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64 rows where experiment.library_layout = "PAIRED", technology = "unknown" and tissue_curation = "Skin"

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devstage_curation 6

devstage_curation_coarse 5

experiment.library_selection 4

experiment.platform 3

tissue_curation_coarse 1

tissue_curation 1

  • Skin · 64 ✖

technology 1

  • unknown · 64 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_layout 1

  • PAIRED · 64 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
9770 9770 ERR5838122 ERX5487778 ERS6337138 ERP119543 PRJEB36360 Transcriptomic analysis of adult skin from 9 Danio species ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27 Other Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21 PUBMED:33277491 Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. Transcriptomic analysis of adult skin from 9 Danio species SAMEA8652584 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652584|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:05 Danio rerio adult skin 5|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:05 Danio rerio adult skin 5|sex:male|tissue type:skin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 5 unspecified 1 TruSeq stranded mRNA Illumina   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP119543 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29 S1385Nr5.1.fastq.gz S1385Nr5.2.fastq.gz fastq fastq 6912206316.0 34306523.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 5 0:100.74 1:100.74 A:1853779551;C:1607929988;G:1658402611;T:1792045990;N:48176 100 100     1853779551 1607929988 1658402611 1792045990 48176 ERX5487778 ERS6337138 ERA4129786 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 2 0.96095 0.962 0.08049 0.07821 0.70654 0.70926 0.51398 0.51064 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-03-21 Adult Adult Skin Surface Structure
9771 9771 ERR5838121 ERX5487777 ERS6337136 ERP119543 PRJEB36360 Transcriptomic analysis of adult skin from 9 Danio species ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27 Other Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21 PUBMED:33277491 Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. Transcriptomic analysis of adult skin from 9 Danio species SAMEA8652582 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652582|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:04 Danio rerio adult skin 4|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:04 Danio rerio adult skin 4|sex:male|tissue type:skin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 4 unspecified 1 TruSeq stranded mRNA Illumina   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP119543 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29 S1385Nr4.1.fastq.gz S1385Nr4.2.fastq.gz fastq fastq 6161942050.0 30595009.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 4 0:100.70 1:100.70 A:1642716052;C:1446485458;G:1490121106;T:1582576605;N:42829 100 100     1642716052 1446485458 1490121106 1582576605 42829 ERX5487777 ERS6337136 ERA4129786 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 2 0.96544 0.96564 0.07368 0.07303 0.70822 0.71092 0.50154 0.50781 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-03-21 Adult Adult Skin Surface Structure
9772 9772 ERR5838120 ERX5487776 ERS6337133 ERP119543 PRJEB36360 Transcriptomic analysis of adult skin from 9 Danio species ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27 Other Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21 PUBMED:33277491 Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. Transcriptomic analysis of adult skin from 9 Danio species SAMEA8652579 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652579|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:03 Danio rerio adult skin 3|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:03 Danio rerio adult skin 3|sex:female|tissue type:skin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 3 unspecified 1 TruSeq stranded mRNA Illumina   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP119543 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29 S1385Nr3.1.fastq.gz S1385Nr3.2.fastq.gz fastq fastq 7422881394.0 36866805.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 3 0:100.67 1:100.67 A:1950275527;C:1768648993;G:1827362519;T:1876542858;N:51497 100 100     1950275527 1768648993 1827362519 1876542858 51497 ERX5487776 ERS6337133 ERA4129786 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 2 0.97031 0.97047 0.04915 0.04817 0.71459 0.71894 0.51089 0.5097 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-03-21 Adult Adult Skin Surface Structure
9773 9773 ERR5838119 ERX5487775 ERS6337132 ERP119543 PRJEB36360 Transcriptomic analysis of adult skin from 9 Danio species ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27 Other Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21 PUBMED:33277491 Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. Transcriptomic analysis of adult skin from 9 Danio species SAMEA8652578 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652578|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:02 Danio rerio adult skin 2|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:02 Danio rerio adult skin 2|sex:female|tissue type:skin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 2 unspecified 1 TruSeq stranded mRNA Illumina   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP119543 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29 S1385Nr2.1.fastq.gz S1385Nr2.2.fastq.gz fastq fastq 7006718028.0 34786110.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 2 0:100.71 1:100.71 A:1847371523;C:1665346769;G:1712373266;T:1781565768;N:60702 100 100     1847371523 1665346769 1712373266 1781565768 60702 ERX5487775 ERS6337132 ERA4129786 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 2 0.96136 0.96039 0.05872 0.05752 0.70325 0.70674 0.46717 0.48218 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-03-21 Adult Adult Skin Surface Structure
9774 9774 ERR5838118 ERX5487774 ERS6337063 ERP119543 PRJEB36360 Transcriptomic analysis of adult skin from 9 Danio species ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27 Other Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21 PUBMED:33277491 Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. Transcriptomic analysis of adult skin from 9 Danio species SAMEA8652509 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652509|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:01 Danio rerio adult skin 1|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:01 Danio rerio adult skin 1|sex:male|tissue type:skin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 1 unspecified 1 TruSeq stranded mRNA Illumina   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP119543 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29 S1385Nr1.1.fastq.gz S1385Nr1.2.fastq.gz fastq fastq 6586457266.0 32719900.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 1 0:100.65 1:100.65 A:1709547533;C:1593125315;G:1617088678;T:1666650824;N:44916 100 100     1709547533 1593125315 1617088678 1666650824 44916 ERX5487774 ERS6337063 ERA4129786 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 2 0.9531 0.95366 0.07763 0.07567 0.71384 0.71634 0.52409 0.52475 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-03-21 Adult Adult Skin Surface Structure
25297 25297 SRR25764099 SRX21486772 SRS18719072 SRP457109 PRJNA1009810 Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish GSE241757 Transcriptome Analysis Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.   pubmed:38265193   Adult itgb4+ basal cells GSM7734879   tissue:epidermal cells|cell type:adult fin epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing Adult itgb4+ basal cells High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values. epidermal cells Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. cell type:adult fin epidermal basal cells|genotype:Tgitgb4:mcherry GSM7734879 GSM7734879: Adult itgb4+ basal cells; Danio rerio; RNA Seq GSM7734879 r1 GSM7734879 1 The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP457109     Adult_itgb4mcherry_S230_R1_001.fastq.gz Adult_itgb4mcherry_S230_R2_001.fastq.gz fastq fastq 5035430000.0 12588575.0 GSM7734879 r1 0:200 1:200 A:1339392170;C:1117195164;G:1254708952;T:1323174485;N:959229 200 200     1339392170 1117195164 1254708952 1323174485 959229 SRX21486772 SRS18719072 SRA1700438 Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology 2 0.01543 0.02468 0.00098 0.00102 0.99318 0.99387 0.47878 0.31718 200 200 T T mates < 9% mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2023-08-28 Adult Adult Skin Surface Structure
25298 25298 SRR25764100 SRX21486771 SRS18719071 SRP457109 PRJNA1009810 Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish GSE241757 Transcriptome Analysis Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.   pubmed:38265193   1 dpf itgb4+ embryonic basal precursors rep2 GSM7734878   tissue:epidermal cells|cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing 1 dpf itgb4+ embryonic basal precursors rep2 High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values. epidermal cells Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry GSM7734878 GSM7734878: 1 dpf itgb4+ embryonic basal precursors rep2; Danio rerio; RNA Seq GSM7734878 r1 GSM7734878 1 The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP457109     itgb4mcherry_2_S229_R1_001.fastq.gz itgb4mcherry_2_S229_R2_001.fastq.gz fastq fastq 6040245600.0 15100614.0 GSM7734878 r1 0:200 1:200 A:1588346322;C:1356558310;G:1524614760;T:1569583583;N:1142625 200 200     1588346322 1356558310 1524614760 1569583583 1142625 SRX21486771 SRS18719071 SRA1700438 Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology 2 0.0156 0.0191 0.00074 0.00093 0.99024 0.99088 0.47058 0.47838 200 200 T T mates < 9% mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2023-08-28 Multi-stage Multi-stage Skin Surface Structure
25299 25299 SRR25764101 SRX21486770 SRS18719070 SRP457109 PRJNA1009810 Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish GSE241757 Transcriptome Analysis Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.   pubmed:38265193   1 dpf itgb4+ embryonic basal precursors rep1 GSM7734877   tissue:epidermal cells|cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing 1 dpf itgb4+ embryonic basal precursors rep1 High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values. epidermal cells Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry GSM7734877 GSM7734877: 1 dpf itgb4+ embryonic basal precursors rep1; Danio rerio; RNA Seq GSM7734877 r1 GSM7734877 1 The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP457109     itgb4mcherry_1_S20_R1_001.fastq.gz itgb4mcherry_1_S20_R2_001.fastq.gz fastq fastq 7055215600.0 17638039.0 GSM7734877 r1 0:200 1:200 A:1894635584;C:1556854856;G:1769420212;T:1825520802;N:8784146 200 200     1894635584 1556854856 1769420212 1825520802 8784146 SRX21486770 SRS18719070 SRA1700438 Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology 2 0.01135 0.01881 0.00043 0.00016 0.9932 0.99543 0.46234 0.43106 200 200 T T mates < 9% mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2023-08-28 Multi-stage Multi-stage Skin Surface Structure
25300 25300 SRR25764102 SRX21486769 SRS18719069 SRP457109 PRJNA1009810 Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish GSE241757 Transcriptome Analysis Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.   pubmed:38265193   1 dpf krt4+ embryonic periderm cells rep2 GSM7734876   tissue:epidermal cells|cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp|geo loc name:missing|collection date:missing 1 dpf krt4+ embryonic periderm cells rep2 High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values. epidermal cells Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp GSM7734876 GSM7734876: 1 dpf krt4+ embryonic periderm cells rep2; Danio rerio; RNA Seq GSM7734876 r1 GSM7734876 1 The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP457109     krt4cre-gfp_2_S4_R2_001.fastq.gz krt4cre-gfp_2_S4_R1_001.fastq.gz fastq fastq 9439207600.0 23598019.0 GSM7734876 r1 0:200 1:200 A:2499982675;C:2086665360;G:2395002073;T:2454282285;N:3275207 200 200     2499982675 2086665360 2395002073 2454282285 3275207 SRX21486769 SRS18719069 SRA1700438 Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology 2 0.44931 0.01877 0.02236 0.00115 0.80012 0.99032 0.45473 0.49453 200 200 B T mate2 technical by mapping diff bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2023-08-28 Multi-stage Multi-stage Skin Surface Structure
25301 25301 SRR25764103 SRX21486768 SRS18719066 SRP457109 PRJNA1009810 Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish GSE241757 Transcriptome Analysis Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.   pubmed:38265193   1 dpf krt4+ embryonic periderm cells rep1 GSM7734875   tissue:epidermal cells|cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp|geo loc name:missing|collection date:missing 1 dpf krt4+ embryonic periderm cells rep1 High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values. epidermal cells Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp GSM7734875 GSM7734875: 1 dpf krt4+ embryonic periderm cells rep1; Danio rerio; RNA Seq GSM7734875 r1 GSM7734875 1 The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP457109     krt4cre-gfp_1_S19_R2_001.fastq.gz krt4cre-gfp_1_S19_R1_001.fastq.gz fastq fastq 6119547200.0 15298868.0 GSM7734875 r1 0:200 1:200 A:1642059769;C:1349462427;G:1535937964;T:1584527048;N:7559992 200 200     1642059769 1349462427 1535937964 1584527048 7559992 SRX21486768 SRS18719066 SRA1700438 Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology 2 0.01112 0.01017 0.0003 0.00014 0.9931 0.99586 0.43605 0.40821 200 200 T T mates < 9% mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2023-08-28 Multi-stage Multi-stage Skin Surface Structure
33837 33837 SRR30763634 SRX26165999 SRS22710780 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin con2 Skin con 3   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin con 3|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin con 3 SK CON 3 SK CON 3 Zebrafish skin at control group     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_con2_Clean_Data1.fq.gz Skin_con2_Clean_Data2.fq.gz fastq fastq 6083362246.0 21717347.0 Skin con2 Clean Data1.fq.gz 0:140.06 1:140.05 A:1575684711;C:1458969719;G:1469933956;T:1578641539;N:132321 140 140     1575684711 1458969719 1469933956 1578641539 132321 SRX26165999 SRS22710780 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33838 33838 SRR30763635 SRX26165998 SRS22710779 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin con1 Skin con 2   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin con 2|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin con 2 SK CON 2 SK CON 2 Zebrafish skin at control group     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_con1_Clean_Data1.fq.gz Skin_con1_Clean_Data2.fq.gz fastq fastq 5776524166.0 20610041.0 Skin con1 Clean Data1.fq.gz 0:140.14 1:140.13 A:1496887200;C:1385008310;G:1395131090;T:1499373290;N:124276 140 140     1496887200 1385008310 1395131090 1499373290 124276 SRX26165998 SRS22710779 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33839 33839 SRR30763636 SRX26165997 SRS22710778 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin con Skin con 1   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin con 1|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin con 1 SK CON 1 SK CON 1 Zebrafish skin at control group     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_con_Clean_Data1.fq.gz Skin_con_Clean_Data2.fq.gz fastq fastq 5304184337.0 18925504.0 Skin con Clean Data1.fq.gz 0:140.14 1:140.13 A:1400015654;C:1245459230;G:1267684230;T:1391013551;N:11672 140 140     1400015654 1245459230 1267684230 1391013551 11672 SRX26165997 SRS22710778 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33840 33840 SRR30763637 SRX26165996 SRS22710777 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin 3dpi2 Skin 3d 3   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 3dpi 3|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin 3d 3 SK 3D 3 SK 3D 3 Zebrafish skin at 3 dpv post immunization with glycoprotein of spring viraemia of carp virus     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_3dpi2_Clean_Data1.fq.gz Skin_3dpi2_Clean_Data2.fq.gz fastq fastq 5528962547.0 19717071.0 Skin 3dpi2 Clean Data1.fq.gz 0:140.21 1:140.20 A:1434889776;C:1319598036;G:1335801562;T:1438550030;N:123143 140 140     1434889776 1319598036 1335801562 1438550030 123143 SRX26165996 SRS22710777 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33841 33841 SRR30763638 SRX26165995 SRS22710776 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin 3dpi1 Skin 3d 2   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 3dpi 2|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin 3d 2 SK 3D 2 SK 3D 2 Zebrafish skin at 3 dpv post immunization with glycoprotein of spring viraemia of carp virus     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_3dpi1_Clean_Data1.fq.gz Skin_3dpi1_Clean_Data2.fq.gz fastq fastq 6045424568.0 21559158.0 Skin 3dpi1 Clean Data1.fq.gz 0:140.21 1:140.20 A:1566211023;C:1442845401;G:1464489674;T:1571745680;N:132790 140 140     1566211023 1442845401 1464489674 1571745680 132790 SRX26165995 SRS22710776 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33842 33842 SRR30763639 SRX26165994 SRS22710775 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin 3dpi Skin 3d 1   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 3dpi 1|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin 3d 1 SK 3D 1 SK 3D 1 Zebrafish skin at 3 dpv post immunization with glycoprotein of spring viraemia of carp virus     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_3dpi_Clean_Data1.fq.gz Skin_3dpi_Clean_Data2.fq.gz fastq fastq 5398897838.0 19388025.0 Skin 3dpi Clean Data1.fq.gz 0:139.24 1:139.23 A:1434301676;C:1260747084;G:1277759027;T:1426077485;N:12566 139 139     1434301676 1260747084 1277759027 1426077485 12566 SRX26165994 SRS22710775 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33843 33843 SRR30763640 SRX26165993 SRS22710774 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin 1dpi2 Skin 1d 3   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 1dpi 3|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin 1d 3 SK 1D 3 SK 1D 3 Zebrafish skin at 1 dpv post immunization with glycoprotein of spring viraemia of carp virus     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_1dpi2_Clean_Data1.fq.gz Skin_1dpi2_Clean_Data2.fq.gz fastq fastq 6317753535.0 22527726.0 Skin 1dpi2 Clean Data1.fq.gz 0:140.23 1:140.22 A:1637469629;C:1508203339;G:1526532646;T:1645411954;N:135967 140 140     1637469629 1508203339 1526532646 1645411954 135967 SRX26165993 SRS22710774 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33844 33844 SRR30763641 SRX26165992 SRS22710773 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin 1dpi1 Skin 1d 2   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 1dpi 2|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin 1d 2 SK 1D 2 SK 1D 2 Zebrafish skin at 1 dpv post immunization with glycoprotein of spring viraemia of carp virus     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_1dpi1_Clean_Data1.fq.gz Skin_1dpi1_Clean_Data2.fq.gz fastq fastq 5665401221.0 20209478.0 Skin 1dpi1 Clean Data1.fq.gz 0:140.17 1:140.16 A:1463485728;C:1359900876;G:1372085350;T:1469804976;N:124291 140 140     1463485728 1359900876 1372085350 1469804976 124291 SRX26165992 SRS22710773 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33845 33845 SRR30763642 SRX26165991 SRS22710772 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin 1dpi Skin 1d 1   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 1dpi 1|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin 1d 1 SK 1D 1 SK 1D 1 Zebrafish skin at 1 dpv post immunization with glycoprotein of spring viraemia of carp virus     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_1dpi_Clean_Data1.fq.gz Skin_1dpi_Clean_Data2.fq.gz fastq fastq 4758945020.0 17104843.0 Skin 1dpi Clean Data1.fq.gz 0:139.12 1:139.11 A:1261511064;C:1113177324;G:1128285977;T:1255959998;N:10657 139 139     1261511064 1113177324 1128285977 1255959998 10657 SRX26165991 SRS22710772 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
36717 36717 SRR835162 SRX271958 SRS416254 SRP021517 PRJNA198908 Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin GSE46387 Transcriptome Analysis In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing   pubmed:23874447   dm 77h 28 399s62 GSM1129620   tissue:melanocytes|hpf dm 77h 28 399s62 Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library melanocytes   This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…   hpf GSM1129620 GSM1129620: dm 77h 28 399s62; Danio rerio; RNA Seq GSM1129620 1   1 This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc… GEO Accession:GSM1129620 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP021517         731276158.0 3620179.0 GSM1129620 r1 0:101 1:101 A:173989639;C:199270484;G:188281318;T:169725601;N:9116 101 101     173989639 199270484 188281318 169725601 9116 SRX271958 SRS416254 SRA074390 GEO Rob Mitra, Genetics, Washington University 2 0.84122 0.79964 0.02274 0.02168 0.89645 0.89073 0.63341 0.63015 101 101 B B biological fallback assumption illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36718 36718 SRR835161 SRX271957 SRS416253 SRP021517 PRJNA198908 Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin GSE46387 Transcriptome Analysis In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing   pubmed:23874447   dm 77h 28 399s61 GSM1129619   tissue:melanocytes|hpf dm 77h 28 399s61 Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library melanocytes   This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…   hpf GSM1129619 GSM1129619: dm 77h 28 399s61; Danio rerio; RNA Seq GSM1129619 1   1 This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc… GEO Accession:GSM1129619 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_28_399s61_CACT.fq.bz2 dm_77h_28_399s62_CACT.fq.bz2 fastq fastq 731276158.0 3620179.0 GSM1129619 r1 0:101 1:101 A:173989639;C:199270484;G:188281318;T:169725601;N:9116 101 101     173989639 199270484 188281318 169725601 9116 SRX271957 SRS416253 SRA074390 GEO Rob Mitra, Genetics, Washington University 2 0.84121 0.79968 0.02287 0.02141 0.89658 0.89051 0.63318 0.63061 101 101 B B biological fallback assumption illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36725 36725 SRR835154 SRX271950 SRS416245 SRP021517 PRJNA198908 Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin GSE46387 Transcriptome Analysis In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing   pubmed:23874447   dm 77h 25 399s62 GSM1129612   tissue:melanocytes|hpf dm 77h 25 399s62 Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library melanocytes   This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…   hpf GSM1129612 GSM1129612: dm 77h 25 399s62; Danio rerio; RNA Seq GSM1129612 1   1 This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc… GEO Accession:GSM1129612 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP021517         1715809008.0 8494104.0 GSM1129612 r1 0:101 1:101 A:405310561;C:444474389;G:467897835;T:398105078;N:21145 101 101     405310561 444474389 467897835 398105078 21145 SRX271950 SRS416245 SRA074390 GEO Rob Mitra, Genetics, Washington University 2 0.66327 0.58026 0.07911 0.07288 0.91721 0.9083 0.56907 0.5363 101 101 B B biological fallback assumption illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36726 36726 SRR835153 SRX271949 SRS416246 SRP021517 PRJNA198908 Gene Expression Analysis of Zebrafish Melanocytes Iridophores and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin GSE46387 Transcriptome Analysis In order to facilitate understanding of pigment cell biology we developed a method to concomitantly purify melanocytes iridophores and retinal pigmented epithelium from zebrafish and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co enrichment in melanocytes and retinal pigmented epithelium as well as in melanocytes and iridophores. We found 214 genes co enriched in melanocytes and retinal pigmented epithelium indicating the shared functions of melanin producing cells. We found 62 genes significantly co enriched in melanocytes and iridophores illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate limiting substrate for purine synthesis phosphoribosyl pyrophosphate thus constituting a guanine cycle. The purification procedure and expression analysis described here along with the accompanying transcriptome wide expression data provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types and will be a useful resource for further studies of pigment cell biology. Overall design: mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing   pubmed:23874447   dm 77h 25 399s61 GSM1129611   tissue:melanocytes|hpf dm 77h 25 399s61 Align sequences using Novoalign to cDNA database Calculate RPKMs from Novoalign output using Perl Genome build: Non redundant database of 25 102 cDNAs generated by Higdon et al 2013 based on NCBI's RefSeq build from 8/29/2012 current RefSeq available at ftp://ftp.ncbi.nlm.nih.gov/refseq/D rerio/mRNA Prot/zebrafish.rna.fna.gz Supplementary files format and content: Excell file containing RPKMs of each library melanocytes   This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc…   hpf GSM1129611 GSM1129611: dm 77h 25 399s61; Danio rerio; RNA Seq GSM1129611 1   1 This study was carried out in accordance with the Washington University Animal Use Committee guidelines under approved protocol #20110236. Zebrafish were reared and bred according to standard protocols. The fish used in this study were homozygous for a temperature sensitive allele of micropthalmia transcription factor mitfavc7. This mutant facilitated the collection of RPE as mitfa is not required for RPE development in zebrafish. Melanocytes iridophores and RPE develop normally at 25°C in mitfavc7. When held at 32°C the neural crest derived melanocytes do not develop but RPE and iridophores develop normally. All melanocyte and iridophore samples were incubated at 25°C prior to collection. Fish were anesthetized with Tricaine rinsed with Ca Mg DPBS Sigma D8537 and immersed in 100mL TrypLE Express Invitrogen 12604039 per 1000 fish. Fish were incubated at 37°C and shaken at 100rpm for 15 20 minutes followed by trituration with a Pasteur pipette to remove eyes from larva. post separation of eyes and larva each group was placed in TrypLE Express and shaken at 100rpm at 37°C for 1 1.5 hr. Dissociated cells were filtered through a 120uM screen into 50 mL tubes. Remaining intact tissue was triturated 10 20 times and again filtered through a 120uM screen into the dissociated cells. Dissociated cells were pelleted in a swinging bucket rotor Eppendorf 5810 R at 500 relative centrifugal force rcf for 5 minutes at 4°C then resuspended in 1mL cold isotonic Percoll Sigma P1644 by gentle pipetting. Isotonic Percoll was prepared by mixing 1 part 10X PBS with 9 parts Percoll. Resuspended cells were transferred to 1.6mL Eppendorf tubes and spun at 2000rcf for 5 minutes at 4°C in a swinging bucket rotor for isopycnic separation. Pigment cells in the pellet were then resuspended in 400µL of ice cold DPBS with 2% fetal calf serum FCS and placed onto preformed Percoll density gradients. Preformed gradients were prepared via centrifugation of 1mL aliquots of isotonic Percoll in 1.6mL tubes at 10 000rc… GEO Accession:GSM1129611 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_25_399s61_TCTT.fq.bz2 dm_77h_25_399s62_TCTT.fq.bz2 fastq fastq 1715809008.0 8494104.0 GSM1129611 r1 0:101 1:101 A:405310561;C:444474389;G:467897835;T:398105078;N:21145 101 101     405310561 444474389 467897835 398105078 21145 SRX271949 SRS416246 SRA074390 GEO Rob Mitra, Genetics, Washington University 2 0.66325 0.58027 0.0792 0.07327 0.91741 0.90847 0.56374 0.53632 101 101 B B biological fallback assumption illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
53011 53011 SRR9662028 SRX6422904 SRS5079694 SRP213938 PRJNA553572 A map of cis regulatory elements and 3D genome structures in zebrafish GSE134055 Other The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.   pubmed:33239788;pubmed:35649578   YueLab RNA Seq Skin rep2 GSM3934896   source name:Tissue|strain:Tuebingen|tissue:Skin YueLab RNA Seq Skin rep2 RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged Tissue   For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions strain:Tuebingen|tissue:Skin GSM3934896 GSM3934896: YueLab RNA Seq Skin rep2; Danio rerio; RNA Seq GSM3934896   1 For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. GEO Accession:GSM3934896 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer   SRP213938     YueLab-RNA-Seq-Skin-rep2_1.fastq.gz YueLab-RNA-Seq-Skin-rep2_2.fastq.gz fastq fastq 3369540489.0 27929926.0 GSM3934896 r1 0:60.47 1:60.17 A:881257889;C:784720097;G:773160075;T:930047288;N:355140 60 60     881257889 784720097 773160075 930047288 355140 SRX6422904 SRS5079694 SRA919194 GEO Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine 2 0.96098 0.96359 0.1219 0.11985 0.69962 0.70161 0.48503 0.4877 61 60 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United States 2019-07-09 Pharyngula Embryo Skin Surface Structure
53012 53012 SRR9662027 SRX6422903 SRS5079693 SRP213938 PRJNA553572 A map of cis regulatory elements and 3D genome structures in zebrafish GSE134055 Other The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.   pubmed:33239788;pubmed:35649578   YueLab RNA Seq Skin rep1 GSM3934895   source name:Tissue|strain:Tuebingen|tissue:Skin YueLab RNA Seq Skin rep1 RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged Tissue   For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions strain:Tuebingen|tissue:Skin GSM3934895 GSM3934895: YueLab RNA Seq Skin rep1; Danio rerio; RNA Seq GSM3934895   1 For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. GEO Accession:GSM3934895 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer   SRP213938     YueLab-RNA-Seq-Skin-rep1_1.fastq.gz YueLab-RNA-Seq-Skin-rep1_2.fastq.gz fastq fastq 2565035707.0 21260839.0 GSM3934895 r1 0:60.48 1:60.17 A:670789880;C:599392091;G:585931498;T:708654706;N:267532 60 60     670789880 599392091 585931498 708654706 267532 SRX6422903 SRS5079693 SRA919194 GEO Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine 2 0.96148 0.96283 0.12215 0.11903 0.70015 0.70114 0.47321 0.47375 60 60 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United States 2019-07-09 Pharyngula Embryo Skin Surface Structure
55982 55982 SRR10895887 SRX7564592 SRS6001802 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 007   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Skin|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100101924 L01 9 CL100101924 L01 9       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100101924_L01_550_1.fq.gz CL100101924_L01_550_2.fq.gz fastq fastq 8780226200.0 87802262.0 CL100101924 L01 550 1.fq.gz 0:100 1:100 A:2363664067;C:1983383192;G:2025795704;T:2396528723;N:10854514 100 100     2363664067 1983383192 2025795704 2396528723 10854514 SRX7564592 SRS6001802 SRA1026516 BGI|BGI-Research BGI 1 0.92686   0.10085   0.70903   0.51488   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Skin Surface Structure
55983 55983 SRR10895888 SRX7564591 SRS6001802 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 007   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Skin|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100101924 L01 8 CL100101924 L01 8       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100101924_L01_549_2.fq.gz CL100101924_L01_549_1.fq.gz fastq fastq 9805051200.0 98050512.0 CL100101924 L01 549 1.fq.gz 0:100 1:100 A:2663706429;C:2193838939;G:2241619945;T:2693859046;N:12026841 100 100     2663706429 2193838939 2241619945 2693859046 12026841 SRX7564591 SRS6001802 SRA1026516 BGI|BGI-Research BGI 1 0.92652   0.0983   0.71043   0.53401   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Skin Surface Structure
55984 55984 SRR10895889 SRX7564590 SRS6001802 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 007   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Skin|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100101924 L01 7 CL100101924 L01 7       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100101924_L01_547_1.fq.gz CL100101924_L01_547_2.fq.gz fastq fastq 9137587600.0 91375876.0 CL100101924 L01 547 1.fq.gz 0:100 1:100 A:2471506783;C:2052808667;G:2096159921;T:2505897469;N:11214760 100 100     2471506783 2052808667 2096159921 2505897469 11214760 SRX7564590 SRS6001802 SRA1026516 BGI|BGI-Research BGI 1 0.93126   0.09864   0.70613   0.51947   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Skin Surface Structure
55985 55985 SRR10895890 SRX7564589 SRS6001802 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 007   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Skin|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100101924 L01 6 CL100101924 L01 6       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100101924_L01_551_1.fq.gz CL100101924_L01_551_2.fq.gz fastq fastq 7665129600.0 76651296.0 CL100101924 L01 551 1.fq.gz 0:100 1:100 A:2062939973;C:1731950056;G:1768675635;T:2092110510;N:9453426 100 100     2062939973 1731950056 1768675635 2092110510 9453426 SRX7564589 SRS6001802 SRA1026516 BGI|BGI-Research BGI 1 0.93022   0.10662   0.70512   0.50773   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Skin Surface Structure
55986 55986 SRR10895892 SRX7564587 SRS6001802 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 007   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Skin|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100101924 L01 5 CL100101924 L01 5       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100101924_L01_548_1.fq.gz CL100101924_L01_548_2.fq.gz fastq fastq 6527814200.0 65278142.0 CL100101924 L01 548 1.fq.gz 0:100 1:100 A:1748761735;C:1483522306;G:1516468410;T:1771028617;N:8033132 100 100     1748761735 1483522306 1516468410 1771028617 8033132 SRX7564587 SRS6001802 SRA1026516 BGI|BGI-Research BGI 1 0.93149   0.09371   0.70542   0.51664   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Skin Surface Structure
59125 59125 SRR11684038 SRX8244841 SRS6592476 SRP259990 PRJNA630162 Zebrafish adult skin mpeg+ cells GSE149788 Transcriptome Analysis We compared hematopoietic and non hematopoietic mpeg1.1+ cells from the skin of wild type fish with non hematopoietic cells from the skin of zebrafish lacking functional csf1r. We reval that non hematopoietic mpeg1.1 cells from wild type and csf1rDM fish show no major differences and likely represent metaphocytes a newly characterized ectoderm derived cell population in the skin. Both non hematopoietic mpeg1.1+ cell populations from wild type and csf1r mutatns show a major downregulations in canonical macrophages signature genes as compared to hematopoietic mpeg1.1 cells from wild type fish. Overall design: Two biological replicates were analyzed for each of 6 conditions three genotypes; two treatments per genotype parent bioproject:PRJNA630158 pubmed:32367800   GFE6 Csf1r mutant.3 GSM4512730   tissue:skin mpeg1.1 GFP+ cells|developmental stage:adult 3mo|genotype:csf1raj4e1/j4e1; csf1rbsa1503/csf1rbsa1503 mpeg1 EGFP; Kdrl:Cre; act2b:loxP STOP loxP DsRedexpress|treatment:untreated GFE6 Csf1r mutant.3 Sequencing and base calling was performed on the IlIllumina Novaseq 6000 Paired end reads were aligned to the GRCz11.94 danio rerio genome using STAR version 2.5.4b software. Annotations Danio rerio.GRCz11.94.gtf were obtained from ftp.Ensembl.org Gene level counts were obtained using HTSeq count version 0.11.0 Differential gene expression analysis: EdgeR Bioconductor. GSEA: GAGE Bioconductor Genome build: GRCz11.94 Supplementary files format and content: CPM values [.csv] semicolon delimited files skin mpeg1.1 GFP+ cells   RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix Standard adult zebrafish rearing conditions in multilink system at 26° C with 12:12 h ligt/dark cycle developmental stage:adult 3mo|genotype:csf1raj4e1/j4e1; csf1rbsa1503/csf1rbsa1503 mpeg1 EGFP; Kdrl:Cre; act2b:loxP STOP loxP DsRedexpress|treatment:untreated GSM4512730 GSM4512730: GFE6 Csf1r mutant.3; Danio rerio; RNA Seq GSM4512730   1 RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix GEO Accession:GSM4512730 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP259990     so-zf94_GFE6-Csf1r-mutant_S6_R2_001.fastq.gz so-zf94_GFE6-Csf1r-mutant_S6_R1_001.fastq.gz fastq fastq 14494840876.0 71756638.0 GSM4512730 r1 0:101 1:101 A:3899647300;C:3479135941;G:3237570754;T:3878261390;N:225491 101 101     3899647300 3479135941 3237570754 3878261390 225491 SRX8244841 SRS6592476 SRA1072141 GEO Erasmus MC 2 0.64161 0.64139 0.26871 0.27571 0.80827 0.80687 0.57871 0.57509 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Netherlands 2020-05-04 Adult Adult Skin Surface Structure
59126 59126 SRR11684037 SRX8244840 SRS6592475 SRP259990 PRJNA630162 Zebrafish adult skin mpeg+ cells GSE149788 Transcriptome Analysis We compared hematopoietic and non hematopoietic mpeg1.1+ cells from the skin of wild type fish with non hematopoietic cells from the skin of zebrafish lacking functional csf1r. We reval that non hematopoietic mpeg1.1 cells from wild type and csf1rDM fish show no major differences and likely represent metaphocytes a newly characterized ectoderm derived cell population in the skin. Both non hematopoietic mpeg1.1+ cell populations from wild type and csf1r mutatns show a major downregulations in canonical macrophages signature genes as compared to hematopoietic mpeg1.1 cells from wild type fish. Overall design: Two biological replicates were analyzed for each of 6 conditions three genotypes; two treatments per genotype parent bioproject:PRJNA630158 pubmed:32367800   GFE5 Csf1r mutant.2 GSM4512729   tissue:skin mpeg1.1 GFP+ cells|developmental stage:adult 3mo|genotype:csf1raj4e1/j4e1; csf1rbsa1503/csf1rbsa1503 tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated GFE5 Csf1r mutant.2 Sequencing and base calling was performed on the IlIllumina Novaseq 6000 Paired end reads were aligned to the GRCz11.94 danio rerio genome using STAR version 2.5.4b software. Annotations Danio rerio.GRCz11.94.gtf were obtained from ftp.Ensembl.org Gene level counts were obtained using HTSeq count version 0.11.0 Differential gene expression analysis: EdgeR Bioconductor. GSEA: GAGE Bioconductor Genome build: GRCz11.94 Supplementary files format and content: CPM values [.csv] semicolon delimited files skin mpeg1.1 GFP+ cells   RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix Standard adult zebrafish rearing conditions in multilink system at 26° C with 12:12 h ligt/dark cycle developmental stage:adult 3mo|genotype:csf1raj4e1/j4e1; csf1rbsa1503/csf1rbsa1503 tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated GSM4512729 GSM4512729: GFE5 Csf1r mutant.2; Danio rerio; RNA Seq GSM4512729   1 RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix GEO Accession:GSM4512729 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP259990     so-zf94_GFE5-Csf1r-mutant_S5_R2_001.fastq.gz so-zf94_GFE5-Csf1r-mutant_S5_R1_001.fastq.gz fastq fastq 13759568552.0 68116676.0 GSM4512729 r1 0:101 1:101 A:3660704043;C:3344175315;G:3105211222;T:3649262807;N:215165 101 101     3660704043 3344175315 3105211222 3649262807 215165 SRX8244840 SRS6592475 SRA1072141 GEO Erasmus MC 2 0.69777 0.70166 0.28564 0.29683 0.79945 0.80022 0.58707 0.58207 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Netherlands 2020-05-04 Adult Adult Skin Surface Structure
59127 59127 SRR11684036 SRX8244839 SRS6592474 SRP259990 PRJNA630162 Zebrafish adult skin mpeg+ cells GSE149788 Transcriptome Analysis We compared hematopoietic and non hematopoietic mpeg1.1+ cells from the skin of wild type fish with non hematopoietic cells from the skin of zebrafish lacking functional csf1r. We reval that non hematopoietic mpeg1.1 cells from wild type and csf1rDM fish show no major differences and likely represent metaphocytes a newly characterized ectoderm derived cell population in the skin. Both non hematopoietic mpeg1.1+ cell populations from wild type and csf1r mutatns show a major downregulations in canonical macrophages signature genes as compared to hematopoietic mpeg1.1 cells from wild type fish. Overall design: Two biological replicates were analyzed for each of 6 conditions three genotypes; two treatments per genotype parent bioproject:PRJNA630158 pubmed:32367800   GFE4 B Switch.1 GSM4512728   tissue:skin mpeg1.1 GFP+; act2b:loxP STOP loxP DsRedexpress+ cells|developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated GFE4 B Switch.1 Sequencing and base calling was performed on the IlIllumina Novaseq 6000 Paired end reads were aligned to the GRCz11.94 danio rerio genome using STAR version 2.5.4b software. Annotations Danio rerio.GRCz11.94.gtf were obtained from ftp.Ensembl.org Gene level counts were obtained using HTSeq count version 0.11.0 Differential gene expression analysis: EdgeR Bioconductor. GSEA: GAGE Bioconductor Genome build: GRCz11.94 Supplementary files format and content: CPM values [.csv] semicolon delimited files skin mpeg1.1 GFP+; act2b:loxP STOP loxP DsRedexpress+ cells   RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix Standard adult zebrafish rearing conditions in multilink system at 26° C with 12:12 h ligt/dark cycle developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated GSM4512728 GSM4512728: GFE4 B Switch.1; Danio rerio; RNA Seq GSM4512728   1 RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix GEO Accession:GSM4512728 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP259990     so-zf94_GFE4-B-Switch_WT_S4_R2_001.fastq.gz so-zf94_GFE4-B-Switch_WT_S4_R1_001.fastq.gz fastq fastq 10963685744.0 54275672.0 GSM4512728 r1 0:101 1:101 A:2843051618;C:2733369632;G:2559200274;T:2827894333;N:169887 101 101     2843051618 2733369632 2559200274 2827894333 169887 SRX8244839 SRS6592474 SRA1072141 GEO Erasmus MC 2 0.81437 0.80007 0.30275 0.3056 0.7933 0.79427 0.60512 0.50903 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Netherlands 2020-05-04 Adult Adult Skin Surface Structure
59128 59128 SRR11684035 SRX8244838 SRS6592477 SRP259990 PRJNA630162 Zebrafish adult skin mpeg+ cells GSE149788 Transcriptome Analysis We compared hematopoietic and non hematopoietic mpeg1.1+ cells from the skin of wild type fish with non hematopoietic cells from the skin of zebrafish lacking functional csf1r. We reval that non hematopoietic mpeg1.1 cells from wild type and csf1rDM fish show no major differences and likely represent metaphocytes a newly characterized ectoderm derived cell population in the skin. Both non hematopoietic mpeg1.1+ cell populations from wild type and csf1r mutatns show a major downregulations in canonical macrophages signature genes as compared to hematopoietic mpeg1.1 cells from wild type fish. Overall design: Two biological replicates were analyzed for each of 6 conditions three genotypes; two treatments per genotype parent bioproject:PRJNA630158 pubmed:32367800   GFE3 B Switch.3 GSM4512727   tissue:skin mpeg1.1 GFP+; act2b:loxP STOP loxP DsRedexpress+ cells|developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated GFE3 B Switch.3 Sequencing and base calling was performed on the IlIllumina Novaseq 6000 Paired end reads were aligned to the GRCz11.94 danio rerio genome using STAR version 2.5.4b software. Annotations Danio rerio.GRCz11.94.gtf were obtained from ftp.Ensembl.org Gene level counts were obtained using HTSeq count version 0.11.0 Differential gene expression analysis: EdgeR Bioconductor. GSEA: GAGE Bioconductor Genome build: GRCz11.94 Supplementary files format and content: CPM values [.csv] semicolon delimited files skin mpeg1.1 GFP+; act2b:loxP STOP loxP DsRedexpress+ cells   RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix Standard adult zebrafish rearing conditions in multilink system at 26° C with 12:12 h ligt/dark cycle developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated GSM4512727 GSM4512727: GFE3 B Switch.3; Danio rerio; RNA Seq GSM4512727   1 RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix GEO Accession:GSM4512727 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP259990     so-zf94_GFE3-B-Switch_WT_S3_R2_001.fastq.gz so-zf94_GFE3-B-Switch_WT_S3_R1_001.fastq.gz fastq fastq 12782078634.0 63277617.0 GSM4512727 r1 0:101 1:101 A:3381512327;C:3122362574;G:2918446203;T:3359558840;N:198690 101 101     3381512327 3122362574 2918446203 3359558840 198690 SRX8244838 SRS6592477 SRA1072141 GEO Erasmus MC 2 0.76741 0.76247 0.29132 0.2981 0.78512 0.78561 0.58337 0.57753 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Netherlands 2020-05-04 Adult Adult Skin Surface Structure
59129 59129 SRR11684034 SRX8244837 SRS6595814 SRP259990 PRJNA630162 Zebrafish adult skin mpeg+ cells GSE149788 Transcriptome Analysis We compared hematopoietic and non hematopoietic mpeg1.1+ cells from the skin of wild type fish with non hematopoietic cells from the skin of zebrafish lacking functional csf1r. We reval that non hematopoietic mpeg1.1 cells from wild type and csf1rDM fish show no major differences and likely represent metaphocytes a newly characterized ectoderm derived cell population in the skin. Both non hematopoietic mpeg1.1+ cell populations from wild type and csf1r mutatns show a major downregulations in canonical macrophages signature genes as compared to hematopoietic mpeg1.1 cells from wild type fish. Overall design: Two biological replicates were analyzed for each of 6 conditions three genotypes; two treatments per genotype parent bioproject:PRJNA630158 pubmed:32367800   GFE2 WT.2 GSM4512726   tissue:skin mpeg1.1 GFP+ cells|developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated GFE2 WT.2 Sequencing and base calling was performed on the IlIllumina Novaseq 6000 Paired end reads were aligned to the GRCz11.94 danio rerio genome using STAR version 2.5.4b software. Annotations Danio rerio.GRCz11.94.gtf were obtained from ftp.Ensembl.org Gene level counts were obtained using HTSeq count version 0.11.0 Differential gene expression analysis: EdgeR Bioconductor. GSEA: GAGE Bioconductor Genome build: GRCz11.94 Supplementary files format and content: CPM values [.csv] semicolon delimited files skin mpeg1.1 GFP+ cells   RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix Standard adult zebrafish rearing conditions in multilink system at 26° C with 12:12 h ligt/dark cycle developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated GSM4512726 GSM4512726: GFE2 WT.2; Danio rerio; RNA Seq GSM4512726   1 RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix GEO Accession:GSM4512726 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP259990     so-zf94_GFE2-WT_S2_R1_001.fastq.gz so-zf94_GFE2-WT_S2_R2_001.fastq.gz fastq fastq 14364066682.0 71109241.0 GSM4512726 r1 0:101 1:101 A:3728039055;C:3584760331;G:3349868256;T:3701175176;N:223864 101 101     3728039055 3584760331 3349868256 3701175176 223864 SRX8244837 SRS6595814 SRA1072141 GEO Erasmus MC 2 0.84099 0.82969 0.32553 0.33066 0.79226 0.79145 0.6061 0.60266 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Netherlands 2020-05-04 Adult Adult Skin Surface Structure
59130 59130 SRR11684033 SRX8244836 SRS6592473 SRP259990 PRJNA630162 Zebrafish adult skin mpeg+ cells GSE149788 Transcriptome Analysis We compared hematopoietic and non hematopoietic mpeg1.1+ cells from the skin of wild type fish with non hematopoietic cells from the skin of zebrafish lacking functional csf1r. We reval that non hematopoietic mpeg1.1 cells from wild type and csf1rDM fish show no major differences and likely represent metaphocytes a newly characterized ectoderm derived cell population in the skin. Both non hematopoietic mpeg1.1+ cell populations from wild type and csf1r mutatns show a major downregulations in canonical macrophages signature genes as compared to hematopoietic mpeg1.1 cells from wild type fish. Overall design: Two biological replicates were analyzed for each of 6 conditions three genotypes; two treatments per genotype parent bioproject:PRJNA630158 pubmed:32367800   GFE1 WT.1 GSM4512725   tissue:skin mpeg1.1 GFP+ cells|developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated GFE1 WT.1 Sequencing and base calling was performed on the IlIllumina Novaseq 6000 Paired end reads were aligned to the GRCz11.94 danio rerio genome using STAR version 2.5.4b software. Annotations Danio rerio.GRCz11.94.gtf were obtained from ftp.Ensembl.org Gene level counts were obtained using HTSeq count version 0.11.0 Differential gene expression analysis: EdgeR Bioconductor. GSEA: GAGE Bioconductor Genome build: GRCz11.94 Supplementary files format and content: CPM values [.csv] semicolon delimited files skin mpeg1.1 GFP+ cells   RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix Standard adult zebrafish rearing conditions in multilink system at 26° C with 12:12 h ligt/dark cycle developmental stage:adult 3mo|genotype:wild type tgmpeg1 EGFP; tgKdrl:Cre; tgact2b:loxP STOP loxP DsRedexpress|treatment:untreated GSM4512725 GSM4512725: GFE1 WT.1; Danio rerio; RNA Seq GSM4512725   1 RNA isolation from FACS sorted cells was perfored using the miRneasy Micro Kit Qiagen following manufacturer's instruction Indexed cDNA libraries were obtained using the Ovation SoLo RNA seq System NuGen TECAN with the SoLo AnyDeplete probe mix GEO Accession:GSM4512725 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP259990     so-zf94_GFE1-WT_S1_R2_001.fastq.gz so-zf94_GFE1-WT_S1_R1_001.fastq.gz fastq fastq 12446480884.0 61616242.0 GSM4512725 r1 0:101 1:101 A:3368704863;C:2968645301;G:2743627645;T:3365306136;N:196939 101 101     3368704863 2968645301 2743627645 3365306136 196939 SRX8244836 SRS6592473 SRA1072141 GEO Erasmus MC 2 0.79126 0.79765 0.31567 0.32746 0.76893 0.76871 0.55753 0.55755 101 101 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Netherlands 2020-05-04 Adult Adult Skin Surface Structure
67672 67672 SRR17247005 SRX13426046 SRS11327039 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         D2   isolate:not collected|age:3mpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate D2|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S342 S342 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     d2_R1.fq.gz d2_R2.fq.gz fastq fastq 6774255900.0 22580853.0 d2 R1.fq.gz 0:150 1:150 A:1901164418;C:1468805326;G:1485945297;T:1918188680;N:152179 150 150     1901164418 1468805326 1485945297 1918188680 152179 SRX13426046 SRS11327039 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.94179 0.94443 0.0891 0.08968 0.7331 0.73513 0.62221 0.62339 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Adult Adult Skin Surface Structure
67673 67673 SRR17247006 SRX13426045 SRS11327038 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         D1   isolate:not collected|age:3mpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate D1|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S341 S341 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     d1_R1.fq.gz d1_R2.fq.gz fastq fastq 5804251200.0 19347504.0 d1 R1.fq.gz 0:150 1:150 A:1651195300;C:1234370632;G:1251804070;T:1666750262;N:130936 150 150     1651195300 1234370632 1251804070 1666750262 130936 SRX13426045 SRS11327038 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.83287 0.83611 0.08737 0.08841 0.7498 0.75162 0.64045 0.66425 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Adult Adult Skin Surface Structure
67674 67674 SRR17247007 SRX13426044 SRS11327036 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         C3   isolate:not collected|age:41dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate C3|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S340 S340 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     c3_R1.fq.gz c3_R2.fq.gz fastq fastq 4841497500.0 16138325.0 c3 R1.fq.gz 0:150 1:150 A:1386818341;C:1017922211;G:1041712160;T:1394940280;N:104508 150 150     1386818341 1017922211 1041712160 1394940280 104508 SRX13426044 SRS11327036 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.90078 0.9042 0.12147 0.12291 0.73184 0.73497 0.57479 0.5555 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67675 67675 SRR17247008 SRX13426043 SRS11327037 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         C2   isolate:not collected|age:41dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate C2|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S339 S339 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     c2_R1.fq.gz c2_R2.fq.gz fastq fastq 7688124900.0 25627083.0 c2 R1.fq.gz 0:150 1:150 A:2102172030;C:1722525598;G:1752732030;T:2110524143;N:171099 150 150     2102172030 1722525598 1752732030 2110524143 171099 SRX13426043 SRS11327037 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.8669 0.86816 0.08761 0.08688 0.70725 0.71145 0.49101 0.48619 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67676 67676 SRR17247009 SRX13426042 SRS11327035 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         C1   isolate:not collected|age:41dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate C1|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S338 S338 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     c1_R1.fq.gz c1_R2.fq.gz fastq fastq 7456776900.0 24855923.0 c1 R1.fq.gz 0:150 1:150 A:2051878608;C:1656315578;G:1687161312;T:2061254398;N:167004 150 150     2051878608 1656315578 1687161312 2061254398 167004 SRX13426042 SRS11327035 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.82556 0.82709 0.09055 0.08946 0.70471 0.70857 0.48138 0.4916 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67677 67677 SRR17247010 SRX13426041 SRS11327033 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         B3   isolate:not collected|age:33dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate B3|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S337 S337 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     b3_R1.fq.gz b3_R2.fq.gz fastq fastq 9228717900.0 30762393.0 b3 R1.fq.gz 0:150 1:150 A:2487982964;C:2099691030;G:2134638107;T:2506202131;N:203668 150 150     2487982964 2099691030 2134638107 2506202131 203668 SRX13426041 SRS11327033 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.66624 0.66885 0.06853 0.06779 0.71887 0.72066 0.4895 0.49681 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67678 67678 SRR17247011 SRX13426040 SRS11327034 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         B2   isolate:not collected|age:33dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate B2|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S336 S336 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     b2_R1.fq.gz b2_R2.fq.gz fastq fastq 6040557600.0 20135192.0 b2 R1.fq.gz 0:150 1:150 A:1664821294;C:1338719408;G:1359251973;T:1677628310;N:136615 150 150     1664821294 1338719408 1359251973 1677628310 136615 SRX13426040 SRS11327034 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.93426 0.93571 0.10066 0.10055 0.69631 0.69897 0.47588 0.46263 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67679 67679 SRR17247012 SRX13426039 SRS11327032 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         B1   isolate:not collected|age:33dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate B1|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S335 S335 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     b1_R1.fq.gz b1_R2.fq.gz fastq fastq 6368555100.0 21228517.0 b1 R1.fq.gz 0:150 1:150 A:1748027301;C:1419234076;G:1440533749;T:1760617536;N:142438 150 150     1748027301 1419234076 1440533749 1760617536 142438 SRX13426039 SRS11327032 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.93385 0.93455 0.09654 0.09586 0.70031 0.70274 0.4679 0.47428 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67680 67680 SRR17247013 SRX13426038 SRS11327030 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         D3   isolate:not collected|age:3mpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate D3|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S343 S343 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     d3_R2.fq.gz d3_R1.fq.gz fastq fastq 4661307000.0 15537690.0 d3 R1.fq.gz 0:150 1:150 A:1335395274;C:980634616;G:990646677;T:1354525081;N:105352 150 150     1335395274 980634616 990646677 1354525081 105352 SRX13426038 SRS11327030 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.55593 0.55991 0.04498 0.04594 0.79884 0.80079 0.51906 0.50799 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Adult Adult Skin Surface Structure
67681 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

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