run_metadata
239 rows where experiment.library_layout = "SINGLE" and tissue_curation = "Skin"
This data as json, CSV (advanced)
| 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 | ||||||||||||||||||||||
| 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 | |||||||||||||||||||
| 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 | |||||||||||||||||||
| 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 | ||||||||||||||||||||||||||
| 38119 | 38119 | SRR1551796 | SRX681416 | SRS685079 | SRP045504 | PRJNA258223 | Danio rerio strain:TL Transcriptome or Gene expression | PRJNA258223 | Other | Transcriptome profiling of keratocytes derived from 2dpf and 4dpf embryos | Transcriptome from 2dpf keratocytes | keratocytes from 2dpf embryos | breed:TL|strain:TL|age:2dpf|biomaterial provider:Julie Theriot Stanford University|sex:not collected|tissue:keratocytes skin|cell type:keratocyte|dev stage:2dpf|BioSampleModel:Model organism or animal | Transcriptome from 2dpf keratocytes replicate 3 | 2dpf 3 | 2dpf 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 | lane3_2dpf629.fastq | fastq | 551787520.0 | 13794688.0 | 2dpf 3 | 0:40 | A:138660463;C:132605577;G:134640312;T:145852714;N:28454 | 40 | 138660463 | 132605577 | 134640312 | 145852714 | 28454 | SRX681416 | SRS685079 | SRA179323 | Stanford University|Julie Theriot | Stanford University | 1 | 0.91375 | 0.21598 | 0.75317 | 0.47881 | 40 | B | usable mapping rate | illumina | early_illumina | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-08-14 | Hatching | Embryo | Skin | Surface Structure | ||||||||||||||||||||||||||
| 38120 | 38120 | SRR1551795 | SRX681415 | SRS685079 | SRP045504 | PRJNA258223 | Danio rerio strain:TL Transcriptome or Gene expression | PRJNA258223 | Other | Transcriptome profiling of keratocytes derived from 2dpf and 4dpf embryos | Transcriptome from 2dpf keratocytes | keratocytes from 2dpf embryos | breed:TL|strain:TL|age:2dpf|biomaterial provider:Julie Theriot Stanford University|sex:not collected|tissue:keratocytes skin|cell type:keratocyte|dev stage:2dpf|BioSampleModel:Model organism or animal | Transcriptome from 2dpf keratocytes | 2dpf 2 | 2dpf 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 | lane1_2dpf.fastq | fastq | 796874112.0 | 22135392.0 | 2dpf 2 | 0:36 | A:209956517;C:184659684;G:185142987;T:216055902;N:1059022 | 36 | 209956517 | 184659684 | 185142987 | 216055902 | 1059022 | SRX681415 | SRS685079 | SRA179323 | Stanford University|Julie Theriot | Stanford University | 1 | 0.89178 | 0.17837 | 0.7609 | 0.49774 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2015-04-07 | Hatching | Embryo | Skin | Surface Structure | ||||||||||||||||||||||||||
| 38121 | 38121 | SRR1551782 | SRX681402 | SRS685079 | SRP045504 | PRJNA258223 | Danio rerio strain:TL Transcriptome or Gene expression | PRJNA258223 | Other | Transcriptome profiling of keratocytes derived from 2dpf and 4dpf embryos | Transcriptome from 2dpf keratocytes | keratocytes from 2dpf embryos | breed:TL|strain:TL|age:2dpf|biomaterial provider:Julie Theriot Stanford University|sex:not collected|tissue:keratocytes skin|cell type:keratocyte|dev stage:2dpf|BioSampleModel:Model organism or animal | 2dpf keratocytes replicate 1 | 2dpf 1 | 2dpf 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>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 | lane6_2dpf.fastq | fastq | 647944118.0 | 17051161.0 | 2dpf 1 | 0:38 | A:145735255;C:167786338;G:186677806;T:141598169;N:6146550 | 38 | 145735255 | 167786338 | 186677806 | 141598169 | 6146550 | SRX681402 | SRS685079 | SRA179323 | Stanford University|Julie Theriot | Stanford University | 1 | 0.7695 | 0.15816 | 0.81491 | 0.44972 | 38 | B | usable mapping rate | illumina | early_illumina | unknown | poly_a | trueseq | bulk | unknown | unknown | United States | 2014-08-14 | Hatching | Embryo | Skin | Surface Structure | ||||||||||||||||||||||||||
| 38389 | 38389 | SRR1821850 | SRX893451 | SRS859516 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin208 36m 3.75nM roten1 8w rep6 | GSM1620997 | source name:total RNA extracted from skin|tissue:skin|age:36 month|treatment:3.75nM roten1|duration:8 weeks | skin208 36m 3.75nM roten1 8w rep6 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:36 month|treatment:3.75nM roten1|duration:8 weeks | GSM1620997 | GSM1620997: skin208 36m 3.75nM roten1 8w rep6; Danio rerio; RNA Seq | GSM1620997 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620997 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 208_skin.fastq.gz | fastq | 1960697700.0 | 39213954.0 | GSM1620997 r1 | 0:50 | A:532792887;C:452528560;G:441240826;T:533522462;N:612965 | 50 | 532792887 | 452528560 | 441240826 | 533522462 | 612965 | SRX893451 | SRS859516 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.92216 | 0.09326 | 0.72147 | 0.49795 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38390 | 38390 | SRR1821849 | SRX893450 | SRS859517 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin207 36m 3.75nM roten1 8w rep5 | GSM1620996 | source name:total RNA extracted from skin|tissue:skin|age:36 month|treatment:3.75nM roten1|duration:8 weeks | skin207 36m 3.75nM roten1 8w rep5 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:36 month|treatment:3.75nM roten1|duration:8 weeks | GSM1620996 | GSM1620996: skin207 36m 3.75nM roten1 8w rep5; Danio rerio; RNA Seq | GSM1620996 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620996 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 207_skin.fastq.gz | fastq | 1644999850.0 | 32899997.0 | GSM1620996 r1 | 0:50 | A:444439104;C:381379643;G:371782441;T:447032625;N:366037 | 50 | 444439104 | 381379643 | 371782441 | 447032625 | 366037 | SRX893450 | SRS859517 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.90733 | 0.0971 | 0.71518 | 0.48175 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38391 | 38391 | SRR1821848 | SRX893449 | SRS859518 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin206 36m 3.75nM roten1 8w rep4 | GSM1620995 | source name:total RNA extracted from skin|tissue:skin|age:36 month|treatment:3.75nM roten1|duration:8 weeks | skin206 36m 3.75nM roten1 8w rep4 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:36 month|treatment:3.75nM roten1|duration:8 weeks | GSM1620995 | GSM1620995: skin206 36m 3.75nM roten1 8w rep4; Danio rerio; RNA Seq | GSM1620995 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620995 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 206_skin.fastq.gz | fastq | 2333175800.0 | 46663516.0 | GSM1620995 r1 | 0:50 | A:629018600;C:541489412;G:532198591;T:629985712;N:483485 | 50 | 629018600 | 541489412 | 532198591 | 629985712 | 483485 | SRX893449 | SRS859518 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.91718 | 0.10454 | 0.70974 | 0.47753 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38392 | 38392 | SRR1821847 | SRX893448 | SRS859519 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin205 36m 3.75nM roten1 8w rep3 | GSM1620994 | source name:total RNA extracted from skin|tissue:skin|age:36 month|treatment:3.75nM roten1|duration:8 weeks | skin205 36m 3.75nM roten1 8w rep3 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:36 month|treatment:3.75nM roten1|duration:8 weeks | GSM1620994 | GSM1620994: skin205 36m 3.75nM roten1 8w rep3; Danio rerio; RNA Seq | GSM1620994 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620994 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 205_skin.fastq.gz | fastq | 1885120700.0 | 37702414.0 | GSM1620994 r1 | 0:50 | A:509247143;C:431669478;G:422352918;T:511569209;N:10281952 | 50 | 509247143 | 431669478 | 422352918 | 511569209 | 10281952 | SRX893448 | SRS859519 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.90066 | 0.107 | 0.71415 | 0.48729 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38393 | 38393 | SRR1821846 | SRX893447 | SRS859520 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin204 36m 3.75nM roten1 8w rep2 | GSM1620993 | source name:total RNA extracted from skin|tissue:skin|age:36 month|treatment:3.75nM roten1|duration:8 weeks | skin204 36m 3.75nM roten1 8w rep2 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:36 month|treatment:3.75nM roten1|duration:8 weeks | GSM1620993 | GSM1620993: skin204 36m 3.75nM roten1 8w rep2; Danio rerio; RNA Seq | GSM1620993 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620993 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 204_skin.fastq.gz | fastq | 2039214400.0 | 40784288.0 | GSM1620993 r1 | 0:50 | A:554630438;C:468936669;G:460030131;T:555276071;N:341091 | 50 | 554630438 | 468936669 | 460030131 | 555276071 | 341091 | SRX893447 | SRS859520 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.91261 | 0.11181 | 0.70832 | 0.4889 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38394 | 38394 | SRR1821845 | SRX893446 | SRS859521 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin203 36m 3.75nM roten1 8w rep1 | GSM1620992 | source name:total RNA extracted from skin|tissue:skin|age:36 month|treatment:3.75nM roten1|duration:8 weeks | skin203 36m 3.75nM roten1 8w rep1 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:36 month|treatment:3.75nM roten1|duration:8 weeks | GSM1620992 | GSM1620992: skin203 36m 3.75nM roten1 8w rep1; Danio rerio; RNA Seq | GSM1620992 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620992 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 203_skin.fastq.gz | fastq | 2169512850.0 | 43390257.0 | GSM1620992 r1 | 0:50 | A:583644936;C:503133232;G:492417551;T:585152349;N:5164782 | 50 | 583644936 | 503133232 | 492417551 | 585152349 | 5164782 | SRX893446 | SRS859521 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.91263 | 0.1004 | 0.71376 | 0.48566 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38395 | 38395 | SRR1821844 | SRX893445 | SRS859522 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin172 36m 3.75nM roten1 3w rep5 | GSM1620991 | source name:total RNA extracted from skin|tissue:skin|age:36 month|treatment:3.75nM roten1|duration:3 weeks | skin172 36m 3.75nM roten1 3w rep5 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:36 month|treatment:3.75nM roten1|duration:3 weeks | GSM1620991 | GSM1620991: skin172 36m 3.75nM roten1 3w rep5; Danio rerio; RNA Seq | GSM1620991 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620991 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 172_skin.fastq.gz | fastq | 1922415800.0 | 38448316.0 | GSM1620991 r1 | 0:50 | A:517025440;C:447202733;G:438389966;T:519578929;N:218732 | 50 | 517025440 | 447202733 | 438389966 | 519578929 | 218732 | SRX893445 | SRS859522 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.92509 | 0.08635 | 0.71747 | 0.48682 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38396 | 38396 | SRR1821843 | SRX893444 | SRS859523 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin171 36m 3.75nM roten1 3w rep4 | GSM1620990 | source name:total RNA extracted from skin|tissue:skin|age:36 month|treatment:3.75nM roten1|duration:3 weeks | skin171 36m 3.75nM roten1 3w rep4 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:36 month|treatment:3.75nM roten1|duration:3 weeks | GSM1620990 | GSM1620990: skin171 36m 3.75nM roten1 3w rep4; Danio rerio; RNA Seq | GSM1620990 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620990 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 171_skin.fastq.gz | fastq | 1795802450.0 | 35916049.0 | GSM1620990 r1 | 0:50 | A:482833890;C:415521773;G:409072097;T:485286706;N:3087984 | 50 | 482833890 | 415521773 | 409072097 | 485286706 | 3087984 | SRX893444 | SRS859523 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.91548 | 0.08856 | 0.71153 | 0.48407 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38397 | 38397 | SRR1821842 | SRX893443 | SRS859524 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin170 36m 3.75nM roten1 3w rep3 | GSM1620989 | source name:total RNA extracted from skin|tissue:skin|age:36 month|treatment:3.75nM roten1|duration:3 weeks | skin170 36m 3.75nM roten1 3w rep3 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:36 month|treatment:3.75nM roten1|duration:3 weeks | GSM1620989 | GSM1620989: skin170 36m 3.75nM roten1 3w rep3; Danio rerio; RNA Seq | GSM1620989 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620989 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 170_skin.fastq.gz | fastq | 1844753700.0 | 36895074.0 | GSM1620989 r1 | 0:50 | A:496864420;C:428934827;G:420432768;T:498397505;N:124180 | 50 | 496864420 | 428934827 | 420432768 | 498397505 | 124180 | SRX893443 | SRS859524 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.92475 | 0.08478 | 0.71123 | 0.5082 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38398 | 38398 | SRR1821841 | SRX893442 | SRS859525 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin169 36m 3.75nM roten1 3w rep2 | GSM1620988 | source name:total RNA extracted from skin|tissue:skin|age:36 month|treatment:3.75nM roten1|duration:3 weeks | skin169 36m 3.75nM roten1 3w rep2 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:36 month|treatment:3.75nM roten1|duration:3 weeks | GSM1620988 | GSM1620988: skin169 36m 3.75nM roten1 3w rep2; Danio rerio; RNA Seq | GSM1620988 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620988 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 169_skin.fastq.gz | fastq | 1832979850.0 | 36659597.0 | GSM1620988 r1 | 0:50 | A:492012429;C:429700408;G:417026859;T:494015583;N:224571 | 50 | 492012429 | 429700408 | 417026859 | 494015583 | 224571 | SRX893442 | SRS859525 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.93738 | 0.07334 | 0.71936 | 0.5123 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38399 | 38399 | SRR1821840 | SRX893441 | SRS859526 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin168 36m 3.75nM roten1 3w rep1 | GSM1620987 | source name:total RNA extracted from skin|tissue:skin|age:36 month|treatment:3.75nM roten1|duration:3 weeks | skin168 36m 3.75nM roten1 3w rep1 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:36 month|treatment:3.75nM roten1|duration:3 weeks | GSM1620987 | GSM1620987: skin168 36m 3.75nM roten1 3w rep1; Danio rerio; RNA Seq | GSM1620987 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620987 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 168_skin.fastq.gz | fastq | 1811602600.0 | 36232052.0 | GSM1620987 r1 | 0:50 | A:482632140;C:422445561;G:412836586;T:485392445;N:8295868 | 50 | 482632140 | 422445561 | 412836586 | 485392445 | 8295868 | SRX893441 | SRS859526 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.9185 | 0.07569 | 0.71368 | 0.49409 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38400 | 38400 | SRR1821839 | SRX893440 | SRS859527 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin188 36m control 8w rep4 | GSM1620986 | source name:total RNA extracted from skin|tissue:skin|age:36 month|treatment:n1|duration:8 weeks | skin188 36m control 8w rep4 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:36 month|treatment:n1|duration:8 weeks | GSM1620986 | GSM1620986: skin188 36m control 8w rep4; Danio rerio; RNA Seq | GSM1620986 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620986 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 188_skin.fastq.gz | fastq | 1797310350.0 | 35946207.0 | GSM1620986 r1 | 0:50 | A:486641633;C:413978398;G:404993329;T:489015902;N:2681088 | 50 | 486641633 | 413978398 | 404993329 | 489015902 | 2681088 | SRX893440 | SRS859527 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.91594 | 0.09158 | 0.72082 | 0.51585 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38401 | 38401 | SRR1821838 | SRX893439 | SRS859528 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin187 36m control 8w rep3 | GSM1620985 | source name:total RNA extracted from skin|tissue:skin|age:36 month|treatment:n1|duration:8 weeks | skin187 36m control 8w rep3 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:36 month|treatment:n1|duration:8 weeks | GSM1620985 | GSM1620985: skin187 36m control 8w rep3; Danio rerio; RNA Seq | GSM1620985 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620985 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 187_skin.fastq.gz | fastq | 1951002950.0 | 39020059.0 | GSM1620985 r1 | 0:50 | A:520701869;C:457907686;G:446812256;T:524196019;N:1385120 | 50 | 520701869 | 457907686 | 446812256 | 524196019 | 1385120 | SRX893439 | SRS859528 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.9211 | 0.07622 | 0.71145 | 0.46944 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38402 | 38402 | SRR1821837 | SRX893438 | SRS859529 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin186 36m control 8w rep2 | GSM1620984 | source name:total RNA extracted from skin|tissue:skin|age:36 month|treatment:n1|duration:8 weeks | skin186 36m control 8w rep2 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:36 month|treatment:n1|duration:8 weeks | GSM1620984 | GSM1620984: skin186 36m control 8w rep2; Danio rerio; RNA Seq | GSM1620984 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620984 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 186_skin.fastq.gz | fastq | 2016117600.0 | 40322352.0 | GSM1620984 r1 | 0:50 | A:545084574;C:465634059;G:454024180;T:546321124;N:5053663 | 50 | 545084574 | 465634059 | 454024180 | 546321124 | 5053663 | SRX893438 | SRS859529 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.91606 | 0.09659 | 0.71246 | 0.52973 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38403 | 38403 | SRR1821836 | SRX893437 | SRS859530 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin185 36m control 8w rep1 | GSM1620983 | source name:total RNA extracted from skin|tissue:skin|age:36 month|treatment:n1|duration:8 weeks | skin185 36m control 8w rep1 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:36 month|treatment:n1|duration:8 weeks | GSM1620983 | GSM1620983: skin185 36m control 8w rep1; Danio rerio; RNA Seq | GSM1620983 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620983 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 185_skin.fastq.gz | fastq | 1862747450.0 | 37254949.0 | GSM1620983 r1 | 0:50 | A:506321471;C:429322966;G:419158880;T:507760233;N:183900 | 50 | 506321471 | 429322966 | 419158880 | 507760233 | 183900 | SRX893437 | SRS859530 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.9187 | 0.09926 | 0.70755 | 0.51593 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38404 | 38404 | SRR1821835 | SRX893436 | SRS859531 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin162 36m control 3w rep3 | GSM1620982 | source name:total RNA extracted from skin|tissue:skin|age:36 month|treatment:n1|duration:3 weeks | skin162 36m control 3w rep3 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:36 month|treatment:n1|duration:3 weeks | GSM1620982 | GSM1620982: skin162 36m control 3w rep3; Danio rerio; RNA Seq | GSM1620982 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620982 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 162_skin.fastq.gz | fastq | 2058728600.0 | 41174572.0 | GSM1620982 r1 | 0:50 | A:545731040;C:487775330;G:479420254;T:545686109;N:115867 | 50 | 545731040 | 487775330 | 479420254 | 545686109 | 115867 | SRX893436 | SRS859531 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.93508 | 0.07365 | 0.70688 | 0.4827 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38405 | 38405 | SRR1821834 | SRX893435 | SRS859532 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin161 36m control 3w rep2 | GSM1620981 | source name:total RNA extracted from skin|tissue:skin|age:36 month|treatment:n1|duration:3 weeks | skin161 36m control 3w rep2 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:36 month|treatment:n1|duration:3 weeks | GSM1620981 | GSM1620981: skin161 36m control 3w rep2; Danio rerio; RNA Seq | GSM1620981 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620981 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 161_skin.fastq.gz | fastq | 1897142450.0 | 37942849.0 | GSM1620981 r1 | 0:50 | A:508043218;C:440251400;G:428510637;T:511046395;N:9290800 | 50 | 508043218 | 440251400 | 428510637 | 511046395 | 9290800 | SRX893435 | SRS859532 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.90644 | 0.0826 | 0.71358 | 0.49573 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38406 | 38406 | SRR1821833 | SRX893434 | SRS859533 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin160 36m control 3w rep1 | GSM1620980 | source name:total RNA extracted from skin|tissue:skin|age:36 month|treatment:n1|duration:3 weeks | skin160 36m control 3w rep1 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:36 month|treatment:n1|duration:3 weeks | GSM1620980 | GSM1620980: skin160 36m control 3w rep1; Danio rerio; RNA Seq | GSM1620980 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620980 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 160_skin.fastq.gz | fastq | 1829692650.0 | 36593853.0 | GSM1620980 r1 | 0:50 | A:493906226;C:425214476;G:414775189;T:495470406;N:326353 | 50 | 493906226 | 425214476 | 414775189 | 495470406 | 326353 | SRX893434 | SRS859533 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.92036 | 0.09412 | 0.71484 | 0.48928 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38407 | 38407 | SRR1821832 | SRX893433 | SRS859534 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin184 12m control 8w rep3 | GSM1620979 | source name:total RNA extracted from skin|tissue:skin|age:12 month|treatment:n1|duration:8 weeks | skin184 12m control 8w rep3 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:12 month|treatment:n1|duration:8 weeks | GSM1620979 | GSM1620979: skin184 12m control 8w rep3; Danio rerio; RNA Seq | GSM1620979 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620979 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 184_skin.fastq.gz | fastq | 1888865600.0 | 37777312.0 | GSM1620979 r1 | 0:50 | A:510384459;C:436312051;G:428261723;T:512241273;N:1666094 | 50 | 510384459 | 436312051 | 428261723 | 512241273 | 1666094 | SRX893433 | SRS859534 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.91542 | 0.0997 | 0.70082 | 0.49633 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38408 | 38408 | SRR1821831 | SRX893432 | SRS859535 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin183 12m control 8w rep2 | GSM1620978 | source name:total RNA extracted from skin|tissue:skin|age:12 month|treatment:n1|duration:8 weeks | skin183 12m control 8w rep2 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:12 month|treatment:n1|duration:8 weeks | GSM1620978 | GSM1620978: skin183 12m control 8w rep2; Danio rerio; RNA Seq | GSM1620978 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620978 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 183_skin.fastq.gz | fastq | 2011969000.0 | 40239380.0 | GSM1620978 r1 | 0:50 | A:541080523;C:469282719;G:455255702;T:544440274;N:1909782 | 50 | 541080523 | 469282719 | 455255702 | 544440274 | 1909782 | SRX893432 | SRS859535 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.92404 | 0.104 | 0.70619 | 0.47963 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38409 | 38409 | SRR1821830 | SRX893431 | SRS859536 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin182 12m control 8w rep1 | GSM1620977 | source name:total RNA extracted from skin|tissue:skin|age:12 month|treatment:n1|duration:8 weeks | skin182 12m control 8w rep1 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:12 month|treatment:n1|duration:8 weeks | GSM1620977 | GSM1620977: skin182 12m control 8w rep1; Danio rerio; RNA Seq | GSM1620977 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620977 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 182_skin.fastq.gz | fastq | 1974072600.0 | 39481452.0 | GSM1620977 r1 | 0:50 | A:532294515;C:457485293;G:447416004;T:532212696;N:4664092 | 50 | 532294515 | 457485293 | 447416004 | 532212696 | 4664092 | SRX893431 | SRS859536 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.91699 | 0.10118 | 0.71163 | 0.49086 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38410 | 38410 | SRR1821829 | SRX893430 | SRS859537 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin159 12m control 3w rep3 | GSM1620976 | source name:total RNA extracted from skin|tissue:skin|age:12 month|treatment:n1|duration:3 weeks | skin159 12m control 3w rep3 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:12 month|treatment:n1|duration:3 weeks | GSM1620976 | GSM1620976: skin159 12m control 3w rep3; Danio rerio; RNA Seq | GSM1620976 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620976 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 159_skin.fastq.gz | fastq | 1887853800.0 | 37757076.0 | GSM1620976 r1 | 0:50 | A:510759018;C:434865500;G:426519929;T:512499569;N:3209784 | 50 | 510759018 | 434865500 | 426519929 | 512499569 | 3209784 | SRX893430 | SRS859537 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.91654 | 0.1023 | 0.70607 | 0.49388 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38411 | 38411 | SRR1821828 | SRX893429 | SRS859538 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin158 12m control 3w rep2 | GSM1620975 | source name:total RNA extracted from skin|tissue:skin|age:12 month|treatment:n1|duration:3 weeks | skin158 12m control 3w rep2 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:12 month|treatment:n1|duration:3 weeks | GSM1620975 | GSM1620975: skin158 12m control 3w rep2; Danio rerio; RNA Seq | GSM1620975 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620975 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 158_skin.fastq.gz | fastq | 1818559300.0 | 36371186.0 | GSM1620975 r1 | 0:50 | A:487547586;C:425039144;G:415674047;T:490148749;N:149774 | 50 | 487547586 | 425039144 | 415674047 | 490148749 | 149774 | SRX893429 | SRS859538 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.93033 | 0.09871 | 0.66103 | 0.48246 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 38412 | 38412 | SRR1821827 | SRX893428 | SRS859539 | SRP055573 | PRJNA276667 | RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age | GSE66362 | Transcriptome Analysis | Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group | pubmed:27135165 | skin157 12m control 3w rep1 | GSM1620974 | source name:total RNA extracted from skin|tissue:skin|age:12 month|treatment:n1|duration:3 weeks | skin157 12m control 3w rep1 | FASTQ files were extracted using Illumina Casava software v1.8.2. | total RNA extracted from skin | Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | Zebrafish Danio rerio were raised under standard conditions. | tissue:skin|age:12 month|treatment:n1|duration:3 weeks | GSM1620974 | GSM1620974: skin157 12m control 3w rep1; Danio rerio; RNA Seq | GSM1620974 | 1 | Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. | GEO Accession:GSM1620974 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP055573 | 157_skin.fastq.gz | fastq | 1855321100.0 | 37106422.0 | GSM1620974 r1 | 0:50 | A:495304825;C:434601244;G:425046390;T:498975673;N:1392968 | 50 | 495304825 | 434601244 | 425046390 | 498975673 | 1392968 | SRX893428 | SRS859539 | SRA244883 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.91768 | 0.09102 | 0.7012 | 0.49299 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2015-02-27 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||
| 39610 | 39610 | SRR1873570 | SRX915250 | SRS870224 | SRP056014 | PRJNA277780 | Identification of small non coding RNAs in zebrafish | GSE66718 | Transcriptome Analysis | MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins. | pubmed:26694924 | skin | GSM1630514 | source name:adult skin 1 year old|strain/background:AB|genotype/variation:wild type|tissue:skin|developmental stage:adult|age:1 year | skin | Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs… | adult skin 1 year old | 100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing. | Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle. | strain/background:AB|genotype/variation:wild type|tissue:skin|developmental stage:adult|age:1 year | GSM1630514 | GSM1630514: skin; Danio rerio; miRNA Seq | GSM1630514 | 1 | 100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing. | GEO Accession:GSM1630514 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | LS454 | 454 GS FLX | SRP056014 | 79232.0 | 1527.0 | GSM1630514 r1 | 0:4 1:47.89 | A:20622;C:23508;G:19017;T:15967;N:118 | 4 | 47 | 20622 | 23508 | 19017 | 15967 | 118 | SRX915250 | SRS870224 | SRA246117 | GEO | University of Aveiro | 1 | 0.0 | 0.0 | 1.0 | 53 | T | under 1.2% mapping rate | legacy | early | 3prime | size_fractionation | unknown | bulk | other_seq | 454 | Portugal | 2015-03-09 | Adult | Adult | Skin | Surface Structure | ||||||||||||||||||||
| 40001 | 40001 | SRR2751044 | SRX1362114 | SRS1125416 | SRP065208 | PRJNA299585 | Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin | GSE74244 | Transcriptome Analysis | Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group | pubmed:29382830 | NH FLI skin 111 | GSM1915550 | source name:total RNA extracted from skin|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:skin | NH FLI skin 111 | Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample | total RNA extracted from skin | Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. | strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:skin | GSM1915550 | GSM1915550: NH FLI skin 111; Danio rerio; RNA Seq | GSM1915550 | 1 | Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. | GEO Accession:GSM1915550 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP065208 | skin_42m_DR111.fq.gz | fastq | 3159101450.0 | 63182029.0 | GSM1915550 r1 | 0:50 | A:848692326;C:737950616;G:722461308;T:849228405;N:768795 | 50 | 848692326 | 737950616 | 722461308 | 849228405 | 768795 | SRX1362114 | SRS1125416 | SRA306458 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.9327 | 0.09435 | 0.70737 | 0.50049 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2015-10-21 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||||
| 40002 | 40002 | SRR2751043 | SRX1362113 | SRS1125415 | SRP065208 | PRJNA299585 | Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin | GSE74244 | Transcriptome Analysis | Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group | pubmed:29382830 | NH FLI skin 109 | GSM1915549 | source name:total RNA extracted from skin|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:skin | NH FLI skin 109 | Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample | total RNA extracted from skin | Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. | strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:skin | GSM1915549 | GSM1915549: NH FLI skin 109; Danio rerio; RNA Seq | GSM1915549 | 1 | Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. | GEO Accession:GSM1915549 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP065208 | skin_42m_DR109.fq.gz | fastq | 2638118700.0 | 52762374.0 | GSM1915549 r1 | 0:50 | A:699567604;C:623885297;G:610871040;T:703405737;N:389022 | 50 | 699567604 | 623885297 | 610871040 | 703405737 | 389022 | SRX1362113 | SRS1125415 | SRA306458 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.93453 | 0.09144 | 0.7191 | 0.47437 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2015-10-21 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||||
| 40003 | 40003 | SRR2751042 | SRX1362112 | SRS1125418 | SRP065208 | PRJNA299585 | Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin | GSE74244 | Transcriptome Analysis | Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group | pubmed:29382830 | NH FLI skin 108 | GSM1915548 | source name:total RNA extracted from skin|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:skin | NH FLI skin 108 | Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample | total RNA extracted from skin | Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. | strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:skin | GSM1915548 | GSM1915548: NH FLI skin 108; Danio rerio; RNA Seq | GSM1915548 | 1 | Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. | GEO Accession:GSM1915548 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP065208 | skin_42m_DR108.fq.gz | fastq | 2354900150.0 | 47098003.0 | GSM1915548 r1 | 0:50 | A:629252405;C:552452722;G:540951538;T:632145411;N:98074 | 50 | 629252405 | 552452722 | 540951538 | 632145411 | 98074 | SRX1362112 | SRS1125418 | SRA306458 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.93959 | 0.09384 | 0.71764 | 0.49807 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2015-10-21 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||||
| 40004 | 40004 | SRR2751041 | SRX1362111 | SRS1125419 | SRP065208 | PRJNA299585 | Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin | GSE74244 | Transcriptome Analysis | Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group | pubmed:29382830 | NH FLI skin 107 | GSM1915547 | source name:total RNA extracted from skin|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:skin | NH FLI skin 107 | Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample | total RNA extracted from skin | Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. | strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:skin | GSM1915547 | GSM1915547: NH FLI skin 107; Danio rerio; RNA Seq | GSM1915547 | 1 | Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. | GEO Accession:GSM1915547 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP065208 | skin_42m_DR107.fq.gz | fastq | 2518777200.0 | 50375544.0 | GSM1915547 r1 | 0:50 | A:678501999;C:582249482;G:579224840;T:678502233;N:298646 | 50 | 678501999 | 582249482 | 579224840 | 678502233 | 298646 | SRX1362111 | SRS1125419 | SRA306458 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.9366 | 0.10967 | 0.71977 | 0.4795 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2015-10-21 | Adult | Adult | Skin | Surface Structure | |||||||||||||||||||
| 40005 | 40005 | SRR2751040 | SRX1362110 | SRS1125417 | SRP065208 | PRJNA299585 | Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin | GSE74244 | Transcriptome Analysis | Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group | pubmed:29382830 | NH FLI skin 106 | GSM1915546 | source name:total RNA extracted from skin|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:skin | NH FLI skin 106 | Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample | total RNA extracted from skin | Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. | strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:skin | GSM1915546 | GSM1915546: NH FLI skin 106; Danio rerio; RNA Seq | GSM1915546 | 1 | Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. | GEO Accession:GSM1915546 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP065208 | skin_42m_DR106.fq.gz | fastq | 2372061450.0 | 47441229.0 | GSM1915546 r1 | 0:50 | A:644690580;C:546357177;G:533675326;T:646884182;N:454185 | 50 | 644690580 | 546357177 | 533675326 | 646884182 | 454185 | SRX1362110 | SRS1125417 | SRA306458 | GEO | Leibniz Institute for Age Research - Fritz Lipmann Institute | 1 | 0.92831 | 0.10593 | 0.70453 | 0.49444 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2015-10-21 | Adult | Adult | Skin | Surface Structure |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;