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398 rows where tissue_curation = "Skin"

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devstage_curation 7

experiment.library_selection 6

devstage_curation_coarse 6

experiment.platform 4

experiment.library_strategy 4

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Skin · 398 ✖
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
3759 3759 ERR1294279 ERX1365625 ERS1067820 ERP014370 PRJEB12848 Danio rerio Mau mutants skin Transcriptome ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265 Other Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects we analyze skin transcriptome of adult wild type TU fish and two mau alleles. ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25     Mau tVBU1/tVBU1 skin transcriptome SAMEA3880686 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 9 vbu13 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 vbu13_GCCAAT_L008_R1_001.fastq.gz fastq 2376143675.0 23526175.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 9 0:101 A:655940769;C:534990399;G:527934646;T:655773043;N:1504818 101       655940769 534990399 527934646 655773043 1504818 ERX1365625 ERS1067820 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.95443   0.10666   0.73176   0.50978   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3760 3760 ERR1294278 ERX1365624 ERS1067820 ERP014370 PRJEB12848 Danio rerio Mau mutants skin Transcriptome ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265 Other Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects we analyze skin transcriptome of adult wild type TU fish and two mau alleles. ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25     Mau tVBU1/tVBU1 skin transcriptome SAMEA3880686 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 8 vbu12 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 vbu12_GTGAAA_L008_R1_001.fastq.gz fastq 1449181835.0 14348335.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 8 0:101 A:399518584;C:327615685;G:323868050;T:397240465;N:939051 101       399518584 327615685 323868050 397240465 939051 ERX1365624 ERS1067820 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.95893   0.09315   0.73464   0.48744   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3761 3761 ERR1294277 ERX1365623 ERS1067820 ERP014370 PRJEB12848 Danio rerio Mau mutants skin Transcriptome ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265 Other Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects we analyze skin transcriptome of adult wild type TU fish and two mau alleles. ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25     Mau tVBU1/tVBU1 skin transcriptome SAMEA3880686 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880686|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VBU1|allele:mau tVBU1/tVBU1|common name:zebrafish|dev stage:adult|sample name:VBU1|tissue type:skin                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 7 vbu11 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 vbu11_GTCCGC_L008_R1_001.fastq.gz fastq 1455235169.0 14408269.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 7 0:101 A:392100064;C:337980617;G:331091626;T:393178582;N:884280 101       392100064 337980617 331091626 393178582 884280 ERX1365623 ERS1067820 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.95485   0.08016   0.72845   0.47549   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3762 3762 ERR1294276 ERX1365622 ERS1067819 ERP014370 PRJEB12848 Danio rerio Mau mutants skin Transcriptome ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265 Other Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects we analyze skin transcriptome of adult wild type TU fish and two mau alleles. ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25     Mau tVE1/tVE1 skin transcriptome SAMEA3880685 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 6 ve13 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 ve13_CCGTCC_L008_R1_001.fastq.gz fastq 1029294030.0 10191030.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:670 6 0:101 A:284612731;C:231451012;G:228443320;T:284135536;N:651431 101       284612731 231451012 228443320 284135536 651431 ERX1365622 ERS1067819 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.93287   0.10726   0.72585   0.4913   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3763 3763 ERR1294275 ERX1365621 ERS1067819 ERP014370 PRJEB12848 Danio rerio Mau mutants skin Transcriptome ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265 Other Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects we analyze skin transcriptome of adult wild type TU fish and two mau alleles. ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25     Mau tVE1/tVE1 skin transcriptome SAMEA3880685 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 5 ve12 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 ve12_ATGTCA_L008_R1_001.fastq.gz fastq 1446322222.0 14320022.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 5 0:101 A:400821160;C:324210104;G:320286425;T:400078485;N:926048 101       400821160 324210104 320286425 400078485 926048 ERX1365621 ERS1067819 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.92778   0.09489   0.73093   0.48493   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3764 3764 ERR1294274 ERX1365620 ERS1067819 ERP014370 PRJEB12848 Danio rerio Mau mutants skin Transcriptome ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265 Other Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects we analyze skin transcriptome of adult wild type TU fish and two mau alleles. ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25     Mau tVE1/tVE1 skin transcriptome SAMEA3880685 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880685|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:VE1|allele:mau tVE1/tVE1|common name:zebrafish|dev stage:adult|sample name:VE1|tissue type:skin                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 4 ve11 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 ve11_AGTTCC_L008_R1_001.fastq.gz fastq 2117238861.0 20962761.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 4 0:101 A:591654664;C:469803769;G:462550117;T:591863795;N:1366516 101       591654664 469803769 462550117 591863795 1366516 ERX1365620 ERS1067819 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.93146   0.09666   0.73501   0.48749   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3765 3765 ERR1294273 ERX1365619 ERS1067818 ERP014370 PRJEB12848 Danio rerio Mau mutants skin Transcriptome ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265 Other Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects we analyze skin transcriptome of adult wild type TU fish and two mau alleles. ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25     WT skin transcriptome SAMEA3880684 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 3 wt3 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 wt3_AGTCAA_L008_R1_001.fastq.gz fastq 2631687411.0 26056311.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 3 0:101 A:734843629;C:584316000;G:577487406;T:733356850;N:1683526 101       734843629 584316000 577487406 733356850 1683526 ERX1365619 ERS1067818 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.95114   0.1036   0.72474   0.48261   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3766 3766 ERR1294272 ERX1365618 ERS1067818 ERP014370 PRJEB12848 Danio rerio Mau mutants skin Transcriptome ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265 Other Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects we analyze skin transcriptome of adult wild type TU fish and two mau alleles. ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25     WT skin transcriptome SAMEA3880684 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 2 wt2 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 wt2_CTTGTA_L008_R1_001.fastq.gz fastq 2093443463.0 20727163.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:669 2 0:101 A:607582034;C:442802229;G:437957089;T:603752294;N:1349817 101       607582034 442802229 437957089 603752294 1349817 ERX1365618 ERS1067818 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.94792   0.10892   0.73277   0.51067   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
3767 3767 ERR1294271 ERX1365617 ERS1067818 ERP014370 PRJEB12848 Danio rerio Mau mutants skin Transcriptome ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-25-02-2016-18:42:00:594-265 Other Mau/Aqp3a dominant mutants of zebrafish Danio rerio are characterized by broken stripes and short fins. To identify signaling pathways affected by mau mutations and leading to pigment patterning defects we analyze skin transcriptome of adult wild type TU fish and two mau alleles. ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2016 02 25     WT skin transcriptome SAMEA3880684 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2016 05 24|ENA last update:2016 02 25|External Id:SAMEA3880684|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2016 05 24T17:02:01Z|INSDC last update:2016 02 25T18:42:06Z|INSDC status:public|Submitter Id:WT|allele:mau +/+|common name:zebrafish|dev stage:adult|sample name:WT|tissue type:skin                 Illumina HiSeq 2000 sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:668 1 wt1 1 Illumina TruSeq RNA   RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2000   ERP014370 Illumina HiSeq 2000 sequencing ENA FIRST PUBLIC:2016 05 24|ENA LAST UPDATE:2018 11 16 wt1_CAGATC_L008_R1_001.fastq.gz fastq 1701561241.0 16847141.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 25 02 2016 18:41:58:668 1 0:101 A:505358711;C:348893979;G:343445186;T:502880170;N:983195 101       505358711 348893979 343445186 502880170 983195 ERX1365617 ERS1067818 ERA567249 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 1 0.94565   0.13032   0.73669   0.50473   101   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2016-02-25 Adult Adult Skin Surface Structure
9770 9770 ERR5838122 ERX5487778 ERS6337138 ERP119543 PRJEB36360 Transcriptomic analysis of adult skin from 9 Danio species ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27 Other Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21 PUBMED:33277491 Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. Transcriptomic analysis of adult skin from 9 Danio species SAMEA8652584 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652584|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:05 Danio rerio adult skin 5|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:05 Danio rerio adult skin 5|sex:male|tissue type:skin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 5 unspecified 1 TruSeq stranded mRNA Illumina   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP119543 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29 S1385Nr5.1.fastq.gz S1385Nr5.2.fastq.gz fastq fastq 6912206316.0 34306523.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 5 0:100.74 1:100.74 A:1853779551;C:1607929988;G:1658402611;T:1792045990;N:48176 100 100     1853779551 1607929988 1658402611 1792045990 48176 ERX5487778 ERS6337138 ERA4129786 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 2 0.96095 0.962 0.08049 0.07821 0.70654 0.70926 0.51398 0.51064 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-03-21 Adult Adult Skin Surface Structure
9771 9771 ERR5838121 ERX5487777 ERS6337136 ERP119543 PRJEB36360 Transcriptomic analysis of adult skin from 9 Danio species ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27 Other Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21 PUBMED:33277491 Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. Transcriptomic analysis of adult skin from 9 Danio species SAMEA8652582 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652582|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:04 Danio rerio adult skin 4|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:04 Danio rerio adult skin 4|sex:male|tissue type:skin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 4 unspecified 1 TruSeq stranded mRNA Illumina   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP119543 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29 S1385Nr4.1.fastq.gz S1385Nr4.2.fastq.gz fastq fastq 6161942050.0 30595009.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 4 0:100.70 1:100.70 A:1642716052;C:1446485458;G:1490121106;T:1582576605;N:42829 100 100     1642716052 1446485458 1490121106 1582576605 42829 ERX5487777 ERS6337136 ERA4129786 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 2 0.96544 0.96564 0.07368 0.07303 0.70822 0.71092 0.50154 0.50781 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-03-21 Adult Adult Skin Surface Structure
9772 9772 ERR5838120 ERX5487776 ERS6337133 ERP119543 PRJEB36360 Transcriptomic analysis of adult skin from 9 Danio species ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27 Other Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21 PUBMED:33277491 Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. Transcriptomic analysis of adult skin from 9 Danio species SAMEA8652579 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652579|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:03 Danio rerio adult skin 3|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:03 Danio rerio adult skin 3|sex:female|tissue type:skin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 3 unspecified 1 TruSeq stranded mRNA Illumina   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP119543 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29 S1385Nr3.1.fastq.gz S1385Nr3.2.fastq.gz fastq fastq 7422881394.0 36866805.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 3 0:100.67 1:100.67 A:1950275527;C:1768648993;G:1827362519;T:1876542858;N:51497 100 100     1950275527 1768648993 1827362519 1876542858 51497 ERX5487776 ERS6337133 ERA4129786 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 2 0.97031 0.97047 0.04915 0.04817 0.71459 0.71894 0.51089 0.5097 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-03-21 Adult Adult Skin Surface Structure
9773 9773 ERR5838119 ERX5487775 ERS6337132 ERP119543 PRJEB36360 Transcriptomic analysis of adult skin from 9 Danio species ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27 Other Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21 PUBMED:33277491 Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. Transcriptomic analysis of adult skin from 9 Danio species SAMEA8652578 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652578|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:02 Danio rerio adult skin 2|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:02 Danio rerio adult skin 2|sex:female|tissue type:skin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 2 unspecified 1 TruSeq stranded mRNA Illumina   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP119543 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29 S1385Nr2.1.fastq.gz S1385Nr2.2.fastq.gz fastq fastq 7006718028.0 34786110.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 2 0:100.71 1:100.71 A:1847371523;C:1665346769;G:1712373266;T:1781565768;N:60702 100 100     1847371523 1665346769 1712373266 1781565768 60702 ERX5487775 ERS6337132 ERA4129786 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 2 0.96136 0.96039 0.05872 0.05752 0.70325 0.70674 0.46717 0.48218 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-03-21 Adult Adult Skin Surface Structure
9774 9774 ERR5838118 ERX5487774 ERS6337063 ERP119543 PRJEB36360 Transcriptomic analysis of adult skin from 9 Danio species ena-STUDY-MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY-22-01-2020-08:38:04:562-27 Other Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. ENA FIRST PUBLIC:2020 03 21|ENA LAST UPDATE:2021 04 21 PUBMED:33277491 Transcriptomic analysis was carried out on adult skin of the flanks for the following nine Danio species: Danio rerio Danio aesculapii Danio nigrofasciatus Danio tinwini Danio kyathit Danio albolineatus Danio choprae Danio margaritatus and Danio erythromicron. Five replicates per species were carried out. Each replicate was derived from a single fish with skin samples coming from both flanks. Paired end stranded RNA Seq was then carried out. Transcriptomic analysis of adult skin from 9 Danio species SAMEA8652509 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY ENA first public:2021 04 30|ENA last update:2021 04 29|External Id:SAMEA8652509|INSDC center alias:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC center name:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|INSDC first public:2021 04 30T00:30:20Z|INSDC last update:2021 04 29T02:45:00Z|INSDC status:public|Submitter Id:01 Danio rerio adult skin 1|collected by:Marco Podobnik|collection date:2019 08 23|common name:zebrafish|dev stage:adult|identified by:Marco Podobnik|isolation source:Tuebingen|sample name:01 Danio rerio adult skin 1|sex:male|tissue type:skin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 1 unspecified 1 TruSeq stranded mRNA Illumina   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP119543 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2021 04 29 S1385Nr1.1.fastq.gz S1385Nr1.2.fastq.gz fastq fastq 6586457266.0 32719900.0 ena RUN MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 28 04 2021 08:27:34:651 1 0:100.65 1:100.65 A:1709547533;C:1593125315;G:1617088678;T:1666650824;N:44916 100 100     1709547533 1593125315 1617088678 1666650824 44916 ERX5487774 ERS6337063 ERA4129786 MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY|European Nucleotide Archive MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY 2 0.9531 0.95366 0.07763 0.07567 0.71384 0.71634 0.52409 0.52475 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2020-03-21 Adult Adult Skin Surface Structure
25297 25297 SRR25764099 SRX21486772 SRS18719072 SRP457109 PRJNA1009810 Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish GSE241757 Transcriptome Analysis Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.   pubmed:38265193   Adult itgb4+ basal cells GSM7734879   tissue:epidermal cells|cell type:adult fin epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing Adult itgb4+ basal cells High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values. epidermal cells Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. cell type:adult fin epidermal basal cells|genotype:Tgitgb4:mcherry GSM7734879 GSM7734879: Adult itgb4+ basal cells; Danio rerio; RNA Seq GSM7734879 r1 GSM7734879 1 The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP457109     Adult_itgb4mcherry_S230_R1_001.fastq.gz Adult_itgb4mcherry_S230_R2_001.fastq.gz fastq fastq 5035430000.0 12588575.0 GSM7734879 r1 0:200 1:200 A:1339392170;C:1117195164;G:1254708952;T:1323174485;N:959229 200 200     1339392170 1117195164 1254708952 1323174485 959229 SRX21486772 SRS18719072 SRA1700438 Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology 2 0.01543 0.02468 0.00098 0.00102 0.99318 0.99387 0.47878 0.31718 200 200 T T mates < 9% mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2023-08-28 Adult Adult Skin Surface Structure
25298 25298 SRR25764100 SRX21486771 SRS18719071 SRP457109 PRJNA1009810 Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish GSE241757 Transcriptome Analysis Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.   pubmed:38265193   1 dpf itgb4+ embryonic basal precursors rep2 GSM7734878   tissue:epidermal cells|cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing 1 dpf itgb4+ embryonic basal precursors rep2 High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values. epidermal cells Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry GSM7734878 GSM7734878: 1 dpf itgb4+ embryonic basal precursors rep2; Danio rerio; RNA Seq GSM7734878 r1 GSM7734878 1 The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP457109     itgb4mcherry_2_S229_R1_001.fastq.gz itgb4mcherry_2_S229_R2_001.fastq.gz fastq fastq 6040245600.0 15100614.0 GSM7734878 r1 0:200 1:200 A:1588346322;C:1356558310;G:1524614760;T:1569583583;N:1142625 200 200     1588346322 1356558310 1524614760 1569583583 1142625 SRX21486771 SRS18719071 SRA1700438 Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology 2 0.0156 0.0191 0.00074 0.00093 0.99024 0.99088 0.47058 0.47838 200 200 T T mates < 9% mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2023-08-28 Multi-stage Multi-stage Skin Surface Structure
25299 25299 SRR25764101 SRX21486770 SRS18719070 SRP457109 PRJNA1009810 Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish GSE241757 Transcriptome Analysis Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.   pubmed:38265193   1 dpf itgb4+ embryonic basal precursors rep1 GSM7734877   tissue:epidermal cells|cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry|geo loc name:missing|collection date:missing 1 dpf itgb4+ embryonic basal precursors rep1 High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values. epidermal cells Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. cell type:embryonic epidermal basal cells|genotype:Tgitgb4:mcherry GSM7734877 GSM7734877: 1 dpf itgb4+ embryonic basal precursors rep1; Danio rerio; RNA Seq GSM7734877 r1 GSM7734877 1 The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP457109     itgb4mcherry_1_S20_R1_001.fastq.gz itgb4mcherry_1_S20_R2_001.fastq.gz fastq fastq 7055215600.0 17638039.0 GSM7734877 r1 0:200 1:200 A:1894635584;C:1556854856;G:1769420212;T:1825520802;N:8784146 200 200     1894635584 1556854856 1769420212 1825520802 8784146 SRX21486770 SRS18719070 SRA1700438 Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology 2 0.01135 0.01881 0.00043 0.00016 0.9932 0.99543 0.46234 0.43106 200 200 T T mates < 9% mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2023-08-28 Multi-stage Multi-stage Skin Surface Structure
25300 25300 SRR25764102 SRX21486769 SRS18719069 SRP457109 PRJNA1009810 Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish GSE241757 Transcriptome Analysis Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.   pubmed:38265193   1 dpf krt4+ embryonic periderm cells rep2 GSM7734876   tissue:epidermal cells|cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp|geo loc name:missing|collection date:missing 1 dpf krt4+ embryonic periderm cells rep2 High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values. epidermal cells Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp GSM7734876 GSM7734876: 1 dpf krt4+ embryonic periderm cells rep2; Danio rerio; RNA Seq GSM7734876 r1 GSM7734876 1 The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP457109     krt4cre-gfp_2_S4_R2_001.fastq.gz krt4cre-gfp_2_S4_R1_001.fastq.gz fastq fastq 9439207600.0 23598019.0 GSM7734876 r1 0:200 1:200 A:2499982675;C:2086665360;G:2395002073;T:2454282285;N:3275207 200 200     2499982675 2086665360 2395002073 2454282285 3275207 SRX21486769 SRS18719069 SRA1700438 Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology 2 0.44931 0.01877 0.02236 0.00115 0.80012 0.99032 0.45473 0.49453 200 200 B T mate2 technical by mapping diff bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2023-08-28 Multi-stage Multi-stage Skin Surface Structure
25301 25301 SRR25764103 SRX21486768 SRS18719066 SRP457109 PRJNA1009810 Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish GSE241757 Transcriptome Analysis Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.   pubmed:38265193   1 dpf krt4+ embryonic periderm cells rep1 GSM7734875   tissue:epidermal cells|cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp|geo loc name:missing|collection date:missing 1 dpf krt4+ embryonic periderm cells rep1 High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values. epidermal cells Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY. The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol. Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding. cell type:embryonic periderm cells|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp GSM7734875 GSM7734875: 1 dpf krt4+ embryonic periderm cells rep1; Danio rerio; RNA Seq GSM7734875 r1 GSM7734875 1 The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP457109     krt4cre-gfp_1_S19_R2_001.fastq.gz krt4cre-gfp_1_S19_R1_001.fastq.gz fastq fastq 6119547200.0 15298868.0 GSM7734875 r1 0:200 1:200 A:1642059769;C:1349462427;G:1535937964;T:1584527048;N:7559992 200 200     1642059769 1349462427 1535937964 1584527048 7559992 SRX21486768 SRS18719066 SRA1700438 Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology 2 0.01112 0.01017 0.0003 0.00014 0.9931 0.99586 0.43605 0.40821 200 200 T T mates < 9% mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Japan 2023-08-28 Multi-stage Multi-stage Skin Surface Structure
32858 32858 SRR29482326 SRX24993370 SRS21694834 SRP515140 PRJNA1126247 Specific oncogene activation of the cell of origin in mucosal melanoma [SORT seq] GSE270356 Other Mucosal melanoma MM is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics we develop a zebrafish model in which all melanocytes experience CCND1 expression and loss of PTEN and TP53. Surprisingly melanoma only develops from melanocytes lining internal organs analogous to the location of patient MM. We find that zebrafish MMs have a unique chromatin landscape from cutaneous melanoma. Internal melanocytes are labeled using a MM specific transcriptional enhancer. Normal zebrafish internal melanocytes share a gene expression signature with MMs. Patient and zebrafish MMs show increased migratory neural crest gene and decreased antigen presentation gene expression consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors allowing this model to be used for MM therapeutic discovery. As this is a non MAPK driven genetically engineered model of melanoma our work also has implications for the 15% of cutaneous melanoma patients who lack MAPK driving mutations. Overall design: Single cell RNA sequencing was done on internal vs. external normal adult zebrafish melanocytes using the SORT seq platform.       Internal melanocytes GSM8340241   source name:Internal melanocytes|tissue:Internal melanocytes|cell type:melanocytes|genotype:mitfa / ; roy / fish injected with mitfa:GFP|geo loc name:missing|collection date:missing Internal melanocytes BWA was used to align paired end read to danRer11. Count tables were generated using MapAndGo. Count tables were corrected using UMI to remove duplicate reads. Transcript counts were adjusted using Poissonian counting statistics to yield the number of UMIs detected per cell. Counts were imported into R using the Seurat suite version 3.0 Assembly: danRer11 Supplementary files format and content: .tsv file contains count matrix file used for data normalization and visualization using Seurat Library strategy: SORT seq Internal melanocytes   Respective tissues were mechanically dissociated digested in TrypLE for 45 min Invitrogen 12563011 40uM filtered spun down and resuspended in FACs buffer dPBS Mg+/Ca+ free with 2% FBS pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina. mitfa / ; roy / zebrafish injected with mitfa:GFP were Raised to maturity to obtain tissues tissue:Internal melanocytes|cell type:melanocytes|genotype:mitfa / ; roy / fish injected with mitfa:GFP GSM8340241 GSM8340241: Internal melanocytes; Danio rerio; OTHER GSM8340241 r1 GSM8340241 1 Respective tissues were mechanically dissociated digested in TrypLE for 45 min Invitrogen 12563011 40uM filtered spun down and resuspended in FACs buffer dPBS Mg+/Ca+ free with 2% FBS pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP515140     HAR-MI-002_H5GCWBGXF_R2.fastq.gz HAR-MI-002_H5GCWBGXF_R1.fastq.gz fastq fastq 2957975418.0 34395063.0 GSM8340241 r1 0:26 1:60 A:738954503;C:560052455;G:520746060;T:1137116132;N:1106268 26 60     738954503 560052455 520746060 1137116132 1106268 SRX24993370 SRS21694834 SRA1904773 Insco Lab, Medical Oncology, Dana Farber Cancer Institute Insco Lab, Medical Oncology, Dana Farber Cancer Institute 2 0.11637 0.84116 0.10894 0.31188 0.98851 0.71526 0.6688 0.60221 26 60 T B sc-like readlen illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   United States 2024-06-20 Undetermined Adult Skin Surface Structure
32859 32859 SRR29482327 SRX24993369 SRS21694833 SRP515140 PRJNA1126247 Specific oncogene activation of the cell of origin in mucosal melanoma [SORT seq] GSE270356 Other Mucosal melanoma MM is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics we develop a zebrafish model in which all melanocytes experience CCND1 expression and loss of PTEN and TP53. Surprisingly melanoma only develops from melanocytes lining internal organs analogous to the location of patient MM. We find that zebrafish MMs have a unique chromatin landscape from cutaneous melanoma. Internal melanocytes are labeled using a MM specific transcriptional enhancer. Normal zebrafish internal melanocytes share a gene expression signature with MMs. Patient and zebrafish MMs show increased migratory neural crest gene and decreased antigen presentation gene expression consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors allowing this model to be used for MM therapeutic discovery. As this is a non MAPK driven genetically engineered model of melanoma our work also has implications for the 15% of cutaneous melanoma patients who lack MAPK driving mutations. Overall design: Single cell RNA sequencing was done on internal vs. external normal adult zebrafish melanocytes using the SORT seq platform.       Cutaneous melanocytes GSM8340240   source name:Cutaneous melanocytes|tissue:Cutaneous melanocytes|cell type:melanocytes|genotype:mitfa / ; roy / fish injected with mitfa:GFP|geo loc name:missing|collection date:missing Cutaneous melanocytes BWA was used to align paired end read to danRer11. Count tables were generated using MapAndGo. Count tables were corrected using UMI to remove duplicate reads. Transcript counts were adjusted using Poissonian counting statistics to yield the number of UMIs detected per cell. Counts were imported into R using the Seurat suite version 3.0 Assembly: danRer11 Supplementary files format and content: .tsv file contains count matrix file used for data normalization and visualization using Seurat Library strategy: SORT seq Cutaneous melanocytes   Respective tissues were mechanically dissociated digested in TrypLE for 45 min Invitrogen 12563011 40uM filtered spun down and resuspended in FACs buffer dPBS Mg+/Ca+ free with 2% FBS pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina. mitfa / ; roy / zebrafish injected with mitfa:GFP were Raised to maturity to obtain tissues tissue:Cutaneous melanocytes|cell type:melanocytes|genotype:mitfa / ; roy / fish injected with mitfa:GFP GSM8340240 GSM8340240: Cutaneous melanocytes; Danio rerio; OTHER GSM8340240 r1 GSM8340240 1 Respective tissues were mechanically dissociated digested in TrypLE for 45 min Invitrogen 12563011 40uM filtered spun down and resuspended in FACs buffer dPBS Mg+/Ca+ free with 2% FBS pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP515140     HAR-MI-001_H5GCWBGXF_R2.fastq.gz HAR-MI-001_H5GCWBGXF_R1.fastq.gz fastq fastq 2680460212.0 31168142.0 GSM8340240 r1 0:26 1:60 A:704357434;C:519158361;G:467098420;T:988838604;N:1007393 26 60     704357434 519158361 467098420 988838604 1007393 SRX24993369 SRS21694833 SRA1904773 Insco Lab, Medical Oncology, Dana Farber Cancer Institute Insco Lab, Medical Oncology, Dana Farber Cancer Institute 2 0.11679 0.81545 0.10693 0.5033 0.9808 0.76404 0.44749 0.57623 26 60 T B sc-like readlen illumina nextseq unknown small_rna trueseq sc single_cell_plate celseq   United States 2024-06-20 Undetermined Adult Skin Surface Structure
33837 33837 SRR30763634 SRX26165999 SRS22710780 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin con2 Skin con 3   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin con 3|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin con 3 SK CON 3 SK CON 3 Zebrafish skin at control group     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_con2_Clean_Data1.fq.gz Skin_con2_Clean_Data2.fq.gz fastq fastq 6083362246.0 21717347.0 Skin con2 Clean Data1.fq.gz 0:140.06 1:140.05 A:1575684711;C:1458969719;G:1469933956;T:1578641539;N:132321 140 140     1575684711 1458969719 1469933956 1578641539 132321 SRX26165999 SRS22710780 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33838 33838 SRR30763635 SRX26165998 SRS22710779 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin con1 Skin con 2   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin con 2|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin con 2 SK CON 2 SK CON 2 Zebrafish skin at control group     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_con1_Clean_Data1.fq.gz Skin_con1_Clean_Data2.fq.gz fastq fastq 5776524166.0 20610041.0 Skin con1 Clean Data1.fq.gz 0:140.14 1:140.13 A:1496887200;C:1385008310;G:1395131090;T:1499373290;N:124276 140 140     1496887200 1385008310 1395131090 1499373290 124276 SRX26165998 SRS22710779 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33839 33839 SRR30763636 SRX26165997 SRS22710778 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin con Skin con 1   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin con 1|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin con 1 SK CON 1 SK CON 1 Zebrafish skin at control group     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_con_Clean_Data1.fq.gz Skin_con_Clean_Data2.fq.gz fastq fastq 5304184337.0 18925504.0 Skin con Clean Data1.fq.gz 0:140.14 1:140.13 A:1400015654;C:1245459230;G:1267684230;T:1391013551;N:11672 140 140     1400015654 1245459230 1267684230 1391013551 11672 SRX26165997 SRS22710778 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33840 33840 SRR30763637 SRX26165996 SRS22710777 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin 3dpi2 Skin 3d 3   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 3dpi 3|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin 3d 3 SK 3D 3 SK 3D 3 Zebrafish skin at 3 dpv post immunization with glycoprotein of spring viraemia of carp virus     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_3dpi2_Clean_Data1.fq.gz Skin_3dpi2_Clean_Data2.fq.gz fastq fastq 5528962547.0 19717071.0 Skin 3dpi2 Clean Data1.fq.gz 0:140.21 1:140.20 A:1434889776;C:1319598036;G:1335801562;T:1438550030;N:123143 140 140     1434889776 1319598036 1335801562 1438550030 123143 SRX26165996 SRS22710777 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33841 33841 SRR30763638 SRX26165995 SRS22710776 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin 3dpi1 Skin 3d 2   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 3dpi 2|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin 3d 2 SK 3D 2 SK 3D 2 Zebrafish skin at 3 dpv post immunization with glycoprotein of spring viraemia of carp virus     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_3dpi1_Clean_Data1.fq.gz Skin_3dpi1_Clean_Data2.fq.gz fastq fastq 6045424568.0 21559158.0 Skin 3dpi1 Clean Data1.fq.gz 0:140.21 1:140.20 A:1566211023;C:1442845401;G:1464489674;T:1571745680;N:132790 140 140     1566211023 1442845401 1464489674 1571745680 132790 SRX26165995 SRS22710776 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33842 33842 SRR30763639 SRX26165994 SRS22710775 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin 3dpi Skin 3d 1   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 3dpi 1|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin 3d 1 SK 3D 1 SK 3D 1 Zebrafish skin at 3 dpv post immunization with glycoprotein of spring viraemia of carp virus     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_3dpi_Clean_Data1.fq.gz Skin_3dpi_Clean_Data2.fq.gz fastq fastq 5398897838.0 19388025.0 Skin 3dpi Clean Data1.fq.gz 0:139.24 1:139.23 A:1434301676;C:1260747084;G:1277759027;T:1426077485;N:12566 139 139     1434301676 1260747084 1277759027 1426077485 12566 SRX26165994 SRS22710775 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33843 33843 SRR30763640 SRX26165993 SRS22710774 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin 1dpi2 Skin 1d 3   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 1dpi 3|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin 1d 3 SK 1D 3 SK 1D 3 Zebrafish skin at 1 dpv post immunization with glycoprotein of spring viraemia of carp virus     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_1dpi2_Clean_Data1.fq.gz Skin_1dpi2_Clean_Data2.fq.gz fastq fastq 6317753535.0 22527726.0 Skin 1dpi2 Clean Data1.fq.gz 0:140.23 1:140.22 A:1637469629;C:1508203339;G:1526532646;T:1645411954;N:135967 140 140     1637469629 1508203339 1526532646 1645411954 135967 SRX26165993 SRS22710774 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33844 33844 SRR30763641 SRX26165992 SRS22710773 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin 1dpi1 Skin 1d 2   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 1dpi 2|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin 1d 2 SK 1D 2 SK 1D 2 Zebrafish skin at 1 dpv post immunization with glycoprotein of spring viraemia of carp virus     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_1dpi1_Clean_Data1.fq.gz Skin_1dpi1_Clean_Data2.fq.gz fastq fastq 5665401221.0 20209478.0 Skin 1dpi1 Clean Data1.fq.gz 0:140.17 1:140.16 A:1463485728;C:1359900876;G:1372085350;T:1469804976;N:124291 140 140     1463485728 1359900876 1372085350 1469804976 124291 SRX26165992 SRS22710773 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33845 33845 SRR30763642 SRX26165991 SRS22710772 SRP534093 PRJNA1163532 Skin as outermost immune organ of vertebrates that elicits robust early immune responses post immunization with glycoprotein of spring viraemia of carp virus PRJNA1163532 Whole Genome Sequencing         Skin 1dpi Skin 1d 1   breed:zebrafish|age:6 month|collection date:2020 01 10|geo loc name:China: Yangling|sex:not collected|tissue:skin|treatment:Skin 1dpi 1|BioSampleModel:Model organism or animal                 Zebrafish skin RNA seq Skin 1d 1 SK 1D 1 SK 1D 1 Zebrafish skin at 1 dpv post immunization with glycoprotein of spring viraemia of carp virus     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP534093     Skin_1dpi_Clean_Data1.fq.gz Skin_1dpi_Clean_Data2.fq.gz fastq fastq 4758945020.0 17104843.0 Skin 1dpi Clean Data1.fq.gz 0:139.12 1:139.11 A:1261511064;C:1113177324;G:1128285977;T:1255959998;N:10657 139 139     1261511064 1113177324 1128285977 1255959998 10657 SRX26165991 SRS22710772 SRA1977051 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-09-22 Adult Adult Skin Surface Structure
33892 33892 SRR30866052 SRX26263961 SRS22803217 SRP536276 PRJNA1168147 Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [scRNA seq] GSE278654 Transcriptome Analysis Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To understand how selective N glycosylation modification performed by mgat4b promote melanocyte development we performed single cell RNA sequencing of mitfa+ve melanophores sorted from the 36hpf staged zebrafish.       m4b mut GSM8552316   tissue:melanocytes|cell type:melanocytes|age:36 hpf|genotype:mgat4b mutant|treatment:No|geo loc name:missing|collection date:missing m4b mut Cellranger mkfastq pipeline was used to generate fastq files The fastq files were then aligned with custom zebrafish reference assembly GRCz11 using cellranger. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including barcodes and features and matrix files melanocytes   The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction   cell type:melanocytes|age:36 hpf|genotype:mgat4b mutant|treatment:No GSM8552316 GSM8552316: m4b mut; Danio rerio; RNA Seq GSM8552316 r1 GSM8552316 1 The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 2000   SRP536276   loader:fastq load.py m4b_mut_S2_L001_I1_001.fastq.gz m4b_mut_S2_L001_I2_001.fastq.gz m4b_mut_S2_L001_R1_001.fastq.gz m4b_mut_S2_L001_R2_001.fastq.gz fastq fastq fastq fastq 18274385040.0 132423080.0 GSM8552316 r1 0:10 1:10 2:28 3:90 A:3788703303;C:2355223955;G:2645521958;T:3126630009;N:1997975 10 10 28 90 3788703303 2355223955 2645521958 3126630009 1997975 SRX26263961 SRS22803217 SRA1984944 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB                       B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown sc single_cell_droplet 10x   India 2024-10-02 Pharyngula Embryo Skin Surface Structure
33893 33893 SRR30866053 SRX26263960 SRS22803216 SRP536276 PRJNA1168147 Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [scRNA seq] GSE278654 Transcriptome Analysis Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To understand how selective N glycosylation modification performed by mgat4b promote melanocyte development we performed single cell RNA sequencing of mitfa+ve melanophores sorted from the 36hpf staged zebrafish.       Control GSM8552315   tissue:melanocytes|cell type:melanocytes|age:36 hpf|genotype:control|treatment:No|geo loc name:missing|collection date:missing Control Cellranger mkfastq pipeline was used to generate fastq files The fastq files were then aligned with custom zebrafish reference assembly GRCz11 using cellranger. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including barcodes and features and matrix files melanocytes   The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction   cell type:melanocytes|age:36 hpf|genotype:control|treatment:No GSM8552315 GSM8552315: Control; Danio rerio; RNA Seq GSM8552315 r1 GSM8552315 1 The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 2000   SRP536276   loader:fastq load.py con_S1_L001_I1_001.fastq.gz con_S1_L001_I2_001.fastq.gz con_S1_L001_R1_001.fastq.gz con_S1_L001_R2_001.fastq.gz fastq fastq fastq fastq 15825218034.0 114675493.0 GSM8552315 r1 0:10 1:10 2:28 3:90 A:3074750870;C:2137365424;G:2401965854;T:2704984993;N:1727229 10 10 28 90 3074750870 2137365424 2401965854 2704984993 1727229 SRX26263960 SRS22803216 SRA1984944 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB                       B   usable mapping rate illumina nextseq_v2 unknown cdna_unspecified unknown sc single_cell_droplet 10x   India 2024-10-02 Pharyngula Embryo Skin Surface Structure
33894 33894 SRR30866028 SRX26263941 SRS22803195 SRP536275 PRJNA1168148 Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq] GSE278653 Transcriptome Analysis Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b we utilized mature melanophores and melanoma cells from the skin of five zebrafish including both MAZERATI wild type and MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of m…       m4b mut melanoma biol rep 2 GSM8552314   source name:skin|tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI|geo loc name:missing|collection date:missing m4b mut melanoma biol rep 2 Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample skin   The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI GSM8552314 GSM8552314: m4b mut melanoma biol rep 2; Danio rerio; RNA Seq GSM8552314 r1 GSM8552314 1 The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP536275     MKO2_S39_R1_001.fastq.gz MKO2_S39_R2_001.fastq.gz fastq fastq 3705364625.0 14164066.0 GSM8552314 r1 0:126.72 1:134.89 A:785806700;C:949078797;G:1178279032;T:784972987;N:7227109 126 134     785806700 949078797 1178279032 784972987 7227109 SRX26263941 SRS22803195 SRA1984938 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB                       B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified trueseq sc_generic bulk bulk   India 2024-10-02 Undetermined Undetermined Skin Surface Structure
33895 33895 SRR30866029 SRX26263940 SRS22803194 SRP536275 PRJNA1168148 Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq] GSE278653 Transcriptome Analysis Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b we utilized mature melanophores and melanoma cells from the skin of five zebrafish including both MAZERATI wild type and MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of m…       m4b mut melanoma biol rep 1 GSM8552313   source name:skin|tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI|geo loc name:missing|collection date:missing m4b mut melanoma biol rep 1 Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample skin   The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI GSM8552313 GSM8552313: m4b mut melanoma biol rep 1; Danio rerio; RNA Seq GSM8552313 r1 GSM8552313 1 The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP536275     MKO1_S38_R1_001.fastq.gz MKO1_S38_R2_001.fastq.gz fastq fastq 4779377372.0 18058294.0 GSM8552313 r1 0:128.72 1:135.94 A:1016908920;C:1236613888;G:1502465334;T:1018053808;N:5335422 128 135     1016908920 1236613888 1502465334 1018053808 5335422 SRX26263940 SRS22803194 SRA1984938 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB                       B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified trueseq sc_generic bulk bulk   India 2024-10-02 Undetermined Undetermined Skin Surface Structure
33896 33896 SRR30866030 SRX26263939 SRS22803193 SRP536275 PRJNA1168148 Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq] GSE278653 Transcriptome Analysis Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b we utilized mature melanophores and melanoma cells from the skin of five zebrafish including both MAZERATI wild type and MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of m…       wild type melanoma control biol rep 2 GSM8552312   source name:skin|tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI|geo loc name:missing|collection date:missing wild type melanoma control biol rep 2 Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample skin   The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI GSM8552312 GSM8552312: wild type melanoma control biol rep 2; Danio rerio; RNA Seq GSM8552312 r1 GSM8552312 1 The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP536275     EV2_S37_R1_001.fastq.gz EV2_S37_R2_001.fastq.gz fastq fastq 5427379509.0 19981504.0 GSM8552312 r1 0:133.16 1:138.46 A:1136639418;C:1414638483;G:1736492639;T:1137614638;N:1994331 133 138     1136639418 1414638483 1736492639 1137614638 1994331 SRX26263939 SRS22803193 SRA1984938 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB                       B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified trueseq sc_generic bulk bulk   India 2024-10-02 Undetermined Undetermined Skin Surface Structure
33897 33897 SRR30866031 SRX26263938 SRS22803192 SRP536275 PRJNA1168148 Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq] GSE278653 Transcriptome Analysis Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b we utilized mature melanophores and melanoma cells from the skin of five zebrafish including both MAZERATI wild type and MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of m…       wild type melanoma control biol rep 1 GSM8552311   source name:skin|tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI|geo loc name:missing|collection date:missing wild type melanoma control biol rep 1 Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample skin   The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI GSM8552311 GSM8552311: wild type melanoma control biol rep 1; Danio rerio; RNA Seq GSM8552311 r1 GSM8552311 1 The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP536275     EV1_S36_R1_001.fastq.gz EV1_S36_R2_001.fastq.gz fastq fastq 5248108957.0 19087024.0 GSM8552311 r1 0:135.12 1:139.84 A:1112163842;C:1354895660;G:1658732932;T:1120342985;N:1973538 135 139     1112163842 1354895660 1658732932 1120342985 1973538 SRX26263938 SRS22803192 SRA1984938 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB                       B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified trueseq sc_generic bulk bulk   India 2024-10-02 Undetermined Undetermined Skin Surface Structure
33898 33898 SRR30866032 SRX26263937 SRS22803191 SRP536275 PRJNA1168148 Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq] GSE278653 Transcriptome Analysis Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b we utilized mature melanophores and melanoma cells from the skin of five zebrafish including both MAZERATI wild type and MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of m…       melanophore biol rep 2 GSM8552310   source name:skin|tissue:skin|cell type:melanophore|genotype:WT|treatment:No|geo loc name:missing|collection date:missing melanophore biol rep 2 Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample skin   The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   tissue:skin|cell type:melanophore|genotype:WT|treatment:No GSM8552310 GSM8552310: melanophore biol rep 2; Danio rerio; RNA Seq GSM8552310 r1 GSM8552310 1 The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP536275     WT2_S41_R1_001.fastq.gz WT2_S41_R2_001.fastq.gz fastq fastq 4636631881.0 16340506.0 GSM8552310 r1 0:140.47 1:143.28 A:1114533149;C:1104066636;G:1293649625;T:1122672029;N:1710442 140 143     1114533149 1104066636 1293649625 1122672029 1710442 SRX26263937 SRS22803191 SRA1984938 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB                       B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified trueseq sc_generic bulk bulk   India 2024-10-02 Undetermined Undetermined Skin Surface Structure
33899 33899 SRR30866033 SRX26263936 SRS22803190 SRP536275 PRJNA1168148 Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq] GSE278653 Transcriptome Analysis Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b we utilized mature melanophores and melanoma cells from the skin of five zebrafish including both MAZERATI wild type and MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of m…       melanophore biol rep 1 GSM8552309   source name:skin|tissue:skin|cell type:melanophore|genotype:WT|treatment:No|geo loc name:missing|collection date:missing melanophore biol rep 1 Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample skin   The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   tissue:skin|cell type:melanophore|genotype:WT|treatment:No GSM8552309 GSM8552309: melanophore biol rep 1; Danio rerio; RNA Seq GSM8552309 r1 GSM8552309 1 The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP536275     WT1_S40_R1_001.fastq.gz WT1_S40_R2_001.fastq.gz fastq fastq 5185761246.0 18118534.0 GSM8552309 r1 0:141.81 1:144.40 A:1231235669;C:1235759770;G:1476864583;T:1240636871;N:1264353 141 144     1231235669 1235759770 1476864583 1240636871 1264353 SRX26263936 SRS22803190 SRA1984938 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB                       B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified trueseq sc_generic bulk bulk   India 2024-10-02 Undetermined Undetermined Skin Surface Structure
36385 36385 SRR516135 SRX156099 SRS346038 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr31 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr31 5m 1 zebrafish Nr31 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013931         1482677008.0 19508908.0 zebrafish Nr31 5m 1 1 0:76 A:385413939;C:354317020;G:354043481;T:388361606;N:540962 76       385413939 354317020 354043481 388361606 540962 SRX156099 SRS346038 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.9273   0.08335   0.67898   0.48956   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36386 36386 SRR516140 SRX156099 SRS346038 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr31 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr31 5m 1 zebrafish Nr31 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013931         388560032.0 5112632.0 zebrafish Nr31 5m 1 2 0:76 A:102207965;C:91473514;G:92119606;T:102551859;N:207088 76       102207965 91473514 92119606 102551859 207088 SRX156099 SRS346038 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92486   0.08531   0.67663   0.49425   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36387 36387 SRR516134 SRX156098 SRS346037 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr30 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr30 5m 1 zebrafish Nr30 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013931         1675582184.0 22047134.0 zebrafish Nr30 5m 1 1 0:76 A:458929887;C:381230210;G:376734439;T:457916852;N:770796 76       458929887 381230210 376734439 457916852 770796 SRX156098 SRS346037 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91832   0.10303   0.71455   0.49444   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36388 36388 SRR516139 SRX156098 SRS346037 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr30 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr30 5m 1 zebrafish Nr30 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013931         477065908.0 6277183.0 zebrafish Nr30 5m 1 2 0:76 A:131927852;C:107181234;G:106214626;T:131489254;N:252942 76       131927852 107181234 106214626 131489254 252942 SRX156098 SRS346037 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91581   0.10754   0.71577   0.49994   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36389 36389 SRR516133 SRX156097 SRS346036 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr29 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr29 5m 1 zebrafish Nr29 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013931         1305047832.0 17171682.0 zebrafish Nr29 5m 1 1 0:76 A:362467093;C:292043132;G:289641844;T:360441501;N:454262 76       362467093 292043132 289641844 360441501 454262 SRX156097 SRS346036 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.90448   0.11905   0.70246   0.47656   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36390 36390 SRR516138 SRX156097 SRS346036 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr29 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr29 5m 1 zebrafish Nr29 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013931     110307_DanioRerio_Nr29_5m_w1_s_1.fq fastq 457287972.0 6016947.0 zebrafish Nr29 5m 1 2 0:76 A:128212070;C:101000378;G:100136000;T:127695086;N:244438 76       128212070 101000378 100136000 127695086 244438 SRX156097 SRS346036 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.90327   0.12466   0.70195   0.49568   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2013-03-11 Adult Adult Skin Surface Structure
36391 36391 SRR516132 SRX156096 SRS346035 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr28 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr28 5m 1 zebrafish Nr28 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013931     110104_DanioRerio_Nr28_5m_l5.fq fastq 778479248.0 10243148.0 zebrafish Nr28 5m 1 1 0:76 A:207103962;C:183338330;G:183353815;T:204420105;N:263036 76       207103962 183338330 183353815 204420105 263036 SRX156096 SRS346035 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91711   0.08403   0.72218   0.46568   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2013-03-11 Adult Adult Skin Surface Structure
36392 36392 SRR516137 SRX156096 SRS346035 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr28 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr28 5m 1 zebrafish Nr28 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013931     110307_DanioRerio_Nr28_5m_w1_s_2.fq fastq 1004119144.0 13212094.0 zebrafish Nr28 5m 1 2 0:76 A:269579079;C:233472158;G:233160786;T:267709479;N:197642 76       269579079 233472158 233160786 267709479 197642 SRX156096 SRS346035 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92125   0.09157   0.72056   0.4782   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2013-03-11 Adult Adult Skin Surface Structure
36393 36393 SRR516131 SRX156095 SRS346034 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr27 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr27 5m 1 zebrafish Nr27 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013931         1689987528.0 22236678.0 zebrafish Nr27 5m 1 1 0:76 A:462852366;C:385867681;G:380635625;T:460044585;N:587271 76       462852366 385867681 380635625 460044585 587271 SRX156095 SRS346034 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91288   0.1015   0.71293   0.488   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36394 36394 SRR516136 SRX156095 SRS346034 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr27 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr27 5m 1 zebrafish Nr27 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013931         421535824.0 5546524.0 zebrafish Nr27 5m 1 2 0:76 A:116434305;C:94958671;G:93876467;T:116039545;N:226836 76       116434305 94958671 93876467 116039545 226836 SRX156095 SRS346034 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.90776   0.10459   0.71399   0.49081   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36395 36395 SRR516130 SRX156094 SRS346033 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr26 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr26 5m 1 zebrafish Nr26 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013931         1633478944.0 21493144.0 zebrafish Nr26 5m 1 1 0:76 A:435251153;C:384938751;G:380973255;T:432171855;N:143930 76       435251153 384938751 380973255 432171855 143930 SRX156094 SRS346033 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92486   0.08081   0.71969   0.50656   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36396 36396 SRR516129 SRX156093 SRS346032 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr25 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr25 5m 1 zebrafish Nr25 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013931     101021_DanioRerio_Nr25_5m_l7.fq fastq 1893537644.0 24914969.0 zebrafish Nr25 5m 1 1 0:76 A:516246577;C:431589332;G:431233057;T:514385629;N:83049 76       516246577 431589332 431233057 514385629 83049 SRX156093 SRS346032 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.89513   0.11188   0.70591   0.47827   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36397 36397 SRR516128 SRX156092 SRS346031 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr23 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr23 5m 1 zebrafish Nr23 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013931     101021_DanioRerio_Nr23_5m_l6.fq fastq 2271040360.0 29882110.0 zebrafish Nr23 5m 1 1 0:76 A:602084142;C:529733757;G:524301688;T:614827528;N:93245 76       602084142 529733757 524301688 614827528 93245 SRX156092 SRS346031 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92194   0.09655   0.70463   0.47059   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2013-03-11 Adult Adult Skin Surface Structure
36398 36398 SRR516127 SRX156091 SRS346030 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr22 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr22 5m 1 zebrafish Nr22 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013931         2812847324.0 37011149.0 zebrafish Nr22 5m 1 1 0:76 A:760320146;C:645617435;G:643672544;T:763112485;N:124714 76       760320146 645617435 643672544 763112485 124714 SRX156091 SRS346030 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.93272   0.08997   0.70755   0.52272   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36399 36399 SRR516126 SRX156090 SRS346029 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 5 month. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 5m skin mRNA zebrafish Nr21 5m                     1 male Danio rerio strain TueAB 5m skin mRNA Illumina GA IIx 76 bp zebrafish Nr21 5m 1 zebrafish Nr21 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013931         2331404728.0 30676378.0 zebrafish Nr21 5m 1 1 0:76 A:630276643;C:539444103;G:529126097;T:632442560;N:115325 76       630276643 539444103 529126097 632442560 115325 SRX156090 SRS346029 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92747   0.10341   0.70414   0.49626   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36400 36400 SRR516125 SRX156089 SRS346028 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 3.5 years. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 3.5y skin mRNA zebrafish Nr18 3.5y                     1 male Danio rerio strain TueAB 3.5y skin mRNA Illumina GA IIx 76 bp zebrafish Nr18 3.5y 1 zebrafish Nr18 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013931         2653618888.0 34916038.0 zebrafish Nr18 3.5y 1 1 0:76 A:728660211;C:598216653;G:601771842;T:724871715;N:98467 76       728660211 598216653 601771842 724871715 98467 SRX156089 SRS346028 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91227   0.10895   0.71802   0.49946   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36401 36401 SRR516124 SRX156088 SRS346027 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 3.5 years. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 3.5y skin mRNA zebrafish Nr14 3.5y                     1 male Danio rerio strain TueAB 3.5y skin mRNA Illumina GA IIx 76 bp zebrafish Nr14 3.5y 1 zebrafish Nr14 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013931         2013201012.0 26489487.0 zebrafish Nr14 3.5y 1 1 0:76 A:554778161;C:456082219;G:445029202;T:557232699;N:78731 76       554778161 456082219 445029202 557232699 78731 SRX156088 SRS346027 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.90845   0.1164   0.71236   0.48939   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36402 36402 SRR516123 SRX156087 SRS346026 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 3.5 years. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 3.5y skin mRNA zebrafish Nr13 3.5y                     1 male Danio rerio strain TueAB 3.5y skin mRNA Illumina GA IIx 76 bp zebrafish Nr13 3.5y 1 zebrafish Nr13 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013931         2680273532.0 35266757.0 zebrafish Nr13 3.5y 1 1 0:76 A:740111520;C:588329849;G:606909161;T:744802954;N:120048 76       740111520 588329849 606909161 744802954 120048 SRX156087 SRS346026 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.85899   0.11949   0.71595   0.48655   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36403 36403 SRR516122 SRX156086 SRS346025 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 3.5 years. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 3.5y skin mRNA zebrafish Nr12 3.5y                     1 male Danio rerio strain TueAB 3.5y skin mRNA Illumina GA IIx 76 bp zebrafish Nr12 3.5y 1 zebrafish Nr12 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013931         2982635200.0 39245200.0 zebrafish Nr12 3.5y 1 1 0:76 A:829678392;C:650275344;G:659157904;T:842323646;N:1199914 76       829678392 650275344 659157904 842323646 1199914 SRX156086 SRS346025 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.88932   0.12521   0.71638   0.53514   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36404 36404 SRR516121 SRX156085 SRS346024 SRP013931 PRJNA169239 Initial analysis of transcript levels in zebrafish with advancing age PRJNA169239 Other This project aims at an initial characterization of changes in gene expression in zebrafish with advancing age. Transcript levels are determined in several tissues of zebrafish with differing ages using RNA seq. Differentially expressed genes are determined to pinpoint genes that are differently regulated in young and old zebrafish. Results will be compared with other species to identify common pathways of ageing.     Wild type zebrafish of the TueAB strain were kept in groups and only males were used for RNA isolation at an age of 3.5 years. Total RNA was isolated from skin using Trizol Invitrogen. 1 male Danio rerio strain TueAB 3.5y skin mRNA zebrafish Nr11 3.5y                     1 male Danio rerio strain TueAB 3.5y skin mRNA Illumina GA IIx 76 bp zebrafish Nr11 3.5y 1 zebrafish Nr11 1 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>76</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013931         2696915708.0 35485733.0 zebrafish Nr11 3.5y 1 1 0:76 A:749305835;C:599264137;G:607414252;T:740194221;N:737263 76       749305835 599264137 607414252 740194221 737263 SRX156085 SRS346024 SRA054207 Leibniz Institute for Age Research - Fritz Lipmann|Genome Analysis Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.86902   0.11557   0.71461   0.49255   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   Germany 2012-06-26 Adult Adult Skin Surface Structure
36712 36712 SRR835167 SRX271963 SRS416259 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 116h 53 GSM1129625   tissue:melanocytes|hpf dm 116h 53 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 GSM1129625 GSM1129625: dm 116h 53; Danio rerio; RNA Seq GSM1129625 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:GSM1129625 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_116h_53_440.fq.bz2 fastq 203842506.0 4853393.0 GSM1129625 r1 0:42 A:49784918;C:48871504;G:45835011;T:59338271;N:12802 42       49784918 48871504 45835011 59338271 12802 SRX271963 SRS416259 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.82741   0.14973   0.84893   0.53644   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36713 36713 SRR835166 SRX271962 SRS416258 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 97h 41 440 GSM1129624   tissue:melanocytes|hpf dm 97h 41 440 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 GSM1129624 GSM1129624: dm 97h 41 440; Danio rerio; RNA Seq GSM1129624 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:GSM1129624 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_97h_41_440.fq.bz2 fastq 199638768.0 4753304.0 GSM1129624 r1 0:42 A:45958194;C:50367228;G:48451580;T:54849238;N:12528 42       45958194 50367228 48451580 54849238 12528 SRX271962 SRS416258 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.85741   0.09897   0.84112   0.53299   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36714 36714 SRR835165 SRX271961 SRS416257 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 FM 351 GSM1129623   tissue:melanocytes|hpf dm 77h FM 351 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 GSM1129623 GSM1129623: dm 77h FM 351; Danio rerio; RNA Seq GSM1129623 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:GSM1129623 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_FM_351_ATT.fq.bz2 fastq 194385384.0 5399594.0 GSM1129623 r1 0:36 A:45805148;C:47931006;G:41165284;T:59482433;N:1513 36       45805148 47931006 41165284 59482433 1513 SRX271961 SRS416257 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.77748   0.07764   0.87687   0.51575   36   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36715 36715 SRR835164 SRX271960 SRS416256 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 52 440 GSM1129622   tissue:melanocytes|hpf dm 77h 52 440 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 GSM1129622 GSM1129622: dm 77h 52 440; Danio rerio; RNA Seq GSM1129622 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:GSM1129622 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_52_440.fq.bz2 fastq 105047586.0 2501133.0 GSM1129622 r1 0:42 A:24711000;C:26459041;G:24869198;T:29001957;N:6390 42       24711000 26459041 24869198 29001957 6390 SRX271960 SRS416256 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.88862   0.09219   0.83611   0.55476   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36716 36716 SRR835163 SRX271959 SRS416255 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 43 440 GSM1129621   tissue:melanocytes|hpf dm 77h 43 440 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 GSM1129621 GSM1129621: dm 77h 43 440; Danio rerio; RNA Seq GSM1129621 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:GSM1129621 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_43_440.fq.bz2 fastq 371553084.0 8846502.0 GSM1129621 r1 0:42 A:84994407;C:91269417;G:87188701;T:108077735;N:22824 42       84994407 91269417 87188701 108077735 22824 SRX271959 SRS416255 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.86495   0.09748   0.83684   0.52833   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval 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
36719 36719 SRR835160 SRX271956 SRS416252 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 28 436 GSM1129618   tissue:melanocytes|hpf dm 77h 28 436 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 GSM1129618 GSM1129618: dm 77h 28 436; Danio rerio; RNA Seq GSM1129618 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:GSM1129618 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_28_436_CACT.fq.bz2 fastq 214752678.0 5113159.0 GSM1129618 r1 0:42 A:50210098;C:62230664;G:49216487;T:52926929;N:168500 42       50210098 62230664 49216487 52926929 168500 SRX271956 SRS416252 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.80956   0.02412   0.87024   0.62475   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36720 36720 SRR835159 SRX271955 SRS416251 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 28 351 GSM1129617   tissue:melanocytes|hpf dm 77h 28 351 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 GSM1129617 GSM1129617: dm 77h 28 351; Danio rerio; RNA Seq GSM1129617 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:GSM1129617 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_28_351_CACT.fq.bz2 fastq 84584556.0 2349571.0 GSM1129617 r1 0:36 A:19843286;C:24761303;G:18855233;T:21124051;N:683 36       19843286 24761303 18855233 21124051 683 SRX271955 SRS416251 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.75246   0.02663   0.87054   0.59024   36   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36721 36721 SRR835158 SRX271954 SRS416250 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 27 436 GSM1129616   tissue:melanocytes|hpf dm 77h 27 436 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 GSM1129616 GSM1129616: dm 77h 27 436; Danio rerio; RNA Seq GSM1129616 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:GSM1129616 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_27_436_TTAT.fq.bz2 fastq 194114466.0 4621773.0 GSM1129616 r1 0:42 A:44579558;C:47759429;G:44539735;T:57080409;N:155335 42       44579558 47759429 44539735 57080409 155335 SRX271954 SRS416250 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.80787   0.04019   0.86263   0.57373   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36722 36722 SRR835157 SRX271953 SRS416249 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 27 351 GSM1129615   tissue:melanocytes|hpf dm 77h 27 351 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 GSM1129615 GSM1129615: dm 77h 27 351; Danio rerio; RNA Seq GSM1129615 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:GSM1129615 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_27_351_TTAT.fq.bz2 fastq 113087304.0 3141314.0 GSM1129615 r1 0:36 A:26171623;C:27323878;G:24871328;T:34719586;N:889 36       26171623 27323878 24871328 34719586 889 SRX271953 SRS416249 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.75375   0.04337   0.85878   0.5311   36   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36723 36723 SRR835156 SRX271952 SRS416248 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 26 433 GSM1129614   tissue:melanocytes|hpf dm 77h 26 433 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 GSM1129614 GSM1129614: dm 77h 26 433; Danio rerio; RNA Seq GSM1129614 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:GSM1129614 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_26_433_AGAT.fq.bz2 fastq 34005804.0 809662.0 GSM1129614 r1 0:42 A:8766789;C:8066807;G:8338043;T:8833768;N:397 42       8766789 8066807 8338043 8833768 397 SRX271952 SRS416248 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.81802   0.05684   0.88787   0.56756   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36724 36724 SRR835155 SRX271951 SRS416247 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 26 351 GSM1129613   tissue:melanocytes|hpf dm 77h 26 351 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 GSM1129613 GSM1129613: dm 77h 26 351; Danio rerio; RNA Seq GSM1129613 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:GSM1129613 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_26_351_AGAT.fq.bz2 fastq 101340432.0 2815012.0 GSM1129613 r1 0:36 A:26592120;C:23518331;G:24503636;T:26725495;N:850 36       26592120 23518331 24503636 26725495 850 SRX271951 SRS416247 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.75158   0.05787   0.88986   0.57167   36   B   usable mapping rate 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
36727 36727 SRR835152 SRX271948 SRS416244 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 25 433 GSM1129610   tissue:melanocytes|hpf dm 77h 25 433 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 GSM1129610 GSM1129610: dm 77h 25 433; Danio rerio; RNA Seq GSM1129610 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:GSM1129610 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_25_433_TCTT.fq.bz2 fastq 489386604.0 11652062.0 GSM1129610 r1 0:42 A:99597908;C:134563195;G:119005661;T:136214210;N:5630 42       99597908 134563195 119005661 136214210 5630 SRX271948 SRS416244 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.79072   0.08396   0.87497   0.51318   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36728 36728 SRR835151 SRX271947 SRS416243 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 25 351 GSM1129609   tissue:melanocytes|hpf dm 77h 25 351 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 GSM1129609 GSM1129609: dm 77h 25 351; Danio rerio; RNA Seq GSM1129609 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:GSM1129609 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_77h_25_351_TCTT.fq.bz2 fastq 98765532.0 2743487.0 GSM1129609 r1 0:36 A:19387910;C:27338385;G:23220852;T:28817575;N:810 36       19387910 27338385 23220852 28817575 810 SRX271947 SRS416243 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.75369   0.08166   0.87667   0.51755   36   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36729 36729 SRR835150 SRX271946 SRS416242 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 58h 45 440 GSM1129608   tissue:melanocytes|hpf dm 58h 45 440 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 GSM1129608 GSM1129608: dm 58h 45 440; Danio rerio; RNA Seq GSM1129608 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:GSM1129608 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_58h_45_440.fq.bz2 fastq 203660982.0 4849071.0 GSM1129608 r1 0:42 A:46576136;C:50204145;G:47522343;T:59345685;N:12673 42       46576136 50204145 47522343 59345685 12673 SRX271946 SRS416242 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.86133   0.0978   0.84565   0.53118   42   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36730 36730 SRR835149 SRX271945 SRS416241 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 58h 23 351 GSM1129607   tissue:melanocytes|hpf dm 58h 23 351 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 GSM1129607 GSM1129607: dm 58h 23 351; Danio rerio; RNA Seq GSM1129607 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:GSM1129607 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP021517     dm_58h_23_351_GAAT.fq.bz2 fastq 106123464.0 2947874.0 GSM1129607 r1 0:36 A:26495114;C:26882652;G:25518440;T:27226454;N:804 36       26495114 26882652 25518440 27226454 804 SRX271945 SRS416241 SRA074390 GEO Rob Mitra, Genetics, Washington University 1 0.78561   0.06331   0.85107   0.46073   36   B   usable mapping rate illumina hiseq_era 3prime poly_a unknown bulk unknown unknown   United States 2013-04-25 Larval Larval Skin Surface Structure
36741 36741 SRR850608 SRX277695 SRS420758 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr18 danrer skin 42months rep5 GSM1141118   source name:total RNA extracted from skin|strain:TuAB|age:42 month|tissue:skin Nr18 danrer skin 42months rep5 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:42 month|tissue:skin GSM1141118 GSM1141118: Nr18 danrer skin 42months rep5; Danio rerio; RNA Seq GSM1141118 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141118 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr18_3.5y_l3_export.fq.gz fastq 3269418540.0 43018665.0 GSM1141118 r1 0:76 A:892486836;C:744426899;G:749230539;T:883114979;N:159287 76       892486836 744426899 749230539 883114979 159287 SRX277695 SRS420758 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91402   0.1106   0.73436   0.4911   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36742 36742 SRR850607 SRX277694 SRS420757 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr14 danrer skin 42months rep4 GSM1141117   source name:total RNA extracted from skin|strain:TuAB|age:42 month|tissue:skin Nr14 danrer skin 42months rep4 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:42 month|tissue:skin GSM1141117 GSM1141117: Nr14 danrer skin 42months rep4; Danio rerio; RNA Seq GSM1141117 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141117 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr14_3.5y_l2_export.fq.gz fastq 2300890044.0 30274869.0 GSM1141117 r1 0:76 A:631736236;C:525065199;G:510761115;T:633208038;N:119456 76       631736236 525065199 510761115 633208038 119456 SRX277694 SRS420757 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.90718   0.11607   0.71997   0.49141   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36743 36743 SRR850606 SRX277693 SRS420790 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr13 danrer skin 42months rep3 GSM1141116   source name:total RNA extracted from skin|strain:TuAB|age:42 month|tissue:skin Nr13 danrer skin 42months rep3 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:42 month|tissue:skin GSM1141116 GSM1141116: Nr13 danrer skin 42months rep3; Danio rerio; RNA Seq GSM1141116 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141116 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr13_3.5y_l1_export.fastq.gz fastq 3508110372.0 46159347.0 GSM1141116 r1 0:76 A:959986155;C:782258637;G:803256847;T:962450623;N:158110 76       959986155 782258637 803256847 962450623 158110 SRX277693 SRS420790 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.85747   0.12068   0.73819   0.4917   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36744 36744 SRR850605 SRX277692 SRS420789 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr12 danrer skin 42months rep2 GSM1141115   source name:total RNA extracted from skin|strain:TuAB|age:42 month|tissue:skin Nr12 danrer skin 42months rep2 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:42 month|tissue:skin GSM1141115 GSM1141115: Nr12 danrer skin 42months rep2; Danio rerio; RNA Seq GSM1141115 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141115 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr12_3.5y_l3_export.fq.gz fastq 3961243804.0 52121629.0 GSM1141115 r1 0:76 A:1092811778;C:874440215;G:892629531;T:1099367104;N:1995176 76       1092811778 874440215 892629531 1099367104 1995176 SRX277692 SRS420789 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.88854   0.12633   0.73746   0.53849   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36745 36745 SRR850604 SRX277691 SRS420788 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr11 danrer skin 42months rep1 GSM1141114   source name:total RNA extracted from skin|strain:TuAB|age:42 month|tissue:skin Nr11 danrer skin 42months rep1 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:42 month|tissue:skin GSM1141114 GSM1141114: Nr11 danrer skin 42months rep1; Danio rerio; RNA Seq GSM1141114 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141114 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr11_3.5y_l2_export.fq.gz fastq 3327777040.0 43786540.0 GSM1141114 r1 0:76 A:920364748;C:745739060;G:758842746;T:901558784;N:1271702 76       920364748 745739060 758842746 901558784 1271702 SRX277691 SRS420788 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.86781   0.11618   0.72888   0.50217   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36746 36746 SRR850603 SRX277690 SRS420756 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr76 danrer skin 24months rep6 GSM1141113   source name:total RNA extracted from skin|strain:TuAB|age:24 month|tissue:skin Nr76 danrer skin 24months rep6 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:24 month|tissue:skin GSM1141113 GSM1141113: Nr76 danrer skin 24months rep6; Danio rerio; RNA Seq GSM1141113 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141113 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr76_2y.fastq.gz fastq 2234765940.0 29404815.0 GSM1141113 r1 0:76 A:582794172;C:524083367;G:547601836;T:579473821;N:812744 76       582794172 524083367 547601836 579473821 812744 SRX277690 SRS420756 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.89808   0.07989   0.73511   0.47456   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36747 36747 SRR850602 SRX277689 SRS420755 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr75 danrer skin 24months rep5 GSM1141112   source name:total RNA extracted from skin|strain:TuAB|age:24 month|tissue:skin Nr75 danrer skin 24months rep5 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:24 month|tissue:skin GSM1141112 GSM1141112: Nr75 danrer skin 24months rep5; Danio rerio; RNA Seq GSM1141112 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141112 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr75_2y.fastq.gz fastq 1000606196.0 13165871.0 GSM1141112 r1 0:76 A:270569436;C:233353660;G:238144829;T:258045669;N:492602 76       270569436 233353660 238144829 258045669 492602 SRX277689 SRS420755 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.8949   0.07966   0.7293   0.47729   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36748 36748 SRR850601 SRX277688 SRS420754 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr73 danrer skin 24months rep4 GSM1141111   source name:total RNA extracted from skin|strain:TuAB|age:24 month|tissue:skin Nr73 danrer skin 24months rep4 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:24 month|tissue:skin GSM1141111 GSM1141111: Nr73 danrer skin 24months rep4; Danio rerio; RNA Seq GSM1141111 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141111 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr73_2y.fastq.gz fastq 2283103688.0 30040838.0 GSM1141111 r1 0:76 A:601138588;C:527906584;G:549863593;T:603391353;N:803570 76       601138588 527906584 549863593 603391353 803570 SRX277688 SRS420754 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.90138   0.08154   0.72598   0.49455   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36749 36749 SRR850600 SRX277687 SRS420787 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr72 danrer skin 24months rep3 GSM1141110   source name:total RNA extracted from skin|strain:TuAB|age:24 month|tissue:skin Nr72 danrer skin 24months rep3 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:24 month|tissue:skin GSM1141110 GSM1141110: Nr72 danrer skin 24months rep3; Danio rerio; RNA Seq GSM1141110 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141110 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr72_2y.fastq.gz fastq 1692545916.0 22270341.0 GSM1141110 r1 0:76 A:447927627;C:393400289;G:405212681;T:445305247;N:700072 76       447927627 393400289 405212681 445305247 700072 SRX277687 SRS420787 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.88704   0.08604   0.72833   0.47215   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36750 36750 SRR850599 SRX277686 SRS420786 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr71 danrer skin 24months rep2 GSM1141109   source name:total RNA extracted from skin|strain:TuAB|age:24 month|tissue:skin Nr71 danrer skin 24months rep2 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:24 month|tissue:skin GSM1141109 GSM1141109: Nr71 danrer skin 24months rep2; Danio rerio; RNA Seq GSM1141109 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141109 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr71_2y.fastq.gz fastq 1897129404.0 24962229.0 GSM1141109 r1 0:76 A:500740954;C:442627409;G:457159802;T:495689680;N:911559 76       500740954 442627409 457159802 495689680 911559 SRX277686 SRS420786 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.88731   0.07537   0.73628   0.4846   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36751 36751 SRR850598 SRX277685 SRS420785 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr70 danrer skin 24months rep1 GSM1141108   source name:total RNA extracted from skin|strain:TuAB|age:24 month|tissue:skin Nr70 danrer skin 24months rep1 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:24 month|tissue:skin GSM1141108 GSM1141108: Nr70 danrer skin 24months rep1; Danio rerio; RNA Seq GSM1141108 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141108 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr70_2y.fastq.gz fastq 2239190508.0 29463033.0 GSM1141108 r1 0:76 A:599665392;C:514113743;G:531871299;T:592730477;N:809597 76       599665392 514113743 531871299 592730477 809597 SRX277685 SRS420785 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.89167   0.09031   0.73515   0.49129   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36752 36752 SRR850597 SRX277684 SRS420784 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr30 danrer skin 5months rep9 GSM1141107   source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin Nr30 danrer skin 5months rep9 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:5 month|tissue:skin GSM1141107 GSM1141107: Nr30 danrer skin 5months rep9; Danio rerio; RNA Seq GSM1141107 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141107 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr30_5m.fastq.gz fastq 2502725752.0 32930602.0 GSM1141107 r1 0:76 A:684745428;C:570860380;G:565883575;T:679750149;N:1486220 76       684745428 570860380 565883575 679750149 1486220 SRX277684 SRS420784 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91789   0.10423   0.7263   0.4909   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36753 36753 SRR850596 SRX277683 SRS420783 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr29 danrer skin 5months rep8 GSM1141106   source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin Nr29 danrer skin 5months rep8 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:5 month|tissue:skin GSM1141106 GSM1141106: Nr29 danrer skin 5months rep8; Danio rerio; RNA Seq GSM1141106 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141106 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr29_5m.fastq.gz fastq 2012479468.0 26479993.0 GSM1141106 r1 0:76 A:558800574;C:450898608;G:447907004;T:553773824;N:1099458 76       558800574 450898608 447907004 553773824 1099458 SRX277683 SRS420783 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.9055   0.1197   0.7119   0.48553   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36754 36754 SRR850595 SRX277682 SRS420782 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr28 danrer skin 5months rep7 GSM1141105   source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin Nr28 danrer skin 5months rep7 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:5 month|tissue:skin GSM1141105 GSM1141105: Nr28 danrer skin 5months rep7; Danio rerio; RNA Seq GSM1141105 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141105 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr28_5m.fastq.gz fastq 2075098224.0 27303924.0 GSM1141105 r1 0:76 A:555062827;C:487427075;G:487360186;T:544381395;N:866741 76       555062827 487427075 487360186 544381395 866741 SRX277682 SRS420782 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91784   0.08866   0.73208   0.47793   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36755 36755 SRR850594 SRX277681 SRS420781 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr27 danrer skin 5months rep6 GSM1141104   source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin Nr27 danrer skin 5months rep6 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:5 month|tissue:skin GSM1141104 GSM1141104: Nr27 danrer skin 5months rep6; Danio rerio; RNA Seq GSM1141104 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141104 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr27_5m.fastq.gz fastq 2415354480.0 31780980.0 GSM1141104 r1 0:76 A:661012615;C:552471296;G:546304105;T:654315033;N:1251431 76       661012615 552471296 546304105 654315033 1251431 SRX277681 SRS420781 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91282   0.104   0.7236   0.48186   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36756 36756 SRR850593 SRX277680 SRS420780 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr26 danrer skin 5months rep5 GSM1141103   source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin Nr26 danrer skin 5months rep5 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:5 month|tissue:skin GSM1141103 GSM1141103: Nr26 danrer skin 5months rep5; Danio rerio; RNA Seq GSM1141103 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141103 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr26_5m_l8_export.fq.gz fastq 1866135464.0 24554414.0 GSM1141103 r1 0:76 A:495417130;C:442746432;G:436942898;T:490685510;N:343494 76       495417130 442746432 436942898 490685510 343494 SRX277680 SRS420780 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92443   0.08023   0.7288   0.48902   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36757 36757 SRR850592 SRX277679 SRS420778 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr25 danrer skin 5months rep4 GSM1141102   source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin Nr25 danrer skin 5months rep4 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:5 month|tissue:skin GSM1141102 GSM1141102: Nr25 danrer skin 5months rep4; Danio rerio; RNA Seq GSM1141102 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141102 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr25_5m_l7_export.fq.gz fastq 2146470508.0 28243033.0 GSM1141102 r1 0:76 A:583770580;C:491677255;G:491536604;T:579365742;N:120327 76       583770580 491677255 491536604 579365742 120327 SRX277679 SRS420778 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.89568   0.11303   0.71778   0.47882   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36758 36758 SRR850591 SRX277678 SRS420779 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr23 danrer skin 5months rep3 GSM1141101   source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin Nr23 danrer skin 5months rep3 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:5 month|tissue:skin GSM1141101 GSM1141101: Nr23 danrer skin 5months rep3; Danio rerio; RNA Seq GSM1141101 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141101 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr23_5m_l6_export.fq.gz fastq 2628691268.0 34588043.0 GSM1141101 r1 0:76 A:693944705;C:617538873;G:611502862;T:705582669;N:122159 76       693944705 617538873 611502862 705582669 122159 SRX277678 SRS420779 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92203   0.09747   0.71378   0.47796   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36759 36759 SRR850590 SRX277677 SRS420777 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr22 danrer skin 5months rep2 GSM1141100   source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin Nr22 danrer skin 5months rep2 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:5 month|tissue:skin GSM1141100 GSM1141100: Nr22 danrer skin 5months rep2; Danio rerio; RNA Seq GSM1141100 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141100 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr22_5m.fastq.gz fastq 3561382724.0 46860299.0 GSM1141100 r1 0:76 A:956105654;C:826498432;G:826128735;T:952426883;N:223020 76       956105654 826498432 826128735 952426883 223020 SRX277677 SRS420777 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.93192   0.09055   0.72876   0.52416   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36760 36760 SRR850589 SRX277676 SRS420776 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr21 danrer skin 5months rep1 GSM1141099   source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin Nr21 danrer skin 5months rep1 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:5 month|tissue:skin GSM1141099 GSM1141099: Nr21 danrer skin 5months rep1; Danio rerio; RNA Seq GSM1141099 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141099 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr21_5m_l4_export.fq.gz fastq 2709932304.0 35657004.0 GSM1141099 r1 0:76 A:730073083;C:631072920;G:619401848;T:729203191;N:181262 76       730073083 631072920 619401848 729203191 181262 SRX277676 SRS420776 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92839   0.10379   0.71392   0.4865   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
38116 38116 SRR1551799 SRX681419 SRS685080 SRP045504 PRJNA258223 Danio rerio strain:TL Transcriptome or Gene expression PRJNA258223 Other Transcriptome profiling of keratocytes derived from 2dpf and 4dpf embryos       keratocytes from 4dpf embryos keratocytes from 4dpf embryos   breed:TL|strain:TL|age:4dpf|biomaterial provider:Julie Theriot Stanford University|sex:not collected|tissue:keratocytes skin|cell type:keratocyte|dev stage:4dpf|BioSampleModel:Model organism or animal                 transcriptome from 4dpf keratocytes replicate 3 4dpf 3 4dpf 3 RNA was extracted from approximately 1 x 105 keratocytes per sample using Trizol Invitrogen. Three biological replicates were collected for each developmental stage. Ribosomal RNA was depleted using the Ribo Zero magnetic kit Epicentre. The remaining mRNA was then fragmented with 8 minutes incubation in 50mM sodium carbonate/bicarbonate 1mM EDTA pH 9.2 at 95 degrees. To prepare cDNA first strand synthesis was performed with Superscript III Invitrogen using random hexamer priming and second strand synthesis was performed with DNA Polymerase I NEB. Illumina libraries were prepared from the cDNA in an automated fashion using the Illumina TruSeq sample prep kit with TruSeq adapters on a SPRIworks System I Beckman Coulter. Sequencing reactions were performed on an Illumina Genome Analyzer IIX according to manufacturer’s instructions to generate 40nt single ended reads.     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP045504     lane4_4dpf707.fastq fastq 1001179200.0 25029480.0 4dpf 3 0:40 A:253770714;C:242097985;G:244642013;T:260557997;N:110491 40       253770714 242097985 244642013 260557997 110491 SRX681419 SRS685080 SRA179326 Stanford University|Julie Theriot Stanford University 1 0.90546   0.2101   0.75185   0.49242   40   B   usable mapping rate illumina early_illumina unknown poly_a trueseq bulk unknown unknown   United States 2015-04-07 Larval Larval Skin Surface Structure
38117 38117 SRR1551798 SRX681418 SRS685080 SRP045504 PRJNA258223 Danio rerio strain:TL Transcriptome or Gene expression PRJNA258223 Other Transcriptome profiling of keratocytes derived from 2dpf and 4dpf embryos       keratocytes from 4dpf embryos keratocytes from 4dpf embryos   breed:TL|strain:TL|age:4dpf|biomaterial provider:Julie Theriot Stanford University|sex:not collected|tissue:keratocytes skin|cell type:keratocyte|dev stage:4dpf|BioSampleModel:Model organism or animal                 Transcriptome from 4dpf keratocytes replicate 2 4dpf 2 4dpf 2 RNA was extracted from approximately 1 x 105 keratocytes per sample using Trizol Invitrogen. Three biological replicates were collected for each developmental stage. Ribosomal RNA was depleted using the Ribo Zero magnetic kit Epicentre. The remaining mRNA was then fragmented with 8 minutes incubation in 50mM sodium carbonate/bicarbonate 1mM EDTA pH 9.2 at 95 degrees. To prepare cDNA first strand synthesis was performed with Superscript III Invitrogen using random hexamer priming and second strand synthesis was performed with DNA Polymerase I NEB. Illumina libraries were prepared from the cDNA in an automated fashion using the Illumina TruSeq sample prep kit with TruSeq adapters on a SPRIworks System I Beckman Coulter. Sequencing reactions were performed on an Illumina Genome Analyzer IIX according to manufacturer’s instructions to generate 40nt single ended reads.     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP045504     lane7_4col.fastq fastq 1700157430.0 44740985.0 4dpf 2 0:38 A:394789834;C:418821057;G:504852317;T:369111176;N:12583046 38       394789834 418821057 504852317 369111176 12583046 SRX681418 SRS685080 SRA179326 Stanford University|Julie Theriot Stanford University 1 0.68441   0.12529   0.8338   0.45494   38   B   usable mapping rate illumina early_illumina unknown poly_a trueseq bulk unknown unknown   United States 2014-08-14 Larval Larval Skin Surface Structure
38118 38118 SRR1551797 SRX681417 SRS685080 SRP045504 PRJNA258223 Danio rerio strain:TL Transcriptome or Gene expression PRJNA258223 Other Transcriptome profiling of keratocytes derived from 2dpf and 4dpf embryos       keratocytes from 4dpf embryos keratocytes from 4dpf embryos   breed:TL|strain:TL|age:4dpf|biomaterial provider:Julie Theriot Stanford University|sex:not collected|tissue:keratocytes skin|cell type:keratocyte|dev stage:4dpf|BioSampleModel:Model organism or animal                 4dpf keratocyte transcriptome replicate 1 4dpf 1 4dpf 1 RNA was extracted from approximately 1 x 105 keratocytes per sample using Trizol Invitrogen. Three biological replicates were collected for each developmental stage. Ribosomal RNA was depleted using the Ribo Zero magnetic kit Epicentre. The remaining mRNA was then fragmented with 8 minutes incubation in 50mM sodium carbonate/bicarbonate 1mM EDTA pH 9.2 at 95 degrees. To prepare cDNA first strand synthesis was performed with Superscript III Invitrogen using random hexamer priming and second strand synthesis was performed with DNA Polymerase I NEB. Illumina libraries were prepared from the cDNA in an automated fashion using the Illumina TruSeq sample prep kit with TruSeq adapters on a SPRIworks System I Beckman Coulter. Sequencing reactions were performed on an Illumina Genome Analyzer IIX according to manufacturer’s instructions to generate 40nt single ended reads.     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>47</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP045504     lane7_1_4dpf.fastq fastq 762138229.0 16215707.0 4dpf 1 0:47 A:183899711;C:180347476;G:190086042;T:189460942;N:18344058 47       183899711 180347476 190086042 189460942 18344058 SRX681417 SRS685080 SRA179326 Stanford University|Julie Theriot Stanford University 1 0.85884   0.2135   0.80077   0.50539   47   B   usable mapping rate illumina early_illumina unknown poly_a trueseq bulk unknown unknown   United States 2014-08-15 Larval Larval 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");;