674 0.46717 0.48218 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-03-21 Adult Adult Skin Surface Structure
9774 9774 ERR5838118 ERX5487774 ERS6337063 ERP119543 PRJEB36360 Transcriptomic analysis of adult skin from 9 Danio species ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27 Other Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21 PUBMED:33277491 Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. Transcriptomic analysis of adult skin from 9 Danio species SAMEA8652509 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652509|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:01 Danio rerio adult skin 1|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:01 Danio rerio adult skin 1|sex:male|tissue type:skin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 1 unspecified 1 TruSeq stranded mRNA Illumina   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP119543 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29 S1385Nr1.1.fastq.gz S1385Nr1.2.fastq.gz fastq fastq 6586457266.0 32719900.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 1 0:100.65 1:100.65 A:1709547533;C:1593125315;G:1617088678;T:1666650824;N:44916 100 100     1709547533 1593125315 1617088678 1666650824 44916 ERX5487774 ERS6337063 ERA4129786 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 2 0.9531 0.95366 0.07763 0.07567 0.71384 0.71634 0.52409 0.52475 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-03-21 Adult Adult Skin Surface Structure
25297 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 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 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 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 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
32858 32858 SRR29482326 SRX24993370 SRS21694834 SRP515140 PRJNA1126247 Specific oncogene activation of the cell of origin in mucosal melanoma [SORT seq] GSE270356 Other Mucosal melanoma MM is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics we develop a zebrafish model in which all melanocytes experience CCND1 expression and loss of PTEN and TP53. Surprisingly melanoma only develops from melanocytes lining internal organs analogous to the location of patient MM. We find that zebrafish MMs have a unique chromatin landscape from cutaneous melanoma. Internal melanocytes are labeled using a MM specific transcriptional enhancer. Normal zebrafish internal melanocytes share a gene expression signature with MMs. Patient and zebrafish MMs show increased migratory neural crest gene and decreased antigen presentation gene expression consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors allowing this model to be used for MM therapeutic discovery. As this is a non MAPK driven genetically engineered model of melanoma our work also has implications for the 15% of cutaneous melanoma patients who lack MAPK driving mutations. Overall design: Single cell RNA sequencing was done on internal vs. external normal adult zebrafish melanocytes using the SORT seq platform.       Internal melanocytes GSM8340241   source name:Internal melanocytes|tissue:Internal melanocytes|cell type:melanocytes|genotype:mitfa / ; roy / fish injected with mitfa:GFP|geo loc name:missing|collection date:missing Internal melanocytes BWA was used to align paired end read to danRer11. Count tables were generated using MapAndGo. Count tables were corrected using UMI to remove duplicate reads. Transcript counts were adjusted using Poissonian counting statistics to yield the number of UMIs detected per cell. Counts were imported into R using the Seurat suite version 3.0 Assembly: danRer11 Supplementary files format and content: .tsv file contains count matrix file used for data normalization and visualization using Seurat Library strategy: SORT seq Internal melanocytes   Respective tissues were mechanically dissociated digested in TrypLE for 45 min Invitrogen 12563011 40uM filtered spun down and resuspended in FACs buffer dPBS Mg+/Ca+ free with 2% FBS pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina. mitfa / ; roy / zebrafish injected with mitfa:GFP were Raised to maturity to obtain tissues tissue:Internal melanocytes|cell type:melanocytes|genotype:mitfa / ; roy / fish injected with mitfa:GFP GSM8340241 GSM8340241: Internal melanocytes; Danio rerio; OTHER GSM8340241 r1 GSM8340241 1 Respective tissues were mechanically dissociated digested in TrypLE for 45 min Invitrogen 12563011 40uM filtered spun down and resuspended in FACs buffer dPBS Mg+/Ca+ free with 2% FBS pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP515140     HAR-MI-002_H5GCWBGXF_R2.fastq.gz HAR-MI-002_H5GCWBGXF_R1.fastq.gz fastq fastq 2957975418.0 34395063.0 GSM8340241 r1 0:26 1:60 A:738954503;C:560052455;G:520746060;T:1137116132;N:1106268 26 60     738954503 560052455 520746060 1137116132 1106268 SRX24993370 SRS21694834 SRA1904773 Insco Lab, Medical Oncology, Dana Farber Cancer Institute Insco Lab, Medical Oncology, Dana Farber Cancer Institute 2 0.11637 0.84116 0.10894 0.31188 0.98851 0.71526 0.6688 0.60221 26 60 T B sc-like readlen illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   United States 2024-06-20 Undetermined Adult Skin Surface Structure
32859 32859 SRR29482327 SRX24993369 SRS21694833 SRP515140 PRJNA1126247 Specific oncogene activation of the cell of origin in mucosal melanoma [SORT seq] GSE270356 Other Mucosal melanoma MM is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics we develop a zebrafish model in which all melanocytes experience CCND1 expression and loss of PTEN and TP53. Surprisingly melanoma only develops from melanocytes lining internal organs analogous to the location of patient MM. We find that zebrafish MMs have a unique chromatin landscape from cutaneous melanoma. Internal melanocytes are labeled using a MM specific transcriptional enhancer. Normal zebrafish internal melanocytes share a gene expression signature with MMs. Patient and zebrafish MMs show increased migratory neural crest gene and decreased antigen presentation gene expression consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors allowing this model to be used for MM therapeutic discovery. As this is a non MAPK driven genetically engineered model of melanoma our work also has implications for the 15% of cutaneous melanoma patients who lack MAPK driving mutations. Overall design: Single cell RNA sequencing was done on internal vs. external normal adult zebrafish melanocytes using the SORT seq platform.       Cutaneous melanocytes GSM8340240   source name:Cutaneous melanocytes|tissue:Cutaneous melanocytes|cell type:melanocytes|genotype:mitfa / ; roy / fish injected with mitfa:GFP|geo loc name:missing|collection date:missing Cutaneous melanocytes BWA was used to align paired end read to danRer11. Count tables were generated using MapAndGo. Count tables were corrected using UMI to remove duplicate reads. Transcript counts were adjusted using Poissonian counting statistics to yield the number of UMIs detected per cell. Counts were imported into R using the Seurat suite version 3.0 Assembly: danRer11 Supplementary files format and content: .tsv file contains count matrix file used for data normalization and visualization using Seurat Library strategy: SORT seq Cutaneous melanocytes   Respective tissues were mechanically dissociated digested in TrypLE for 45 min Invitrogen 12563011 40uM filtered spun down and resuspended in FACs buffer dPBS Mg+/Ca+ free with 2% FBS pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina. mitfa / ; roy / zebrafish injected with mitfa:GFP were Raised to maturity to obtain tissues tissue:Cutaneous melanocytes|cell type:melanocytes|genotype:mitfa / ; roy / fish injected with mitfa:GFP GSM8340240 GSM8340240: Cutaneous melanocytes; Danio rerio; OTHER GSM8340240 r1 GSM8340240 1 Respective tissues were mechanically dissociated digested in TrypLE for 45 min Invitrogen 12563011 40uM filtered spun down and resuspended in FACs buffer dPBS Mg+/Ca+ free with 2% FBS pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP515140     HAR-MI-001_H5GCWBGXF_R2.fastq.gz HAR-MI-001_H5GCWBGXF_R1.fastq.gz fastq fastq 2680460212.0 31168142.0 GSM8340240 r1 0:26 1:60 A:704357434;C:519158361;G:467098420;T:988838604;N:1007393 26 60     704357434 519158361 467098420 988838604 1007393 SRX24993369 SRS21694833 SRA1904773 Insco Lab, Medical Oncology, Dana Farber Cancer Institute Insco Lab, Medical Oncology, Dana Farber Cancer Institute 2 0.11679 0.81545 0.10693 0.5033 0.9808 0.76404 0.44749 0.57623 26 60 T B sc-like readlen illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   United States 2024-06-20 Undetermined Adult Skin Surface Structure
33837 33837 SRR30763634 SRX26165999 SRS22710780 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin con2 Skin con 3   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin con 3|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin con 3 SK CON 3 SK CON 3 Zebrafish skin at control group     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_con2_Clean_Data1.fq.gz Skin_con2_Clean_Data2.fq.gz fastq fastq 6083362246.0 21717347.0 Skin con2 Clean Data1.fq.gz 0:140.06 1:140.05 A:1575684711;C:1458969719;G:1469933956;T:1578641539;N:132321 140 140     1575684711 1458969719 1469933956 1578641539 132321 SRX26165999 SRS22710780 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33838 33838 SRR30763635 SRX26165998 SRS22710779 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin con1 Skin con 2   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin con 2|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin con 2 SK CON 2 SK CON 2 Zebrafish skin at control group     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_con1_Clean_Data1.fq.gz Skin_con1_Clean_Data2.fq.gz fastq fastq 5776524166.0 20610041.0 Skin con1 Clean Data1.fq.gz 0:140.14 1:140.13 A:1496887200;C:1385008310;G:1395131090;T:1499373290;N:124276 140 140     1496887200 1385008310 1395131090 1499373290 124276 SRX26165998 SRS22710779 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33839 33839 SRR30763636 SRX26165997 SRS22710778 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin con Skin con 1   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin con 1|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin con 1 SK CON 1 SK CON 1 Zebrafish skin at control group     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_con_Clean_Data1.fq.gz Skin_con_Clean_Data2.fq.gz fastq fastq 5304184337.0 18925504.0 Skin con Clean Data1.fq.gz 0:140.14 1:140.13 A:1400015654;C:1245459230;G:1267684230;T:1391013551;N:11672 140 140     1400015654 1245459230 1267684230 1391013551 11672 SRX26165997 SRS22710778 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33840 33840 SRR30763637 SRX26165996 SRS22710777 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin 3dpi2 Skin 3d 3   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 3dpi 3|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin 3d 3 SK 3D 3 SK 3D 3 Zebrafish skin at 3 dpv post immunization with glycoprotein of spring viraemia of carp virus     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_3dpi2_Clean_Data1.fq.gz Skin_3dpi2_Clean_Data2.fq.gz fastq fastq 5528962547.0 19717071.0 Skin 3dpi2 Clean Data1.fq.gz 0:140.21 1:140.20 A:1434889776;C:1319598036;G:1335801562;T:1438550030;N:123143 140 140     1434889776 1319598036 1335801562 1438550030 123143 SRX26165996 SRS22710777 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33841 33841 SRR30763638 SRX26165995 SRS22710776 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin 3dpi1 Skin 3d 2   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 3dpi 2|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin 3d 2 SK 3D 2 SK 3D 2 Zebrafish skin at 3 dpv post immunization with glycoprotein of spring viraemia of carp virus     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_3dpi1_Clean_Data1.fq.gz Skin_3dpi1_Clean_Data2.fq.gz fastq fastq 6045424568.0 21559158.0 Skin 3dpi1 Clean Data1.fq.gz 0:140.21 1:140.20 A:1566211023;C:1442845401;G:1464489674;T:1571745680;N:132790 140 140     1566211023 1442845401 1464489674 1571745680 132790 SRX26165995 SRS22710776 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33842 33842 SRR30763639 SRX26165994 SRS22710775 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin 3dpi Skin 3d 1   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 3dpi 1|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin 3d 1 SK 3D 1 SK 3D 1 Zebrafish skin at 3 dpv post immunization with glycoprotein of spring viraemia of carp virus     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_3dpi_Clean_Data1.fq.gz Skin_3dpi_Clean_Data2.fq.gz fastq fastq 5398897838.0 19388025.0 Skin 3dpi Clean Data1.fq.gz 0:139.24 1:139.23 A:1434301676;C:1260747084;G:1277759027;T:1426077485;N:12566 139 139     1434301676 1260747084 1277759027 1426077485 12566 SRX26165994 SRS22710775 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33843 33843 SRR30763640 SRX26165993 SRS22710774 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin 1dpi2 Skin 1d 3   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 1dpi 3|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin 1d 3 SK 1D 3 SK 1D 3 Zebrafish skin at 1 dpv post immunization with glycoprotein of spring viraemia of carp virus     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_1dpi2_Clean_Data1.fq.gz Skin_1dpi2_Clean_Data2.fq.gz fastq fastq 6317753535.0 22527726.0 Skin 1dpi2 Clean Data1.fq.gz 0:140.23 1:140.22 A:1637469629;C:1508203339;G:1526532646;T:1645411954;N:135967 140 140     1637469629 1508203339 1526532646 1645411954 135967 SRX26165993 SRS22710774 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33844 33844 SRR30763641 SRX26165992 SRS22710773 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin 1dpi1 Skin 1d 2   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 1dpi 2|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin 1d 2 SK 1D 2 SK 1D 2 Zebrafish skin at 1 dpv post immunization with glycoprotein of spring viraemia of carp virus     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_1dpi1_Clean_Data1.fq.gz Skin_1dpi1_Clean_Data2.fq.gz fastq fastq 5665401221.0 20209478.0 Skin 1dpi1 Clean Data1.fq.gz 0:140.17 1:140.16 A:1463485728;C:1359900876;G:1372085350;T:1469804976;N:124291 140 140     1463485728 1359900876 1372085350 1469804976 124291 SRX26165992 SRS22710773 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33845 33845 SRR30763642 SRX26165991 SRS22710772 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin 1dpi Skin 1d 1   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 1dpi 1|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin 1d 1 SK 1D 1 SK 1D 1 Zebrafish skin at 1 dpv post immunization with glycoprotein of spring viraemia of carp virus     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_1dpi_Clean_Data1.fq.gz Skin_1dpi_Clean_Data2.fq.gz fastq fastq 4758945020.0 17104843.0 Skin 1dpi Clean Data1.fq.gz 0:139.12 1:139.11 A:1261511064;C:1113177324;G:1128285977;T:1255959998;N:10657 139 139     1261511064 1113177324 1128285977 1255959998 10657 SRX26165991 SRS22710772 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33892 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 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 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 m…       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 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 m…       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 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 m…       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 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 m…       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 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 m…       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 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 m…       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 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 000rc…   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 000rc… 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 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 000rc…   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 000rc… 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 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 000rc…   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 000rc… 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 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 000rc…   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 000rc… 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
55982 55982 SRR10895887 SRX7564592 SRS6001802 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 007   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Skin|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100101924 L01 9 CL100101924 L01 9       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100101924_L01_550_1.fq.gz CL100101924_L01_550_2.fq.gz fastq fastq 8780226200.0 87802262.0 CL100101924 L01 550 1.fq.gz 0:100 1:100 A:2363664067;C:1983383192;G:2025795704;T:2396528723;N:10854514 100 100     2363664067 1983383192 2025795704 2396528723 10854514 SRX7564592 SRS6001802 SRA1026516 BGI|BGI-Research BGI 1 0.92686   0.10085   0.70903   0.51488   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Skin Surface Structure
55983 55983 SRR10895888 SRX7564591 SRS6001802 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 007   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Skin|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100101924 L01 8 CL100101924 L01 8       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100101924_L01_549_2.fq.gz CL100101924_L01_549_1.fq.gz fastq fastq 9805051200.0 98050512.0 CL100101924 L01 549 1.fq.gz 0:100 1:100 A:2663706429;C:2193838939;G:2241619945;T:2693859046;N:12026841 100 100     2663706429 2193838939 2241619945 2693859046 12026841 SRX7564591 SRS6001802 SRA1026516 BGI|BGI-Research BGI 1 0.92652   0.0983   0.71043   0.53401   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Skin Surface Structure
55984 55984 SRR10895889 SRX7564590 SRS6001802 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 007   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Skin|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100101924 L01 7 CL100101924 L01 7       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100101924_L01_547_1.fq.gz CL100101924_L01_547_2.fq.gz fastq fastq 9137587600.0 91375876.0 CL100101924 L01 547 1.fq.gz 0:100 1:100 A:2471506783;C:2052808667;G:2096159921;T:2505897469;N:11214760 100 100     2471506783 2052808667 2096159921 2505897469 11214760 SRX7564590 SRS6001802 SRA1026516 BGI|BGI-Research BGI 1 0.93126   0.09864   0.70613   0.51947   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Skin Surface Structure
55985 55985 SRR10895890 SRX7564589 SRS6001802 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 007   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Skin|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100101924 L01 6 CL100101924 L01 6       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100101924_L01_551_1.fq.gz CL100101924_L01_551_2.fq.gz fastq fastq 7665129600.0 76651296.0 CL100101924 L01 551 1.fq.gz 0:100 1:100 A:2062939973;C:1731950056;G:1768675635;T:2092110510;N:9453426 100 100     2062939973 1731950056 1768675635 2092110510 9453426 SRX7564589 SRS6001802 SRA1026516 BGI|BGI-Research BGI 1 0.93022   0.10662   0.70512   0.50773   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Skin Surface Structure
55986 55986 SRR10895892 SRX7564587 SRS6001802 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 007   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Skin|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100101924 L01 5 CL100101924 L01 5       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100101924_L01_548_1.fq.gz CL100101924_L01_548_2.fq.gz fastq fastq 6527814200.0 65278142.0 CL100101924 L01 548 1.fq.gz 0:100 1:100 A:1748761735;C:1483522306;G:1516468410;T:1771028617;N:8033132 100 100     1748761735 1483522306 1516468410 1771028617 8033132 SRX7564587 SRS6001802 SRA1026516 BGI|BGI-Research BGI 1 0.93149   0.09371   0.70542   0.51664   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Skin Surface Structure
56585 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. … 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. … 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 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. … 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. … 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 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. … 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. … 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 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. … 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. … 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 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. … 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. … 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 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. … 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. … 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 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. … 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. … 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 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. … 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. … 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
67672 67672 SRR17247005 SRX13426046 SRS11327039 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         D2   isolate:not collected|age:3mpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate D2|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S342 S342 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     d2_R1.fq.gz d2_R2.fq.gz fastq fastq 6774255900.0 22580853.0 d2 R1.fq.gz 0:150 1:150 A:1901164418;C:1468805326;G:1485945297;T:1918188680;N:152179 150 150     1901164418 1468805326 1485945297 1918188680 152179 SRX13426046 SRS11327039 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.94179 0.94443 0.0891 0.08968 0.7331 0.73513 0.62221 0.62339 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Adult Adult Skin Surface Structure
67673 67673 SRR17247006 SRX13426045 SRS11327038 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         D1   isolate:not collected|age:3mpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate D1|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S341 S341 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     d1_R1.fq.gz d1_R2.fq.gz fastq fastq 5804251200.0 19347504.0 d1 R1.fq.gz 0:150 1:150 A:1651195300;C:1234370632;G:1251804070;T:1666750262;N:130936 150 150     1651195300 1234370632 1251804070 1666750262 130936 SRX13426045 SRS11327038 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.83287 0.83611 0.08737 0.08841 0.7498 0.75162 0.64045 0.66425 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Adult Adult Skin Surface Structure
67674 67674 SRR17247007 SRX13426044 SRS11327036 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         C3   isolate:not collected|age:41dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate C3|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S340 S340 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     c3_R1.fq.gz c3_R2.fq.gz fastq fastq 4841497500.0 16138325.0 c3 R1.fq.gz 0:150 1:150 A:1386818341;C:1017922211;G:1041712160;T:1394940280;N:104508 150 150     1386818341 1017922211 1041712160 1394940280 104508 SRX13426044 SRS11327036 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.90078 0.9042 0.12147 0.12291 0.73184 0.73497 0.57479 0.5555 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67675 67675 SRR17247008 SRX13426043 SRS11327037 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         C2   isolate:not collected|age:41dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate C2|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S339 S339 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     c2_R1.fq.gz c2_R2.fq.gz fastq fastq 7688124900.0 25627083.0 c2 R1.fq.gz 0:150 1:150 A:2102172030;C:1722525598;G:1752732030;T:2110524143;N:171099 150 150     2102172030 1722525598 1752732030 2110524143 171099 SRX13426043 SRS11327037 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.8669 0.86816 0.08761 0.08688 0.70725 0.71145 0.49101 0.48619 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67676 67676 SRR17247009 SRX13426042 SRS11327035 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         C1   isolate:not collected|age:41dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate C1|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S338 S338 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     c1_R1.fq.gz c1_R2.fq.gz fastq fastq 7456776900.0 24855923.0 c1 R1.fq.gz 0:150 1:150 A:2051878608;C:1656315578;G:1687161312;T:2061254398;N:167004 150 150     2051878608 1656315578 1687161312 2061254398 167004 SRX13426042 SRS11327035 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.82556 0.82709 0.09055 0.08946 0.70471 0.70857 0.48138 0.4916 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67677 67677 SRR17247010 SRX13426041 SRS11327033 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         B3   isolate:not collected|age:33dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate B3|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S337 S337 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     b3_R1.fq.gz b3_R2.fq.gz fastq fastq 9228717900.0 30762393.0 b3 R1.fq.gz 0:150 1:150 A:2487982964;C:2099691030;G:2134638107;T:2506202131;N:203668 150 150     2487982964 2099691030 2134638107 2506202131 203668 SRX13426041 SRS11327033 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.66624 0.66885 0.06853 0.06779 0.71887 0.72066 0.4895 0.49681 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67678 67678 SRR17247011 SRX13426040 SRS11327034 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         B2   isolate:not collected|age:33dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate B2|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S336 S336 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     b2_R1.fq.gz b2_R2.fq.gz fastq fastq 6040557600.0 20135192.0 b2 R1.fq.gz 0:150 1:150 A:1664821294;C:1338719408;G:1359251973;T:1677628310;N:136615 150 150     1664821294 1338719408 1359251973 1677628310 136615 SRX13426040 SRS11327034 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.93426 0.93571 0.10066 0.10055 0.69631 0.69897 0.47588 0.46263 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67679 67679 SRR17247012 SRX13426039 SRS11327032 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         B1   isolate:not collected|age:33dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate B1|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S335 S335 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     b1_R1.fq.gz b1_R2.fq.gz fastq fastq 6368555100.0 21228517.0 b1 R1.fq.gz 0:150 1:150 A:1748027301;C:1419234076;G:1440533749;T:1760617536;N:142438 150 150     1748027301 1419234076 1440533749 1760617536 142438 SRX13426039 SRS11327032 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.93385 0.93455 0.09654 0.09586 0.70031 0.70274 0.4679 0.47428 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67680 67680 SRR17247013 SRX13426038 SRS11327030 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         D3   isolate:not collected|age:3mpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate D3|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S343 S343 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     d3_R2.fq.gz d3_R1.fq.gz fastq fastq 4661307000.0 15537690.0 d3 R1.fq.gz 0:150 1:150 A:1335395274;C:980634616;G:990646677;T:1354525081;N:105352 150 150     1335395274 980634616 990646677 1354525081 105352 SRX13426038 SRS11327030 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.55593 0.55991 0.04498 0.04594 0.79884 0.80079 0.51906 0.50799 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Adult Adult Skin Surface Structure

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;