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,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,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,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,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,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,SRR25764099,SRX21486772,SRS18719072,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,Adult itgb4+ basal cells,GSM7734879,,tissue:epidermal cells|cell type:adult fin epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing,Adult itgb4+ basal cells,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:adult fin epidermal basal cells|genotype:Tgitgb4:mcherry,GSM7734879,GSM7734879: Adult itgb4+ basal cells; Danio rerio; RNA Seq,GSM7734879 r1,GSM7734879,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,Adult_itgb4mcherry_S230_R1_001.fastq.gz Adult_itgb4mcherry_S230_R2_001.fastq.gz,fastq fastq,5035430000.0,12588575.0,GSM7734879 r1,0:200 1:200,A:1339392170;C:1117195164;G:1254708952;T:1323174485;N:959229,200,200,,,1339392170,1117195164,1254708952,1323174485,959229,SRX21486772,SRS18719072,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.01543,0.02468,0.00098,0.00102,0.99318,0.99387,0.47878,0.31718,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Adult,Adult,Skin,Surface Structure
25298,SRR25764100,SRX21486771,SRS18719071,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,1 dpf itgb4+ embryonic basal precursors rep2,GSM7734878,,tissue:epidermal cells|cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing,1 dpf itgb4+ embryonic basal precursors rep2,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry,GSM7734878,GSM7734878: 1 dpf itgb4+ embryonic basal precursors rep2; Danio rerio; RNA Seq,GSM7734878 r1,GSM7734878,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,itgb4mcherry_2_S229_R1_001.fastq.gz itgb4mcherry_2_S229_R2_001.fastq.gz,fastq fastq,6040245600.0,15100614.0,GSM7734878 r1,0:200 1:200,A:1588346322;C:1356558310;G:1524614760;T:1569583583;N:1142625,200,200,,,1588346322,1356558310,1524614760,1569583583,1142625,SRX21486771,SRS18719071,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.0156,0.0191,0.00074,0.00093,0.99024,0.99088,0.47058,0.47838,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Multi-stage,Multi-stage,Skin,Surface Structure
25299,SRR25764101,SRX21486770,SRS18719070,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,1 dpf itgb4+ embryonic basal precursors rep1,GSM7734877,,tissue:epidermal cells|cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing,1 dpf itgb4+ embryonic basal precursors rep1,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry,GSM7734877,GSM7734877: 1 dpf itgb4+ embryonic basal precursors rep1; Danio rerio; RNA Seq,GSM7734877 r1,GSM7734877,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,itgb4mcherry_1_S20_R1_001.fastq.gz itgb4mcherry_1_S20_R2_001.fastq.gz,fastq fastq,7055215600.0,17638039.0,GSM7734877 r1,0:200 1:200,A:1894635584;C:1556854856;G:1769420212;T:1825520802;N:8784146,200,200,,,1894635584,1556854856,1769420212,1825520802,8784146,SRX21486770,SRS18719070,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.01135,0.01881,0.00043,0.00016,0.9932,0.99543,0.46234,0.43106,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Multi-stage,Multi-stage,Skin,Surface Structure
25300,SRR25764102,SRX21486769,SRS18719069,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,1 dpf krt4+ embryonic periderm cells rep2,GSM7734876,,tissue:epidermal cells|cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp|geo loc name:missing|collection date:missing,1 dpf krt4+ embryonic periderm cells rep2,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp,GSM7734876,GSM7734876: 1 dpf krt4+ embryonic periderm cells rep2; Danio rerio; RNA Seq,GSM7734876 r1,GSM7734876,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,krt4cre-gfp_2_S4_R2_001.fastq.gz krt4cre-gfp_2_S4_R1_001.fastq.gz,fastq fastq,9439207600.0,23598019.0,GSM7734876 r1,0:200 1:200,A:2499982675;C:2086665360;G:2395002073;T:2454282285;N:3275207,200,200,,,2499982675,2086665360,2395002073,2454282285,3275207,SRX21486769,SRS18719069,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.44931,0.01877,0.02236,0.00115,0.80012,0.99032,0.45473,0.49453,200,200,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Multi-stage,Multi-stage,Skin,Surface Structure
25301,SRR25764103,SRX21486768,SRS18719066,SRP457109,PRJNA1009810,Live tracking of basal stem cells of the epidermis during growth  homeostasis  and injury response in zebrafish,GSE241757,Transcriptome Analysis,Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however  this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here  we report integrin b4 itgb4 is a useful marker for basal cell labelling  irrespective of the body region  stage  and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells  including those in fins  became quiescent in the adult stage  genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate  depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf  we isolated itgb4+ basal precursors  krt4+ periderm cells from zebrafish embryos at 1 dpf  and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors  embryonic periderm  and adult basal cells.,,pubmed:38265193,,1 dpf krt4+ embryonic periderm cells rep1,GSM7734875,,tissue:epidermal cells|cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp|geo loc name:missing|collection date:missing,1 dpf krt4+ embryonic periderm cells rep1,High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id  length  Genebank id  RNA type  gene name  product  raw count  RPKM and TPM values.,epidermal cells,Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.,Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.,cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp,GSM7734875,GSM7734875: 1 dpf krt4+ embryonic periderm cells rep1; Danio rerio; RNA Seq,GSM7734875 r1,GSM7734875,1,The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP457109,,,krt4cre-gfp_1_S19_R2_001.fastq.gz krt4cre-gfp_1_S19_R1_001.fastq.gz,fastq fastq,6119547200.0,15298868.0,GSM7734875 r1,0:200 1:200,A:1642059769;C:1349462427;G:1535937964;T:1584527048;N:7559992,200,200,,,1642059769,1349462427,1535937964,1584527048,7559992,SRX21486768,SRS18719066,SRA1700438,"Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology","Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology",2,0.01112,0.01017,0.0003,0.00014,0.9931,0.99586,0.43605,0.40821,200,200,T,T,mates < 9% mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2023-08-28,Multi-stage,Multi-stage,Skin,Surface Structure
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,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,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,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,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,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,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,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,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
36717,SRR835162,SRX271958,SRS416254,SRP021517,PRJNA198908,Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin,GSE46387,Transcriptome Analysis,In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing,,pubmed:23874447,,dm 77h 28 399s62,GSM1129620,,tissue:melanocytes|hpf,dm 77h 28 399s62,Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library,melanocytes,,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,,hpf,GSM1129620,GSM1129620: dm 77h 28 399s62; Danio rerio; RNA Seq,GSM1129620 1,,1,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,GEO Accession:GSM1129620,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP021517,,,,,731276158.0,3620179.0,GSM1129620 r1,0:101 1:101,A:173989639;C:199270484;G:188281318;T:169725601;N:9116,101,101,,,173989639,199270484,188281318,169725601,9116,SRX271958,SRS416254,SRA074390,GEO,"Rob Mitra, Genetics, Washington University",2,0.84122,0.79964,0.02274,0.02168,0.89645,0.89073,0.63341,0.63015,101,101,B,B,biological fallback assumption,illumina,hiseq_era,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2013-04-25,Larval,Larval,Skin,Surface Structure
36718,SRR835161,SRX271957,SRS416253,SRP021517,PRJNA198908,Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin,GSE46387,Transcriptome Analysis,In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing,,pubmed:23874447,,dm 77h 28 399s61,GSM1129619,,tissue:melanocytes|hpf,dm 77h 28 399s61,Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library,melanocytes,,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,,hpf,GSM1129619,GSM1129619: dm 77h 28 399s61; Danio rerio; RNA Seq,GSM1129619 1,,1,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,GEO Accession:GSM1129619,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP021517,,,dm_77h_28_399s61_CACT.fq.bz2 dm_77h_28_399s62_CACT.fq.bz2,fastq fastq,731276158.0,3620179.0,GSM1129619 r1,0:101 1:101,A:173989639;C:199270484;G:188281318;T:169725601;N:9116,101,101,,,173989639,199270484,188281318,169725601,9116,SRX271957,SRS416253,SRA074390,GEO,"Rob Mitra, Genetics, Washington University",2,0.84121,0.79968,0.02287,0.02141,0.89658,0.89051,0.63318,0.63061,101,101,B,B,biological fallback assumption,illumina,hiseq_era,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2013-04-25,Larval,Larval,Skin,Surface Structure
36725,SRR835154,SRX271950,SRS416245,SRP021517,PRJNA198908,Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin,GSE46387,Transcriptome Analysis,In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing,,pubmed:23874447,,dm 77h 25 399s62,GSM1129612,,tissue:melanocytes|hpf,dm 77h 25 399s62,Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library,melanocytes,,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,,hpf,GSM1129612,GSM1129612: dm 77h 25 399s62; Danio rerio; RNA Seq,GSM1129612 1,,1,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,GEO Accession:GSM1129612,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP021517,,,,,1715809008.0,8494104.0,GSM1129612 r1,0:101 1:101,A:405310561;C:444474389;G:467897835;T:398105078;N:21145,101,101,,,405310561,444474389,467897835,398105078,21145,SRX271950,SRS416245,SRA074390,GEO,"Rob Mitra, Genetics, Washington University",2,0.66327,0.58026,0.07911,0.07288,0.91721,0.9083,0.56907,0.5363,101,101,B,B,biological fallback assumption,illumina,hiseq_era,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2013-04-25,Larval,Larval,Skin,Surface Structure
36726,SRR835153,SRX271949,SRS416246,SRP021517,PRJNA198908,Gene Expression Analysis of Zebrafish Melanocytes  Iridophores  and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin,GSE46387,Transcriptome Analysis,In order to facilitate understanding of pigment cell biology  we developed a method to concomitantly purify melanocytes  iridophores  and retinal pigmented epithelium from zebrafish  and analyzed their transcriptomes.  Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium  as well as in melanocytes and iridophores.  We found 214 genes co enriched in melanocytes and retinal pigmented epithelium  indicating the shared functions of melanin producing cells.  We found 62 genes significantly co enriched in melanocytes and iridophores  illustrative of their shared developmental origins from the neural crest.  This is also the first analysis of the iridophore transcriptome.  Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment.  We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis  phosphoribosyl pyrophosphate  thus constituting a guanine cycle.  The purification procedure and expression analysis described here  along with the accompanying transcriptome wide expression data  provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types  and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing,,pubmed:23874447,,dm 77h 25 399s61,GSM1129611,,tissue:melanocytes|hpf,dm 77h 25 399s61,Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013  based on NCBI's RefSeq build from 8/29/2012  current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library,melanocytes,,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,,hpf,GSM1129611,GSM1129611: dm 77h 25 399s61; Danio rerio; RNA Seq,GSM1129611 1,,1,This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236.  Zebrafish were reared and bred according to standard protocols.  The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor  mitfavc7.  This mutant facilitated the collection of RPE  as mitfa is not required for RPE development in zebrafish.  Melanocytes  iridophores  and RPE develop normally at 25°C in mitfavc7.  When held at 32°C  the neural crest derived melanocytes do not develop  but RPE and iridophores develop normally.  All melanocyte and iridophore samples were incubated at 25°C prior to collection.  Fish were anesthetized with Tricaine  rinsed with Ca   Mg  DPBS Sigma  D8537  and immersed in 100mL TrypLE Express Invitrogen  12604039 per 1000 fish.  Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes  followed by trituration with a Pasteur pipette to remove eyes from larva.  post separation of eyes and larva  each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr.  Dissociated cells were filtered through a 120uM screen into 50 mL tubes.  Remaining intact tissue was triturated 10 20 times  and again filtered through a 120uM screen into the dissociated cells.  Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C  then resuspended in 1mL cold isotonic Percoll Sigma  P1644 by gentle pipetting.  Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll.  Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation.  Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS  and placed onto preformed Percoll density gradients.  Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rcf for 15 minutes at 4°C in a fixed angle micro centrifuge Eppendorf 5415 R.  Tubes containing preformed Percoll gradients with overlying cell suspensions were centrifuged in a swinging bucket rotor at 2000rcf for 10 minutes at 4°C.  Following centrifugation  overlying Percoll was aspirated  leaving the final 100µL containing the pigment cell pellet.  Cells were resuspended with 50µL of cold DPBS with 2% FCS and transferred to a clean 1.6mL tube containing 500µL of cold DPBS with 2% FCS  and kept on ice until mRNA extraction or FACS.      FACS   We used the inherent properties of the pigmented cells to perform Fluorescence Activated Cell Sorting FACS.  Following resuspension in 500µL cold DPBS with 2% FCS  the enriched cell populations were screened through a 30uM cell filter Partec  04 0042 2316.  Cells were analyzed and sorted with a Dako MoFlo cell sorter using a 120uM nozzle at a drop drive DD frequency of 22390Hz.  Cells were illuminated using a 488 nm laser.  Cells were gated on two attributes to separate cells from each other and from cellular debris.  Cellular debris was detected using forward and side scatter  selecting against the smallest particles 1µm or less.  Cells were sorted based on detection using 510 530nm and 575 595nm filters  corresponding to FL1 and FL2 in Figure 1D  respectively.  When excited by the 488 nm laser  the autofluorescence of iridophores is clearly detectable in these channels as a group of cells extending at a 45 degree line in the upper right quadrant.  Melanocytes and RPE do not autofluoresce with this intensity when excited by the 488nm laser  and cluster at the lower left of the FACS plot.  Cells were collected into ice cold DPBS with 2% FCS and kept on ice until mRNA extraction. Pigment cell cDNA library construction was as follows.  For mRNA extraction the Dynabeads® mRNA DIRECT Kit Invitrogen was used per manufacturer's instructions.  Following mRNA elution from the Dynabeads  first strand cDNA synthesis was performed using MMLV reverse transcriptase Clontech using an anchored polyT primer tailed with a universal primer sequence See Table S3 for primer sequences and Figure 2 for pigment cell cDNA library construction overview.  A universal primer sequence was also added to the three prime end of the first strand by template switching  allowing for PCR amplification of the resultant cDNA  [43 44].  Following PCR amplification using the high fidelity polymerase LA Taq TaKaRa   PCR cycle: 95C for 1 minute  followed by 20 cycles of 98C for 25 seconds  60C for 1 minute  68C for 20 minutes  cDNA was digested with AluI and RsaI restriction enzymes NEB.  Blunt end enzymatic fragmentation of cDNA was used instead of sonication and gel extraction to minimize loss of sample material and eliminate the end repair step of Illumina library preparation.  Since this reduced representation strategy might miss short cDNAs that lack both restriction sites  we sought to avoid this by including enzyme recognition sites within the cDNA amplification primers.  This allows for the inclusion of short cDNAs in our libraries.  Standard Illumina library preparations followed  performed by the Genome Technology Access Center GTAC at Washington University in St. Louis http://gtac.wustl.edu.  In brief  a single A was added to the 3’ end of each strand  Y adapters ligated  and library enrichment PCR performed  followed by gel extraction size selection for fragments ranging from 200 400 base pairs in length.  Illumina library construction of pooled 3dpf embryos was performed by GTAC from total RNA extracted with Trizol reagent as previously described [45].  No PCR amplification of whole embryo cDNA was performed prior to Illumina adapter ligation and library enrichment.  Sequencing was performed on the GAIIX Illumina platform.,GEO Accession:GSM1129611,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP021517,,,dm_77h_25_399s61_TCTT.fq.bz2 dm_77h_25_399s62_TCTT.fq.bz2,fastq fastq,1715809008.0,8494104.0,GSM1129611 r1,0:101 1:101,A:405310561;C:444474389;G:467897835;T:398105078;N:21145,101,101,,,405310561,444474389,467897835,398105078,21145,SRX271949,SRS416246,SRA074390,GEO,"Rob Mitra, Genetics, Washington University",2,0.66325,0.58027,0.0792,0.07327,0.91741,0.90847,0.56374,0.53632,101,101,B,B,biological fallback assumption,illumina,hiseq_era,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2013-04-25,Larval,Larval,Skin,Surface Structure
53011,SRR9662028,SRX6422904,SRS5079694,SRP213938,PRJNA553572,A map of cis regulatory elements and 3D genome structures in zebrafish,GSE134055,Other,The zebrafish has been widely used for the study of human disease and development  as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome  however  has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects  we performed RNA seq  ATAC seq  ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall  we have identified 235 596 cis regulatory elements  which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish  human  and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore  through the analysis of Hi C data in zebrafish brain and muscle  we observed different levels of 3D genome organization  including compartment  topological associating domains TADs  and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and  embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3  RNA Seq  11 of them were examined using ATAC seq  WGBS and ChIP seq H3K9me3 and H3K9me2  and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that  for the samples GSM4661977 GSM4662088  [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.,,pubmed:33239788;pubmed:35649578,,YueLab RNA Seq Skin rep2,GSM3934896,,source name:Tissue|strain:Tuebingen|tissue:Skin,YueLab RNA Seq Skin rep2,RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following  setting: ChIP seq q value <10e 2  p value<10e 5  Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged,Tissue,,For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.,Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions,strain:Tuebingen|tissue:Skin,GSM3934896,GSM3934896: YueLab RNA Seq Skin rep2; Danio rerio; RNA Seq,GSM3934896,,1,For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.,GEO Accession:GSM3934896,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer,,SRP213938,,,YueLab-RNA-Seq-Skin-rep2_1.fastq.gz YueLab-RNA-Seq-Skin-rep2_2.fastq.gz,fastq fastq,3369540489.0,27929926.0,GSM3934896 r1,0:60.47 1:60.17,A:881257889;C:784720097;G:773160075;T:930047288;N:355140,60,60,,,881257889,784720097,773160075,930047288,355140,SRX6422904,SRS5079694,SRA919194,GEO,"Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine",2,0.96098,0.96359,0.1219,0.11985,0.69962,0.70161,0.48503,0.4877,61,60,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-07-09,Pharyngula,Embryo,Skin,Surface Structure
53012,SRR9662027,SRX6422903,SRS5079693,SRP213938,PRJNA553572,A map of cis regulatory elements and 3D genome structures in zebrafish,GSE134055,Other,The zebrafish has been widely used for the study of human disease and development  as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome  however  has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects  we performed RNA seq  ATAC seq  ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall  we have identified 235 596 cis regulatory elements  which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish  human  and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore  through the analysis of Hi C data in zebrafish brain and muscle  we observed different levels of 3D genome organization  including compartment  topological associating domains TADs  and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and  embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3  RNA Seq  11 of them were examined using ATAC seq  WGBS and ChIP seq H3K9me3 and H3K9me2  and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that  for the samples GSM4661977 GSM4662088  [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.,,pubmed:33239788;pubmed:35649578,,YueLab RNA Seq Skin rep1,GSM3934895,,source name:Tissue|strain:Tuebingen|tissue:Skin,YueLab RNA Seq Skin rep1,RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following  setting: ChIP seq q value <10e 2  p value<10e 5  Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged,Tissue,,For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.,Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions,strain:Tuebingen|tissue:Skin,GSM3934895,GSM3934895: YueLab RNA Seq Skin rep1; Danio rerio; RNA Seq,GSM3934895,,1,For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.,GEO Accession:GSM3934895,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer,,SRP213938,,,YueLab-RNA-Seq-Skin-rep1_1.fastq.gz YueLab-RNA-Seq-Skin-rep1_2.fastq.gz,fastq fastq,2565035707.0,21260839.0,GSM3934895 r1,0:60.48 1:60.17,A:670789880;C:599392091;G:585931498;T:708654706;N:267532,60,60,,,670789880,599392091,585931498,708654706,267532,SRX6422903,SRS5079693,SRA919194,GEO,"Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine",2,0.96148,0.96283,0.12215,0.11903,0.70015,0.70114,0.47321,0.47375,60,60,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-07-09,Pharyngula,Embryo,Skin,Surface Structure
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,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,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,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,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
59125,SRR11684038,SRX8244841,SRS6592476,SRP259990,PRJNA630162,Zebrafish adult skin mpeg+ cells,GSE149788,Transcriptome Analysis,We compared hematopoietic and non hematopoietic mpeg1.1+ cells from the skin of wild type fish with non hematopoietic cells from the skin of zebrafish lacking functional csf1r. We reval that non hematopoietic mpeg1.1 cells from wild type and csf1rDM fish show no major differences and likely represent metaphocytes  a newly characterized ectoderm derived cell population in the skin. Both non hematopoietic mpeg1.1+ cell populations from wild type and csf1r mutatns show a major downregulations in canonical macrophages signature genes as compared to hematopoietic mpeg1.1 cells from wild type fish. Overall design: Two biological replicates were analyzed for each of 6 conditions three genotypes; two treatments per genotype,parent bioproject:PRJNA630158,pubmed:32367800,,GFE6 Csf1r mutant.3,GSM4512730,,tissue:skin mpeg1.1 GFP+ cells|developmental stage:adult 3mo|genotype:csf1raj4e1/j4e1; csf1rbsa1503/csf1rbsa1503 mpeg1 EGFP; Kdrl:Cre; act2b:loxP STOP loxP DsRedexpress|treatment:untreated,GFE6 Csf1r mutant.3,Sequencing and base calling was performed on the IlIllumina Novaseq 6000 Paired end reads were aligned to the GRCz11.94 danio rerio genome using  STAR version 2.5.4b software. Annotations Danio rerio.GRCz11.94.gtf were obtained from ftp.Ensembl.org Gene level counts were obtained using HTSeq count version 0.11.0 Differential gene expression analysis: EdgeR Bioconductor. GSEA: GAGE Bioconductor Genome build: GRCz11.94 Supplementary files format and content: CPM values [.csv] semicolon delimited files,skin mpeg1.1 GFP+ cells,,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,Standard adult zebrafish rearing conditions in multilink system at  26° C  with 12:12 h ligt/dark cycle,developmental stage:adult 3mo|genotype:csf1raj4e1/j4e1; csf1rbsa1503/csf1rbsa1503 mpeg1 EGFP; Kdrl:Cre; act2b:loxP STOP loxP DsRedexpress|treatment:untreated,GSM4512730,GSM4512730: GFE6 Csf1r mutant.3; Danio rerio; RNA Seq,GSM4512730,,1,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,GEO Accession:GSM4512730,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP259990,,,so-zf94_GFE6-Csf1r-mutant_S6_R2_001.fastq.gz so-zf94_GFE6-Csf1r-mutant_S6_R1_001.fastq.gz,fastq fastq,14494840876.0,71756638.0,GSM4512730 r1,0:101 1:101,A:3899647300;C:3479135941;G:3237570754;T:3878261390;N:225491,101,101,,,3899647300,3479135941,3237570754,3878261390,225491,SRX8244841,SRS6592476,SRA1072141,GEO,Erasmus MC,2,0.64161,0.64139,0.26871,0.27571,0.80827,0.80687,0.57871,0.57509,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2020-05-04,Adult,Adult,Skin,Surface Structure
59126,SRR11684037,SRX8244840,SRS6592475,SRP259990,PRJNA630162,Zebrafish adult skin mpeg+ cells,GSE149788,Transcriptome Analysis,We compared hematopoietic and non hematopoietic mpeg1.1+ cells from the skin of wild type fish with non hematopoietic cells from the skin of zebrafish lacking functional csf1r. We reval that non hematopoietic mpeg1.1 cells from wild type and csf1rDM fish show no major differences and likely represent metaphocytes  a newly characterized ectoderm derived cell population in the skin. Both non hematopoietic mpeg1.1+ cell populations from wild type and csf1r mutatns show a major downregulations in canonical macrophages signature genes as compared to hematopoietic mpeg1.1 cells from wild type fish. Overall design: Two biological replicates were analyzed for each of 6 conditions three genotypes; two treatments per genotype,parent bioproject:PRJNA630158,pubmed:32367800,,GFE5 Csf1r mutant.2,GSM4512729,,tissue:skin mpeg1.1 GFP+ cells|developmental stage:adult 3mo|genotype:csf1raj4e1/j4e1; csf1rbsa1503/csf1rbsa1503 tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated,GFE5 Csf1r mutant.2,Sequencing and base calling was performed on the IlIllumina Novaseq 6000 Paired end reads were aligned to the GRCz11.94 danio rerio genome using  STAR version 2.5.4b software. Annotations Danio rerio.GRCz11.94.gtf were obtained from ftp.Ensembl.org Gene level counts were obtained using HTSeq count version 0.11.0 Differential gene expression analysis: EdgeR Bioconductor. GSEA: GAGE Bioconductor Genome build: GRCz11.94 Supplementary files format and content: CPM values [.csv] semicolon delimited files,skin mpeg1.1 GFP+ cells,,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,Standard adult zebrafish rearing conditions in multilink system at  26° C  with 12:12 h ligt/dark cycle,developmental stage:adult 3mo|genotype:csf1raj4e1/j4e1; csf1rbsa1503/csf1rbsa1503 tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated,GSM4512729,GSM4512729: GFE5 Csf1r mutant.2; Danio rerio; RNA Seq,GSM4512729,,1,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,GEO Accession:GSM4512729,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP259990,,,so-zf94_GFE5-Csf1r-mutant_S5_R2_001.fastq.gz so-zf94_GFE5-Csf1r-mutant_S5_R1_001.fastq.gz,fastq fastq,13759568552.0,68116676.0,GSM4512729 r1,0:101 1:101,A:3660704043;C:3344175315;G:3105211222;T:3649262807;N:215165,101,101,,,3660704043,3344175315,3105211222,3649262807,215165,SRX8244840,SRS6592475,SRA1072141,GEO,Erasmus MC,2,0.69777,0.70166,0.28564,0.29683,0.79945,0.80022,0.58707,0.58207,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2020-05-04,Adult,Adult,Skin,Surface Structure
59127,SRR11684036,SRX8244839,SRS6592474,SRP259990,PRJNA630162,Zebrafish adult skin mpeg+ cells,GSE149788,Transcriptome Analysis,We compared hematopoietic and non hematopoietic mpeg1.1+ cells from the skin of wild type fish with non hematopoietic cells from the skin of zebrafish lacking functional csf1r. We reval that non hematopoietic mpeg1.1 cells from wild type and csf1rDM fish show no major differences and likely represent metaphocytes  a newly characterized ectoderm derived cell population in the skin. Both non hematopoietic mpeg1.1+ cell populations from wild type and csf1r mutatns show a major downregulations in canonical macrophages signature genes as compared to hematopoietic mpeg1.1 cells from wild type fish. Overall design: Two biological replicates were analyzed for each of 6 conditions three genotypes; two treatments per genotype,parent bioproject:PRJNA630158,pubmed:32367800,,GFE4 B Switch.1,GSM4512728,,tissue:skin mpeg1.1 GFP+; act2b:loxP STOP loxP DsRedexpress+ cells|developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated,GFE4 B Switch.1,Sequencing and base calling was performed on the IlIllumina Novaseq 6000 Paired end reads were aligned to the GRCz11.94 danio rerio genome using  STAR version 2.5.4b software. Annotations Danio rerio.GRCz11.94.gtf were obtained from ftp.Ensembl.org Gene level counts were obtained using HTSeq count version 0.11.0 Differential gene expression analysis: EdgeR Bioconductor. GSEA: GAGE Bioconductor Genome build: GRCz11.94 Supplementary files format and content: CPM values [.csv] semicolon delimited files,skin mpeg1.1 GFP+;  act2b:loxP STOP loxP DsRedexpress+ cells,,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,Standard adult zebrafish rearing conditions in multilink system at  26° C  with 12:12 h ligt/dark cycle,developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated,GSM4512728,GSM4512728: GFE4 B Switch.1; Danio rerio; RNA Seq,GSM4512728,,1,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,GEO Accession:GSM4512728,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP259990,,,so-zf94_GFE4-B-Switch_WT_S4_R2_001.fastq.gz so-zf94_GFE4-B-Switch_WT_S4_R1_001.fastq.gz,fastq fastq,10963685744.0,54275672.0,GSM4512728 r1,0:101 1:101,A:2843051618;C:2733369632;G:2559200274;T:2827894333;N:169887,101,101,,,2843051618,2733369632,2559200274,2827894333,169887,SRX8244839,SRS6592474,SRA1072141,GEO,Erasmus MC,2,0.81437,0.80007,0.30275,0.3056,0.7933,0.79427,0.60512,0.50903,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2020-05-04,Adult,Adult,Skin,Surface Structure
59128,SRR11684035,SRX8244838,SRS6592477,SRP259990,PRJNA630162,Zebrafish adult skin mpeg+ cells,GSE149788,Transcriptome Analysis,We compared hematopoietic and non hematopoietic mpeg1.1+ cells from the skin of wild type fish with non hematopoietic cells from the skin of zebrafish lacking functional csf1r. We reval that non hematopoietic mpeg1.1 cells from wild type and csf1rDM fish show no major differences and likely represent metaphocytes  a newly characterized ectoderm derived cell population in the skin. Both non hematopoietic mpeg1.1+ cell populations from wild type and csf1r mutatns show a major downregulations in canonical macrophages signature genes as compared to hematopoietic mpeg1.1 cells from wild type fish. Overall design: Two biological replicates were analyzed for each of 6 conditions three genotypes; two treatments per genotype,parent bioproject:PRJNA630158,pubmed:32367800,,GFE3 B Switch.3,GSM4512727,,tissue:skin mpeg1.1 GFP+; act2b:loxP STOP loxP DsRedexpress+ cells|developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated,GFE3 B Switch.3,Sequencing and base calling was performed on the IlIllumina Novaseq 6000 Paired end reads were aligned to the GRCz11.94 danio rerio genome using  STAR version 2.5.4b software. Annotations Danio rerio.GRCz11.94.gtf were obtained from ftp.Ensembl.org Gene level counts were obtained using HTSeq count version 0.11.0 Differential gene expression analysis: EdgeR Bioconductor. GSEA: GAGE Bioconductor Genome build: GRCz11.94 Supplementary files format and content: CPM values [.csv] semicolon delimited files,skin mpeg1.1 GFP+;  act2b:loxP STOP loxP DsRedexpress+ cells,,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,Standard adult zebrafish rearing conditions in multilink system at  26° C  with 12:12 h ligt/dark cycle,developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated,GSM4512727,GSM4512727: GFE3 B Switch.3; Danio rerio; RNA Seq,GSM4512727,,1,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,GEO Accession:GSM4512727,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP259990,,,so-zf94_GFE3-B-Switch_WT_S3_R2_001.fastq.gz so-zf94_GFE3-B-Switch_WT_S3_R1_001.fastq.gz,fastq fastq,12782078634.0,63277617.0,GSM4512727 r1,0:101 1:101,A:3381512327;C:3122362574;G:2918446203;T:3359558840;N:198690,101,101,,,3381512327,3122362574,2918446203,3359558840,198690,SRX8244838,SRS6592477,SRA1072141,GEO,Erasmus MC,2,0.76741,0.76247,0.29132,0.2981,0.78512,0.78561,0.58337,0.57753,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2020-05-04,Adult,Adult,Skin,Surface Structure
59129,SRR11684034,SRX8244837,SRS6595814,SRP259990,PRJNA630162,Zebrafish adult skin mpeg+ cells,GSE149788,Transcriptome Analysis,We compared hematopoietic and non hematopoietic mpeg1.1+ cells from the skin of wild type fish with non hematopoietic cells from the skin of zebrafish lacking functional csf1r. We reval that non hematopoietic mpeg1.1 cells from wild type and csf1rDM fish show no major differences and likely represent metaphocytes  a newly characterized ectoderm derived cell population in the skin. Both non hematopoietic mpeg1.1+ cell populations from wild type and csf1r mutatns show a major downregulations in canonical macrophages signature genes as compared to hematopoietic mpeg1.1 cells from wild type fish. Overall design: Two biological replicates were analyzed for each of 6 conditions three genotypes; two treatments per genotype,parent bioproject:PRJNA630158,pubmed:32367800,,GFE2 WT.2,GSM4512726,,tissue:skin mpeg1.1 GFP+ cells|developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated,GFE2 WT.2,Sequencing and base calling was performed on the IlIllumina Novaseq 6000 Paired end reads were aligned to the GRCz11.94 danio rerio genome using  STAR version 2.5.4b software. Annotations Danio rerio.GRCz11.94.gtf were obtained from ftp.Ensembl.org Gene level counts were obtained using HTSeq count version 0.11.0 Differential gene expression analysis: EdgeR Bioconductor. GSEA: GAGE Bioconductor Genome build: GRCz11.94 Supplementary files format and content: CPM values [.csv] semicolon delimited files,skin mpeg1.1 GFP+ cells,,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,Standard adult zebrafish rearing conditions in multilink system at  26° C  with 12:12 h ligt/dark cycle,developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated,GSM4512726,GSM4512726: GFE2 WT.2; Danio rerio; RNA Seq,GSM4512726,,1,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,GEO Accession:GSM4512726,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP259990,,,so-zf94_GFE2-WT_S2_R1_001.fastq.gz so-zf94_GFE2-WT_S2_R2_001.fastq.gz,fastq fastq,14364066682.0,71109241.0,GSM4512726 r1,0:101 1:101,A:3728039055;C:3584760331;G:3349868256;T:3701175176;N:223864,101,101,,,3728039055,3584760331,3349868256,3701175176,223864,SRX8244837,SRS6595814,SRA1072141,GEO,Erasmus MC,2,0.84099,0.82969,0.32553,0.33066,0.79226,0.79145,0.6061,0.60266,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2020-05-04,Adult,Adult,Skin,Surface Structure
59130,SRR11684033,SRX8244836,SRS6592473,SRP259990,PRJNA630162,Zebrafish adult skin mpeg+ cells,GSE149788,Transcriptome Analysis,We compared hematopoietic and non hematopoietic mpeg1.1+ cells from the skin of wild type fish with non hematopoietic cells from the skin of zebrafish lacking functional csf1r. We reval that non hematopoietic mpeg1.1 cells from wild type and csf1rDM fish show no major differences and likely represent metaphocytes  a newly characterized ectoderm derived cell population in the skin. Both non hematopoietic mpeg1.1+ cell populations from wild type and csf1r mutatns show a major downregulations in canonical macrophages signature genes as compared to hematopoietic mpeg1.1 cells from wild type fish. Overall design: Two biological replicates were analyzed for each of 6 conditions three genotypes; two treatments per genotype,parent bioproject:PRJNA630158,pubmed:32367800,,GFE1 WT.1,GSM4512725,,tissue:skin mpeg1.1 GFP+ cells|developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated,GFE1 WT.1,Sequencing and base calling was performed on the IlIllumina Novaseq 6000 Paired end reads were aligned to the GRCz11.94 danio rerio genome using  STAR version 2.5.4b software. Annotations Danio rerio.GRCz11.94.gtf were obtained from ftp.Ensembl.org Gene level counts were obtained using HTSeq count version 0.11.0 Differential gene expression analysis: EdgeR Bioconductor. GSEA: GAGE Bioconductor Genome build: GRCz11.94 Supplementary files format and content: CPM values [.csv] semicolon delimited files,skin mpeg1.1 GFP+ cells,,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,Standard adult zebrafish rearing conditions in multilink system at  26° C  with 12:12 h ligt/dark cycle,developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated,GSM4512725,GSM4512725: GFE1 WT.1; Danio rerio; RNA Seq,GSM4512725,,1,RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix,GEO Accession:GSM4512725,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP259990,,,so-zf94_GFE1-WT_S1_R2_001.fastq.gz so-zf94_GFE1-WT_S1_R1_001.fastq.gz,fastq fastq,12446480884.0,61616242.0,GSM4512725 r1,0:101 1:101,A:3368704863;C:2968645301;G:2743627645;T:3365306136;N:196939,101,101,,,3368704863,2968645301,2743627645,3365306136,196939,SRX8244836,SRS6592473,SRA1072141,GEO,Erasmus MC,2,0.79126,0.79765,0.31567,0.32746,0.76893,0.76871,0.55753,0.55755,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2020-05-04,Adult,Adult,Skin,Surface Structure
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,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,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,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,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,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,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,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,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
67681,SRR17247014,SRX13426037,SRS11327031,SRP351072,PRJNA789095,Danio rerio Raw sequence reads,PRJNA789095,Whole Genome Sequencing,normal of RNA seq of danio rerio,,,,,A2,,isolate:not collected|age:17dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate A2|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of danio rerio,S334,S334,normal RNA seq of danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP351072,,,A2_S58_R1_001.fastq.gz A2_S58_R2_001.fastq.gz,fastq fastq,5616555000.0,18721850.0,A2 S58 R1 001.fastq.gz,0:150 1:150,A:1448598133;C:1350283389;G:1368707125;T:1446502716;N:2463637,150,150,,,1448598133,1350283389,1368707125,1446502716,2463637,SRX13426037,SRS11327031,SRA1344321,shanghai ocean university|college of marine sciences,shanghai ocean university,2,0.96958,0.97206,0.03246,0.03194,0.74659,0.74809,0.48122,0.48632,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-12-16,Larval,Larval,Skin,Surface Structure
67682,SRR17247015,SRX13426036,SRS11327029,SRP351072,PRJNA789095,Danio rerio Raw sequence reads,PRJNA789095,Whole Genome Sequencing,normal of RNA seq of danio rerio,,,,,A1,,isolate:not collected|age:17dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate A1|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of danio rerio,S333,S333,normal RNA seq of danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP351072,,,A1_S57_R1_001.fastq.gz A1_S57_R2_001.fastq.gz,fastq fastq,4007594400.0,13358648.0,A1 S57 R1 001.fastq.gz,0:150 1:150,A:1045509577;C:951632697;G:972694338;T:1035964441;N:1793347,150,150,,,1045509577,951632697,972694338,1035964441,1793347,SRX13426036,SRS11327029,SRA1344321,shanghai ocean university|college of marine sciences,shanghai ocean university,2,0.96027,0.96204,0.03269,0.03149,0.76686,0.76749,0.44581,0.46233,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2021-12-16,Larval,Larval,Skin,Surface Structure
70110,SRR19561930,SRX15614020,SRS13314715,SRP378802,PRJNA846110,Danio rerio Raw sequence reads,PRJNA846110,Other,Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio,,,,Dr13 3,Dr13 3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:13 replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female 45 13 3 skin,45 13 3 skin,45 13 3 skin,All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2  Vazyme Biotech Co.  Ltd  NR612 02  and subjected to 150bp paired end sequencing on a Novaseq 6052 illumina platform.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP378802,,,45-13-3-skin-RNA_R1.fq.gz 45-13-3-skin-RNA_R2.fq.gz,fastq fastq,8803960200.0,29346534.0,45 13 3 skin RNA R1.fq.gz,0:150 1:150,A:2331850157;C:2044379248;G:2068899530;T:2358671653;N:159612,150,150,,,2331850157,2044379248,2068899530,2358671653,159612,SRX15614020,SRS13314715,SRA1432943,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,2,0.94093,0.93983,0.07299,0.07323,0.70956,0.7175,0.49542,0.49282,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-06-07,Adult,Adult,Skin,Surface Structure
70117,SRR19561937,SRX15614013,SRS13314714,SRP378802,PRJNA846110,Danio rerio Raw sequence reads,PRJNA846110,Other,Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio,,,,Dr13 2,Dr13 2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:13 replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female 40 13 2 skin,40 13 2 skin,40 13 2 skin,All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2  Vazyme Biotech Co.  Ltd  NR612 02  and subjected to 150bp paired end sequencing on a Novaseq 6046 illumina platform.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP378802,,,40-13-2-skin-RNA_R1.fq.gz 40-13-2-skin-RNA_R2.fq.gz,fastq fastq,7384104300.0,24613681.0,40 13 2 skin RNA R1.fq.gz,0:150 1:150,A:1946285906;C:1723958270;G:1744031915;T:1969696634;N:131575,150,150,,,1946285906,1723958270,1744031915,1969696634,131575,SRX15614013,SRS13314714,SRA1432943,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,2,0.93711,0.93654,0.07583,0.07619,0.70329,0.71106,0.49506,0.48489,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-06-07,Adult,Adult,Skin,Surface Structure
70123,SRR19561943,SRX15614007,SRS13314713,SRP378802,PRJNA846110,Danio rerio Raw sequence reads,PRJNA846110,Other,Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio,,,,Dr13 1,Dr13 1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:13 replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female 35 13 1 skin,35 13 1 skin,35 13 1 skin,All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2  Vazyme Biotech Co.  Ltd  NR612 02  and subjected to 150bp paired end sequencing on a Novaseq 6040 illumina platform.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP378802,,,35-13-1-skin-RNA_R1.fq.gz 35-13-1-skin-RNA_R2.fq.gz,fastq fastq,7048170000.0,23493900.0,35 13 1 skin RNA R1.fq.gz,0:150 1:150,A:1853436919;C:1646809377;G:1671470350;T:1876315196;N:138158,150,150,,,1853436919,1646809377,1671470350,1876315196,138158,SRX15614007,SRS13314713,SRA1432943,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,2,0.94089,0.9437,0.07696,0.07752,0.71269,0.71672,0.48203,0.48846,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-06-07,Adult,Adult,Skin,Surface Structure
70124,SRR19561944,SRX15614006,SRS13314707,SRP378802,PRJNA846110,Danio rerio Raw sequence reads,PRJNA846110,Other,Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio,,,,Dr27 1,Dr27 1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:27 replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female 5 27 1 skin,5 27 1 skin,5 27 1 skin,All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2  Vazyme Biotech Co.  Ltd  NR612 02  and subjected to 150bp paired end sequencing on a Novaseq 6004 illumina platform.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP378802,,,5-27-1-skin-RNA_R1.fq.gz 5-27-1-skin-RNA_R2.fq.gz,fastq fastq,7896213300.0,26320711.0,5 27 1 skin RNA R1.fq.gz,0:150 1:150,A:2053107057;C:1861415213;G:1895292332;T:2086241112;N:157586,150,150,,,2053107057,1861415213,1895292332,2086241112,157586,SRX15614006,SRS13314707,SRA1432943,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,2,0.94616,0.94573,0.06222,0.062,0.70711,0.71299,0.46446,0.4685,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-06-07,Adult,Adult,Skin,Surface Structure
70130,SRR19561950,SRX15614000,SRS13314712,SRP378802,PRJNA846110,Danio rerio Raw sequence reads,PRJNA846110,Other,Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio,,,,Dr18 3,Dr18 3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:18 replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female 30 18 3 skin,30 18 3 skin,30 18 3 skin,All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2  Vazyme Biotech Co.  Ltd  NR612 02  and subjected to 150bp paired end sequencing on a Novaseq 6034 illumina platform.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP378802,,,30-18-3-skin-RNA_R1.fq.gz 30-18-3-skin-RNA_R2.fq.gz,fastq fastq,8332988400.0,27776628.0,30 18 3 skin RNA R1.fq.gz,0:150 1:150,A:2171684017;C:1969633232;G:1983804591;T:2207704640;N:161920,150,150,,,2171684017,1969633232,1983804591,2207704640,161920,SRX15614000,SRS13314712,SRA1432943,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,2,0.94853,0.94998,0.06705,0.06721,0.70828,0.71338,0.50912,0.51354,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-06-07,Adult,Adult,Skin,Surface Structure
70137,SRR19561957,SRX15613993,SRS13314711,SRP378802,PRJNA846110,Danio rerio Raw sequence reads,PRJNA846110,Other,Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio,,,,Dr18 2,Dr18 2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:18 replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female 25 18 2 skin,25 18 2 skin,25 18 2 skin,All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2  Vazyme Biotech Co.  Ltd  NR612 02  and subjected to 150bp paired end sequencing on a Novaseq 6028 illumina platform.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP378802,,,25-18-2-skin-RNA_R1.fq.gz 25-18-2-skin-RNA_R2.fq.gz,fastq fastq,7904881200.0,26349604.0,25 18 2 skin RNA R1.fq.gz,0:150 1:150,A:2072962586;C:1858401810;G:1869931908;T:2103432362;N:152534,150,150,,,2072962586,1858401810,1869931908,2103432362,152534,SRX15613993,SRS13314711,SRA1432943,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,2,0.94613,0.94717,0.07133,0.0724,0.71035,0.71539,0.49748,0.4888,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-06-07,Adult,Adult,Skin,Surface Structure
70143,SRR19561963,SRX15613987,SRS13314710,SRP378802,PRJNA846110,Danio rerio Raw sequence reads,PRJNA846110,Other,Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio,,,,Dr18 1,Dr18 1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:18 replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female 20 18 1 skin,20 18 1 skin,20 18 1 skin,All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2  Vazyme Biotech Co.  Ltd  NR612 02  and subjected to 150bp paired end sequencing on a Novaseq 6022 illumina platform.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP378802,,,20-18-1-skin-RNA_R1.fq.gz 20-18-1-skin-RNA_R2.fq.gz,fastq fastq,6302723700.0,21009079.0,20 18 1 skin RNA R1.fq.gz,0:150 1:150,A:1658019159;C:1467864572;G:1495349428;T:1681368226;N:122315,150,150,,,1658019159,1467864572,1495349428,1681368226,122315,SRX15613987,SRS13314710,SRA1432943,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,2,0.94106,0.94262,0.07248,0.07365,0.69727,0.70128,0.49998,0.49553,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-06-07,Adult,Adult,Skin,Surface Structure
70150,SRR19561970,SRX15613980,SRS13314709,SRP378802,PRJNA846110,Danio rerio Raw sequence reads,PRJNA846110,Other,Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio,,,,Dr27 3,Dr27 3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:27 replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female 15 27 3 skin,15 27 3 skin,15 27 3 skin,All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2  Vazyme Biotech Co.  Ltd  NR612 02  and subjected to 150bp paired end sequencing on a Novaseq 6016 illumina platform.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP378802,,,15-27-3-skin-RNA_R1.fq.gz 15-27-3-skin-RNA_R2.fq.gz,fastq fastq,7913211900.0,26377373.0,15 27 3 skin RNA R1.fq.gz,0:150 1:150,A:2076008636;C:1844679397;G:1885171351;T:2107194429;N:158087,150,150,,,2076008636,1844679397,1885171351,2107194429,158087,SRX15613980,SRS13314709,SRA1432943,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,2,0.94254,0.94213,0.06887,0.06809,0.71192,0.71701,0.47169,0.47147,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-06-07,Adult,Adult,Skin,Surface Structure
70156,SRR19561976,SRX15613974,SRS13314708,SRP378802,PRJNA846110,Danio rerio Raw sequence reads,PRJNA846110,Other,Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio,,,,Dr27 2,Dr27 2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:27 replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female 10 27 2 skin,10 27 2 skin,10 27 2 skin,All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2  Vazyme Biotech Co.  Ltd  NR612 02  and subjected to 150bp paired end sequencing on a Novaseq 6010 illumina platform.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP378802,,,10-27-2-skin-RNA_R1.fq.gz 10-27-2-skin-RNA_R2.fq.gz,fastq fastq,7498714500.0,24995715.0,10 27 2 skin RNA R1.fq.gz,0:150 1:150,A:1911552417;C:1806172582;G:1833987572;T:1946852984;N:148945,150,150,,,1911552417,1806172582,1833987572,1946852984,148945,SRX15613974,SRS13314708,SRA1432943,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,2,0.95554,0.95451,0.05031,0.04915,0.72754,0.73385,0.4814,0.46469,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-06-07,Adult,Adult,Skin,Surface Structure
71771,SRR22094615,SRX18074634,SRS15579669,SRP405171,PRJNA893397,RNA sequencing of the zebrafish superficial epithelial cells,PRJNA893397,Other,"We discovered that the superficial epithelial cells SECs of zebrafish larvae could adapt a unique kind of cell division during rapid growth conditions. We termed it ""asynthetic fission"". We determined that asynthetic fission occurs in the absence of DNA replication  generating progeny cells with reduced genome size. Here  we aim to define the transcriptional landscape of the SECs during asynthetic fission by applying RNA sequencing.",,,replicate,SEC 21dpf r,SEC 21dpf r,,strain:EK|age:21dpf|dev stage:21dpf|sex:NA|tissue:skin superficial epithelial cell|BioSampleModel:Model organism or animal,,,,,,,,,RNA sequencing of zebrafish:superficial epithelial cells 21dpf replicate,LTS21 YW06,LTS21 YW06,100  150 larvae at 2 dpf  6 dpf  14 dpf  and 21 dpf were first rinsed with 1x DPBS Gibco  14190 144  then digested with collagenase Sigma  C9891 and 0.25% trypsin EDTA Sigma  T4049. Digestion was stopped with DMEM Gibco  11995 065 with 10% NCS and rinsed with 1 x DPBS. Then  cells were suspended in DMEM 10% NCS and filtered with a 35 m cell strainer tube. Dissociated cells were stained with PI 1 g/ml for 106 cells per mL for 5 min in the dark. All EGFP+ and PI  cells were sorted by FACSAria IIIu BD Biosciences. Cells were directly sorted in buffer RLT supplemented with 1%  mercapto ethanol provided in RNeasy Micro kit Qiagen and stored in  80 C until RNA extraction was performed. Total 2 replicates for each timepoint were collected. RNA extraction was carried out using RNeasy Micro kit according to manufacturers instructions. Sequencing was performed by the NGS High Throughput Genomics Core in Biodiversity Research Center  Academia Sinica  Taiwan using Illumina NextSeq2000 with paired end 2 x 150 bp chemistry and a library selection of low input stranded RNA library preparation  Poly A.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 2000,,SRP405171,,,LTS21_YW06_S8_L001_R1_001.fastq.gz LTS21_YW06_S8_L001_R2_001.fastq.gz,fastq fastq,18884108924.0,62530162.0,LTS21 YW06 S8 L001 R1 001.fastq.gz,0:151 1:151,A:4928408237;C:4582387963;G:4378535805;T:4978379185;N:16397734,151,151,,,4928408237,4582387963,4378535805,4978379185,16397734,SRX18074634,SRS15579669,SRA1530145,Academia Sinica|Institute of Cellular and Organismic Biology,Academia Sinica,2,0.78046,0.77311,0.03967,0.03852,0.76834,0.76962,0.48776,0.49055,151,151,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,poly_a,unknown,bulk,unknown,unknown,,Taiwan,2022-10-29,Larval,Larval,Skin,Surface Structure
71772,SRR22094620,SRX18074633,SRS15579668,SRP405171,PRJNA893397,RNA sequencing of the zebrafish superficial epithelial cells,PRJNA893397,Other,"We discovered that the superficial epithelial cells SECs of zebrafish larvae could adapt a unique kind of cell division during rapid growth conditions. We termed it ""asynthetic fission"". We determined that asynthetic fission occurs in the absence of DNA replication  generating progeny cells with reduced genome size. Here  we aim to define the transcriptional landscape of the SECs during asynthetic fission by applying RNA sequencing.",,,,SEC 21dpf,Zebrafish SEC 21dpf,,strain:EK|age:21dpf|dev stage:21dpf|sex:NA|tissue:Skin|BioSampleModel:Model organism or animal,,,,,,,,,RNA sequencing of zebrafish:superficial epithelial cells 21dpf,LTS21 YW05,LTS21 YW05,100  150 larvae at 2 dpf  6 dpf  14 dpf  and 21 dpf were first rinsed with 1x DPBS Gibco  14190 144  then digested with collagenase Sigma  C9891 and 0.25% trypsin EDTA Sigma  T4049. Digestion was stopped with DMEM Gibco  11995 065 with 10% NCS and rinsed with 1 x DPBS. Then  cells were suspended in DMEM 10% NCS and filtered with a 35 m cell strainer tube. Dissociated cells were stained with PI 1 g/ml for 106 cells per mL for 5 min in the dark. All EGFP+ and PI  cells were sorted by FACSAria IIIu BD Biosciences. Cells were directly sorted in buffer RLT supplemented with 1%  mercapto ethanol provided in RNeasy Micro kit Qiagen and stored in  80 C until RNA extraction was performed. Total 2 replicates for each timepoint were collected. RNA extraction was carried out using RNeasy Micro kit according to manufacturers instructions. Sequencing was performed by the NGS High Throughput Genomics Core in Biodiversity Research Center  Academia Sinica  Taiwan using Illumina NextSeq2000 with paired end 2 x 150 bp chemistry and a library selection of low input stranded RNA library preparation  Poly A.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 2000,,SRP405171,,,LTS21_YW05_S7_L001_R1_001.fastq.gz LTS21_YW05_S7_L001_R2_001.fastq.gz,fastq fastq,19711202968.0,65268884.0,LTS21 YW05 S7 L001 R1 001.fastq.gz,0:151 1:151,A:5117592567;C:4797244360;G:4551347423;T:5228007671;N:17010947,151,151,,,5117592567,4797244360,4551347423,5228007671,17010947,SRX18074633,SRS15579668,SRA1530145,Academia Sinica|Institute of Cellular and Organismic Biology,Academia Sinica,2,0.76712,0.76186,0.039,0.03769,0.76637,0.76692,0.45633,0.4647,151,151,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,poly_a,unknown,bulk,unknown,unknown,,Taiwan,2022-10-29,Larval,Larval,Skin,Surface Structure
71773,SRR22094616,SRX18074632,SRS15579667,SRP405171,PRJNA893397,RNA sequencing of the zebrafish superficial epithelial cells,PRJNA893397,Other,"We discovered that the superficial epithelial cells SECs of zebrafish larvae could adapt a unique kind of cell division during rapid growth conditions. We termed it ""asynthetic fission"". We determined that asynthetic fission occurs in the absence of DNA replication  generating progeny cells with reduced genome size. Here  we aim to define the transcriptional landscape of the SECs during asynthetic fission by applying RNA sequencing.",,,replicate,SEC 14dpf r,SEC 14dpf r,,strain:EK|age:14dpf|dev stage:14dpf|sex:NA|tissue:skin superficial epithelial cell|BioSampleModel:Model organism or animal,,,,,,,,,RNA sequencing of zebrafish:superficial epithelial cells 14dpf replicate,LTS21 YW04,LTS21 YW04,100  150 larvae at 2 dpf  6 dpf  14 dpf  and 21 dpf were first rinsed with 1x DPBS Gibco  14190 144  then digested with collagenase Sigma  C9891 and 0.25% trypsin EDTA Sigma  T4049. Digestion was stopped with DMEM Gibco  11995 065 with 10% NCS and rinsed with 1 x DPBS. Then  cells were suspended in DMEM 10% NCS and filtered with a 35 m cell strainer tube. Dissociated cells were stained with PI 1 g/ml for 106 cells per mL for 5 min in the dark. All EGFP+ and PI  cells were sorted by FACSAria IIIu BD Biosciences. Cells were directly sorted in buffer RLT supplemented with 1%  mercapto ethanol provided in RNeasy Micro kit Qiagen and stored in  80 C until RNA extraction was performed. Total 2 replicates for each timepoint were collected. RNA extraction was carried out using RNeasy Micro kit according to manufacturers instructions. Sequencing was performed by the NGS High Throughput Genomics Core in Biodiversity Research Center  Academia Sinica  Taiwan using Illumina NextSeq2000 with paired end 2 x 150 bp chemistry and a library selection of low input stranded RNA library preparation  Poly A.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 2000,,SRP405171,,,LTS21_YW04_S6_L001_R1_001.fastq.gz LTS21_YW04_S6_L001_R2_001.fastq.gz,fastq fastq,18505626216.0,61276908.0,LTS21 YW04 S6 L001 R1 001.fastq.gz,0:151 1:151,A:4873584588;C:4461374730;G:4234634486;T:4920008051;N:16024361,151,151,,,4873584588,4461374730,4234634486,4920008051,16024361,SRX18074632,SRS15579667,SRA1530145,Academia Sinica|Institute of Cellular and Organismic Biology,Academia Sinica,2,0.76819,0.76283,0.05352,0.05251,0.76765,0.76838,0.50479,0.49192,151,151,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,poly_a,unknown,bulk,unknown,unknown,,Taiwan,2022-10-29,Larval,Larval,Skin,Surface Structure
71774,SRR22094619,SRX18074631,SRS15579666,SRP405171,PRJNA893397,RNA sequencing of the zebrafish superficial epithelial cells,PRJNA893397,Other,"We discovered that the superficial epithelial cells SECs of zebrafish larvae could adapt a unique kind of cell division during rapid growth conditions. We termed it ""asynthetic fission"". We determined that asynthetic fission occurs in the absence of DNA replication  generating progeny cells with reduced genome size. Here  we aim to define the transcriptional landscape of the SECs during asynthetic fission by applying RNA sequencing.",,,,SEC 14dpf,Zebrafish SEC 14dpf,,strain:EK|age:14dpf|dev stage:14dpf|sex:NA|tissue:Skin|BioSampleModel:Model organism or animal,,,,,,,,,RNA sequencing of zebrafish:superficial epithelial cells 14dpf,LTS21 YW03,LTS21 YW03,100  150 larvae at 2 dpf  6 dpf  14 dpf  and 21 dpf were first rinsed with 1x DPBS Gibco  14190 144  then digested with collagenase Sigma  C9891 and 0.25% trypsin EDTA Sigma  T4049. Digestion was stopped with DMEM Gibco  11995 065 with 10% NCS and rinsed with 1 x DPBS. Then  cells were suspended in DMEM 10% NCS and filtered with a 35 m cell strainer tube. Dissociated cells were stained with PI 1 g/ml for 106 cells per mL for 5 min in the dark. All EGFP+ and PI  cells were sorted by FACSAria IIIu BD Biosciences. Cells were directly sorted in buffer RLT supplemented with 1%  mercapto ethanol provided in RNeasy Micro kit Qiagen and stored in  80 C until RNA extraction was performed. Total 2 replicates for each timepoint were collected. RNA extraction was carried out using RNeasy Micro kit according to manufacturers instructions. Sequencing was performed by the NGS High Throughput Genomics Core in Biodiversity Research Center  Academia Sinica  Taiwan using Illumina NextSeq2000 with paired end 2 x 150 bp chemistry and a library selection of low input stranded RNA library preparation  Poly A.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 2000,,SRP405171,,,LTS21_YW03_S5_L001_R1_001.fastq.gz LTS21_YW03_S5_L001_R2_001.fastq.gz,fastq fastq,20010150956.0,66258778.0,LTS21 YW03 S5 L001 R1 001.fastq.gz,0:151 1:151,A:5185539519;C:4876294580;G:4677668447;T:5253656025;N:16992385,151,151,,,5185539519,4876294580,4677668447,5253656025,16992385,SRX18074631,SRS15579666,SRA1530145,Academia Sinica|Institute of Cellular and Organismic Biology,Academia Sinica,2,0.78205,0.77596,0.04076,0.03939,0.78248,0.78293,0.4586,0.46807,151,151,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,poly_a,unknown,bulk,unknown,unknown,,Taiwan,2022-10-29,Larval,Larval,Skin,Surface Structure
71775,SRR22094617,SRX18074630,SRS15579665,SRP405171,PRJNA893397,RNA sequencing of the zebrafish superficial epithelial cells,PRJNA893397,Other,"We discovered that the superficial epithelial cells SECs of zebrafish larvae could adapt a unique kind of cell division during rapid growth conditions. We termed it ""asynthetic fission"". We determined that asynthetic fission occurs in the absence of DNA replication  generating progeny cells with reduced genome size. Here  we aim to define the transcriptional landscape of the SECs during asynthetic fission by applying RNA sequencing.",,,replicate,SEC 6dpf r,SEC 6dpf r,,strain:EK|age:6dpf|dev stage:6dpf|sex:NA|tissue:skin superficial epithelial cell|BioSampleModel:Model organism or animal,,,,,,,,,RNA sequencing of zebrafish:superficial epithelial cells 6dpf replicate,LTS21 YW02,LTS21 YW02,100  150 larvae at 2 dpf  6 dpf  14 dpf  and 21 dpf were first rinsed with 1x DPBS Gibco  14190 144  then digested with collagenase Sigma  C9891 and 0.25% trypsin EDTA Sigma  T4049. Digestion was stopped with DMEM Gibco  11995 065 with 10% NCS and rinsed with 1 x DPBS. Then  cells were suspended in DMEM 10% NCS and filtered with a 35 m cell strainer tube. Dissociated cells were stained with PI 1 g/ml for 106 cells per mL for 5 min in the dark. All EGFP+ and PI  cells were sorted by FACSAria IIIu BD Biosciences. Cells were directly sorted in buffer RLT supplemented with 1%  mercapto ethanol provided in RNeasy Micro kit Qiagen and stored in  80 C until RNA extraction was performed. Total 2 replicates for each timepoint were collected. RNA extraction was carried out using RNeasy Micro kit according to manufacturers instructions. Sequencing was performed by the NGS High Throughput Genomics Core in Biodiversity Research Center  Academia Sinica  Taiwan using Illumina NextSeq2000 with paired end 2 x 150 bp chemistry and a library selection of low input stranded RNA library preparation  Poly A.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 2000,,SRP405171,,,LTS21_YW02_S4_L001_R1_001.fastq.gz LTS21_YW02_S4_L001_R2_001.fastq.gz,fastq fastq,20220291918.0,66954609.0,LTS21 YW02 S4 L001 R1 001.fastq.gz,0:151 1:151,A:5407749316;C:4807063001;G:4510753168;T:5477213837;N:17512596,151,151,,,5407749316,4807063001,4510753168,5477213837,17512596,SRX18074630,SRS15579665,SRA1530145,Academia Sinica|Institute of Cellular and Organismic Biology,Academia Sinica,2,0.74742,0.74156,0.05378,0.05283,0.75118,0.75183,0.49329,0.49679,151,151,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,poly_a,unknown,bulk,unknown,unknown,,Taiwan,2022-10-29,Larval,Larval,Skin,Surface Structure
71776,SRR22094618,SRX18074629,SRS15579664,SRP405171,PRJNA893397,RNA sequencing of the zebrafish superficial epithelial cells,PRJNA893397,Other,"We discovered that the superficial epithelial cells SECs of zebrafish larvae could adapt a unique kind of cell division during rapid growth conditions. We termed it ""asynthetic fission"". We determined that asynthetic fission occurs in the absence of DNA replication  generating progeny cells with reduced genome size. Here  we aim to define the transcriptional landscape of the SECs during asynthetic fission by applying RNA sequencing.",,,,SEC 6dpf,Zebrafish SEC 6dpf,,strain:EK|age:6dpf|dev stage:6dpf|sex:NA|tissue:Skin|BioSampleModel:Model organism or animal,,,,,,,,,RNA sequencing of zebrafish:superficial epithelial cells 6dpf,LTS21 YG02,LTS21 YG02,100  150 larvae at 2 dpf  6 dpf  14 dpf  and 21 dpf were first rinsed with 1x DPBS Gibco  14190 144  then digested with collagenase Sigma  C9891 and 0.25% trypsin EDTA Sigma  T4049. Digestion was stopped with DMEM Gibco  11995 065 with 10% NCS and rinsed with 1 x DPBS. Then  cells were suspended in DMEM 10% NCS and filtered with a 35 m cell strainer tube. Dissociated cells were stained with PI 1 g/ml for 106 cells per mL for 5 min in the dark. All EGFP+ and PI  cells were sorted by FACSAria IIIu BD Biosciences. Cells were directly sorted in buffer RLT supplemented with 1%  mercapto ethanol provided in RNeasy Micro kit Qiagen and stored in  80 C until RNA extraction was performed. Total 2 replicates for each timepoint were collected. RNA extraction was carried out using RNeasy Micro kit according to manufacturers instructions. Sequencing was performed by the NGS High Throughput Genomics Core in Biodiversity Research Center  Academia Sinica  Taiwan using Illumina NextSeq2000 with paired end 2 x 150 bp chemistry and a library selection of low input stranded RNA library preparation  Poly A.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 2000,,SRP405171,,,LTS21_YG02_S2_L001_R1_001.fastq.gz LTS21_YG02_S2_L001_R2_001.fastq.gz,fastq fastq,20584419962.0,68160331.0,LTS21 YG02 S2 L001 R1 001.fastq.gz,0:151 1:151,A:5411222042;C:4935924238;G:4703040707;T:5516534305;N:17698670,151,151,,,5411222042,4935924238,4703040707,5516534305,17698670,SRX18074629,SRS15579664,SRA1530145,Academia Sinica|Institute of Cellular and Organismic Biology,Academia Sinica,2,0.76895,0.7633,0.03985,0.03893,0.76481,0.76607,0.46945,0.46388,151,151,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,poly_a,unknown,bulk,unknown,unknown,,Taiwan,2022-10-29,Larval,Larval,Skin,Surface Structure
71777,SRR22094621,SRX18074628,SRS15579663,SRP405171,PRJNA893397,RNA sequencing of the zebrafish superficial epithelial cells,PRJNA893397,Other,"We discovered that the superficial epithelial cells SECs of zebrafish larvae could adapt a unique kind of cell division during rapid growth conditions. We termed it ""asynthetic fission"". We determined that asynthetic fission occurs in the absence of DNA replication  generating progeny cells with reduced genome size. Here  we aim to define the transcriptional landscape of the SECs during asynthetic fission by applying RNA sequencing.",,,replicate,SEC 2dpf r,SEC 2dpf r,,strain:EK|age:2dpf|dev stage:2dpf|sex:NA|tissue:skin superficial epithelial cell|BioSampleModel:Model organism or animal,,,,,,,,,RNA sequencing of zebrafish:superficial epithelial cells 2dpf replicate,LTS21 YW01,LTS21 YW01,100  150 larvae at 2 dpf  6 dpf  14 dpf  and 21 dpf were first rinsed with 1x DPBS Gibco  14190 144  then digested with collagenase Sigma  C9891 and 0.25% trypsin EDTA Sigma  T4049. Digestion was stopped with DMEM Gibco  11995 065 with 10% NCS and rinsed with 1 x DPBS. Then  cells were suspended in DMEM 10% NCS and filtered with a 35 m cell strainer tube. Dissociated cells were stained with PI 1 g/ml for 106 cells per mL for 5 min in the dark. All EGFP+ and PI  cells were sorted by FACSAria IIIu BD Biosciences. Cells were directly sorted in buffer RLT supplemented with 1%  mercapto ethanol provided in RNeasy Micro kit Qiagen and stored in  80 C until RNA extraction was performed. Total 2 replicates for each timepoint were collected. RNA extraction was carried out using RNeasy Micro kit according to manufacturers instructions. Sequencing was performed by the NGS High Throughput Genomics Core in Biodiversity Research Center  Academia Sinica  Taiwan using Illumina NextSeq2000 with paired end 2 x 150 bp chemistry and a library selection of low input stranded RNA library preparation  Poly A.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 2000,,SRP405171,,,LTS21_YW01_S3_L001_R1_001.fastq.gz LTS21_YW01_S3_L001_R2_001.fastq.gz,fastq fastq,19999530824.0,66223612.0,LTS21 YW01 S3 L001 R1 001.fastq.gz,0:151 1:151,A:5239226851;C:4832853944;G:4579224440;T:5331222900;N:17002689,151,151,,,5239226851,4832853944,4579224440,5331222900,17002689,SRX18074628,SRS15579663,SRA1530145,Academia Sinica|Institute of Cellular and Organismic Biology,Academia Sinica,2,0.77399,0.76874,0.04763,0.04655,0.75035,0.75087,0.423,0.42383,151,151,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,poly_a,unknown,bulk,unknown,unknown,,Taiwan,2022-10-29,Hatching,Embryo,Skin,Surface Structure
71778,SRR22094622,SRX18074627,SRS15579662,SRP405171,PRJNA893397,RNA sequencing of the zebrafish superficial epithelial cells,PRJNA893397,Other,"We discovered that the superficial epithelial cells SECs of zebrafish larvae could adapt a unique kind of cell division during rapid growth conditions. We termed it ""asynthetic fission"". We determined that asynthetic fission occurs in the absence of DNA replication  generating progeny cells with reduced genome size. Here  we aim to define the transcriptional landscape of the SECs during asynthetic fission by applying RNA sequencing.",,,,SEC 2dpf,Zebrafish SEC 2dpf,,strain:EK|age:2dpf|dev stage:2dpf|sex:NA|tissue:Skin|BioSampleModel:Model organism or animal,,,,,,,,,RNA sequencing of zebrafish:superficial epithelial cells 2dpf,LTS21 YG01,LTS21 YG01,100  150 larvae at 2 dpf  6 dpf  14 dpf  and 21 dpf were first rinsed with 1x DPBS Gibco  14190 144  then digested with collagenase Sigma  C9891 and 0.25% trypsin EDTA Sigma  T4049. Digestion was stopped with DMEM Gibco  11995 065 with 10% NCS and rinsed with 1 x DPBS. Then  cells were suspended in DMEM 10% NCS and filtered with a 35 m cell strainer tube. Dissociated cells were stained with PI 1 g/ml for 106 cells per mL for 5 min in the dark. All EGFP+ and PI  cells were sorted by FACSAria IIIu BD Biosciences. Cells were directly sorted in buffer RLT supplemented with 1%  mercapto ethanol provided in RNeasy Micro kit Qiagen and stored in  80 C until RNA extraction was performed. Total 2 replicates for each timepoint were collected. RNA extraction was carried out using RNeasy Micro kit according to manufacturers instructions. Sequencing was performed by the NGS High Throughput Genomics Core in Biodiversity Research Center  Academia Sinica  Taiwan using Illumina NextSeq2000 with paired end 2 x 150 bp chemistry and a library selection of low input stranded RNA library preparation  Poly A.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 2000,,SRP405171,,,LTS21_YG01_S1_L001_R1_001.fastq.gz LTS21_YG01_S1_L001_R2_001.fastq.gz,fastq fastq,18171646530.0,60171015.0,LTS21 YG01 S1 L001 R1 001.fastq.gz,0:151 1:151,A:4727063040;C:4426085600;G:4200458773;T:4802148545;N:15890572,151,151,,,4727063040,4426085600,4200458773,4802148545,15890572,SRX18074627,SRS15579662,SRA1530145,Academia Sinica|Institute of Cellular and Organismic Biology,Academia Sinica,2,0.76303,0.75602,0.03268,0.03163,0.78427,0.78484,0.3601,0.35972,151,151,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,poly_a,unknown,bulk,unknown,unknown,,Taiwan,2022-10-29,Hatching,Embryo,Skin,Surface Structure