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32 rows where experiment.platform = "ILLUMINA", technology = "bulk" and tissue_curation = "Skin"

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devstage_curation_coarse 2

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tissue_curation 1

  • Skin · 32 ✖

technology 1

  • bulk · 32 ✖

experiment.platform 1

  • ILLUMINA · 32 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

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
33894 33894 SRR30866028 SRX26263941 SRS22803195 SRP536275 PRJNA1168148 Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq] GSE278653 Transcriptome Analysis Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b we utilized mature melanophores and melanoma cells from the skin of five zebrafish including both MAZERATI wild type and MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of m…       m4b mut melanoma biol rep 2 GSM8552314   source name:skin|tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI|geo loc name:missing|collection date:missing m4b mut melanoma biol rep 2 Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample skin   The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI GSM8552314 GSM8552314: m4b mut melanoma biol rep 2; Danio rerio; RNA Seq GSM8552314 r1 GSM8552314 1 The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP536275     MKO2_S39_R1_001.fastq.gz MKO2_S39_R2_001.fastq.gz fastq fastq 3705364625.0 14164066.0 GSM8552314 r1 0:126.72 1:134.89 A:785806700;C:949078797;G:1178279032;T:784972987;N:7227109 126 134     785806700 949078797 1178279032 784972987 7227109 SRX26263941 SRS22803195 SRA1984938 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB                       B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified trueseq sc_generic bulk bulk   India 2024-10-02 Undetermined Undetermined Skin Surface Structure
33895 33895 SRR30866029 SRX26263940 SRS22803194 SRP536275 PRJNA1168148 Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq] GSE278653 Transcriptome Analysis Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b we utilized mature melanophores and melanoma cells from the skin of five zebrafish including both MAZERATI wild type and MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of m…       m4b mut melanoma biol rep 1 GSM8552313   source name:skin|tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI|geo loc name:missing|collection date:missing m4b mut melanoma biol rep 1 Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample skin   The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI GSM8552313 GSM8552313: m4b mut melanoma biol rep 1; Danio rerio; RNA Seq GSM8552313 r1 GSM8552313 1 The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP536275     MKO1_S38_R1_001.fastq.gz MKO1_S38_R2_001.fastq.gz fastq fastq 4779377372.0 18058294.0 GSM8552313 r1 0:128.72 1:135.94 A:1016908920;C:1236613888;G:1502465334;T:1018053808;N:5335422 128 135     1016908920 1236613888 1502465334 1018053808 5335422 SRX26263940 SRS22803194 SRA1984938 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB                       B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified trueseq sc_generic bulk bulk   India 2024-10-02 Undetermined Undetermined Skin Surface Structure
33896 33896 SRR30866030 SRX26263939 SRS22803193 SRP536275 PRJNA1168148 Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq] GSE278653 Transcriptome Analysis Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b we utilized mature melanophores and melanoma cells from the skin of five zebrafish including both MAZERATI wild type and MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of m…       wild type melanoma control biol rep 2 GSM8552312   source name:skin|tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI|geo loc name:missing|collection date:missing wild type melanoma control biol rep 2 Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample skin   The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI GSM8552312 GSM8552312: wild type melanoma control biol rep 2; Danio rerio; RNA Seq GSM8552312 r1 GSM8552312 1 The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP536275     EV2_S37_R1_001.fastq.gz EV2_S37_R2_001.fastq.gz fastq fastq 5427379509.0 19981504.0 GSM8552312 r1 0:133.16 1:138.46 A:1136639418;C:1414638483;G:1736492639;T:1137614638;N:1994331 133 138     1136639418 1414638483 1736492639 1137614638 1994331 SRX26263939 SRS22803193 SRA1984938 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB                       B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified trueseq sc_generic bulk bulk   India 2024-10-02 Undetermined Undetermined Skin Surface Structure
33897 33897 SRR30866031 SRX26263938 SRS22803192 SRP536275 PRJNA1168148 Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq] GSE278653 Transcriptome Analysis Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b we utilized mature melanophores and melanoma cells from the skin of five zebrafish including both MAZERATI wild type and MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of m…       wild type melanoma control biol rep 1 GSM8552311   source name:skin|tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI|geo loc name:missing|collection date:missing wild type melanoma control biol rep 1 Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample skin   The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI GSM8552311 GSM8552311: wild type melanoma control biol rep 1; Danio rerio; RNA Seq GSM8552311 r1 GSM8552311 1 The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP536275     EV1_S36_R1_001.fastq.gz EV1_S36_R2_001.fastq.gz fastq fastq 5248108957.0 19087024.0 GSM8552311 r1 0:135.12 1:139.84 A:1112163842;C:1354895660;G:1658732932;T:1120342985;N:1973538 135 139     1112163842 1354895660 1658732932 1120342985 1973538 SRX26263938 SRS22803192 SRA1984938 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB                       B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified trueseq sc_generic bulk bulk   India 2024-10-02 Undetermined Undetermined Skin Surface Structure
33898 33898 SRR30866032 SRX26263937 SRS22803191 SRP536275 PRJNA1168148 Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq] GSE278653 Transcriptome Analysis Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b we utilized mature melanophores and melanoma cells from the skin of five zebrafish including both MAZERATI wild type and MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of m…       melanophore biol rep 2 GSM8552310   source name:skin|tissue:skin|cell type:melanophore|genotype:WT|treatment:No|geo loc name:missing|collection date:missing melanophore biol rep 2 Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample skin   The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   tissue:skin|cell type:melanophore|genotype:WT|treatment:No GSM8552310 GSM8552310: melanophore biol rep 2; Danio rerio; RNA Seq GSM8552310 r1 GSM8552310 1 The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP536275     WT2_S41_R1_001.fastq.gz WT2_S41_R2_001.fastq.gz fastq fastq 4636631881.0 16340506.0 GSM8552310 r1 0:140.47 1:143.28 A:1114533149;C:1104066636;G:1293649625;T:1122672029;N:1710442 140 143     1114533149 1104066636 1293649625 1122672029 1710442 SRX26263937 SRS22803191 SRA1984938 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB                       B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified trueseq sc_generic bulk bulk   India 2024-10-02 Undetermined Undetermined Skin Surface Structure
33899 33899 SRR30866033 SRX26263936 SRS22803190 SRP536275 PRJNA1168148 Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq] GSE278653 Transcriptome Analysis Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b we utilized mature melanophores and melanoma cells from the skin of five zebrafish including both MAZERATI wild type and MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of m…       melanophore biol rep 1 GSM8552309   source name:skin|tissue:skin|cell type:melanophore|genotype:WT|treatment:No|geo loc name:missing|collection date:missing melanophore biol rep 1 Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample skin   The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   tissue:skin|cell type:melanophore|genotype:WT|treatment:No GSM8552309 GSM8552309: melanophore biol rep 1; Danio rerio; RNA Seq GSM8552309 r1 GSM8552309 1 The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP536275     WT1_S40_R1_001.fastq.gz WT1_S40_R2_001.fastq.gz fastq fastq 5185761246.0 18118534.0 GSM8552309 r1 0:141.81 1:144.40 A:1231235669;C:1235759770;G:1476864583;T:1240636871;N:1264353 141 144     1231235669 1235759770 1476864583 1240636871 1264353 SRX26263936 SRS22803190 SRA1984938 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB                       B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified trueseq sc_generic bulk bulk   India 2024-10-02 Undetermined Undetermined Skin Surface Structure
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
69552 69552 SRR18901596 SRX14979865 SRS12729755 SRP371883 PRJNA831276 Lipid droplets are a metabolic vulnerability in melanoma GSE201378 Transcriptome Analysis Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake an increased number of lipid droplets and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma   pubmed:37268606   sgDGAT1a 3 bulk RNAseq GSM6062270   source name:Skin|tissue:Skin|cell type:melanoma|genotype:DGAT1a knockout sgDGAT1a 3 bulk RNAseq Sequencing reads underwent quality control with FASTQC 0.11.9 trimming with TRIMMOMATIC 14.0.1 and aligned using Salmon 1.4.0 to the danio rerio GRCz11. Data analysis was conducted in R version 4.0.5. Differential expression and normalized counts were calculated using DESeq2 1.30.1 using default parameters. Normalized counts derived from DESeq2 processing. Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11 Skin   Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.   tissue:Skin|cell type:melanoma|genotype:DGAT1a knockout GSM6062270 GSM6062270: sgDGAT1a 3 bulk RNAseq; Danio rerio; RNA Seq GSM6062270 r1 GSM6062270 1 Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP371883   loader:fastq load.py DGAT1a_3_R1.fastq.gz DGAT1a_3_R2.fastq.gz fastq fastq 6999632088.0 34651644.0 GSM6062270 r1 0:101 1:101 A:1966677410;C:1379731640;G:1488012081;T:2165132052;N:78905 101 101     1966677410 1379731640 1488012081 2165132052 78905 SRX14979865 SRS12729755 SRA1408865 Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.92364 0.83987 0.12298 0.10958 0.7289 0.75205 0.55329 0.53686 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter sc_generic bulk bulk   United States 2022-04-23 Undetermined Undetermined Skin Surface Structure
69553 69553 SRR18901597 SRX14979864 SRS12729754 SRP371883 PRJNA831276 Lipid droplets are a metabolic vulnerability in melanoma GSE201378 Transcriptome Analysis Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake an increased number of lipid droplets and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma   pubmed:37268606   sgDGAT1a 2 bulk RNAseq GSM6062269   source name:Skin|tissue:Skin|cell type:melanoma|genotype:DGAT1a knockout sgDGAT1a 2 bulk RNAseq Sequencing reads underwent quality control with FASTQC 0.11.9 trimming with TRIMMOMATIC 14.0.1 and aligned using Salmon 1.4.0 to the danio rerio GRCz11. Data analysis was conducted in R version 4.0.5. Differential expression and normalized counts were calculated using DESeq2 1.30.1 using default parameters. Normalized counts derived from DESeq2 processing. Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11 Skin   Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.   tissue:Skin|cell type:melanoma|genotype:DGAT1a knockout GSM6062269 GSM6062269: sgDGAT1a 2 bulk RNAseq; Danio rerio; RNA Seq GSM6062269 r1 GSM6062269 1 Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP371883   loader:fastq load.py DGAT1a_2_R1.fastq.gz DGAT1a_2_R2.fastq.gz fastq fastq 8251144500.0 40847250.0 GSM6062269 r1 0:101 1:101 A:2347333328;C:1614724681;G:1750159235;T:2538833381;N:93875 101 101     2347333328 1614724681 1750159235 2538833381 93875 SRX14979864 SRS12729754 SRA1408865 Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.91689 0.85062 0.17154 0.15832 0.7135 0.73357 0.55242 0.53573 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter sc_generic bulk bulk   United States 2022-04-23 Undetermined Undetermined Skin Surface Structure
69554 69554 SRR18901598 SRX14979863 SRS12729783 SRP371883 PRJNA831276 Lipid droplets are a metabolic vulnerability in melanoma GSE201378 Transcriptome Analysis Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake an increased number of lipid droplets and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma   pubmed:37268606   sgDGAT1a 1 bulk RNAseq GSM6062268   source name:Skin|tissue:Skin|cell type:melanoma|genotype:DGAT1a knockout sgDGAT1a 1 bulk RNAseq Sequencing reads underwent quality control with FASTQC 0.11.9 trimming with TRIMMOMATIC 14.0.1 and aligned using Salmon 1.4.0 to the danio rerio GRCz11. Data analysis was conducted in R version 4.0.5. Differential expression and normalized counts were calculated using DESeq2 1.30.1 using default parameters. Normalized counts derived from DESeq2 processing. Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11 Skin   Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.   tissue:Skin|cell type:melanoma|genotype:DGAT1a knockout GSM6062268 GSM6062268: sgDGAT1a 1 bulk RNAseq; Danio rerio; RNA Seq GSM6062268 r1 GSM6062268 1 Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP371883   loader:fastq load.py DGAT1a_1_R1.fastq.gz DGAT1a_1_R2.fastq.gz fastq fastq 18660768484.0 92380042.0 GSM6062268 r1 0:101 1:101 A:5305116678;C:3630125100;G:3862694653;T:5862619976;N:212077 101 101     5305116678 3630125100 3862694653 5862619976 212077 SRX14979863 SRS12729783 SRA1408865 Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.91727 0.83321 0.16534 0.14775 0.71037 0.73594 0.53932 0.52443 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter sc_generic bulk bulk   United States 2022-04-23 Undetermined Undetermined Skin Surface Structure
69555 69555 SRR18901599 SRX14979862 SRS12729753 SRP371883 PRJNA831276 Lipid droplets are a metabolic vulnerability in melanoma GSE201378 Transcriptome Analysis Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake an increased number of lipid droplets and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma   pubmed:37268606   sgNT 3 bulk RNAseq GSM6062267   source name:Skin|tissue:Skin|cell type:melanoma|genotype:WT sgNT 3 bulk RNAseq Sequencing reads underwent quality control with FASTQC 0.11.9 trimming with TRIMMOMATIC 14.0.1 and aligned using Salmon 1.4.0 to the danio rerio GRCz11. Data analysis was conducted in R version 4.0.5. Differential expression and normalized counts were calculated using DESeq2 1.30.1 using default parameters. Normalized counts derived from DESeq2 processing. Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11 Skin   Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.   tissue:Skin|cell type:melanoma|genotype:WT GSM6062267 GSM6062267: sgNT 3 bulk RNAseq; Danio rerio; RNA Seq GSM6062267 r1 GSM6062267 1 Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP371883   loader:fastq load.py NT_3_R1.fastq.gz NT_3_R2.fastq.gz fastq fastq 11541383120.0 57135560.0 GSM6062267 r1 0:101 1:101 A:3251133156;C:2311327780;G:2454133526;T:3524658644;N:130014 101 101     3251133156 2311327780 2454133526 3524658644 130014 SRX14979862 SRS12729753 SRA1408865 Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.91632 0.84851 0.15351 0.14147 0.71366 0.73294 0.51256 0.49995 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter sc_generic bulk bulk   United States 2022-04-23 Undetermined Undetermined Skin Surface Structure
69556 69556 SRR18901600 SRX14979861 SRS12729752 SRP371883 PRJNA831276 Lipid droplets are a metabolic vulnerability in melanoma GSE201378 Transcriptome Analysis Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake an increased number of lipid droplets and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma   pubmed:37268606   sgNT 2 bulk RNAseq GSM6062266   source name:Skin|tissue:Skin|cell type:melanoma|genotype:WT sgNT 2 bulk RNAseq Sequencing reads underwent quality control with FASTQC 0.11.9 trimming with TRIMMOMATIC 14.0.1 and aligned using Salmon 1.4.0 to the danio rerio GRCz11. Data analysis was conducted in R version 4.0.5. Differential expression and normalized counts were calculated using DESeq2 1.30.1 using default parameters. Normalized counts derived from DESeq2 processing. Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11 Skin   Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.   tissue:Skin|cell type:melanoma|genotype:WT GSM6062266 GSM6062266: sgNT 2 bulk RNAseq; Danio rerio; RNA Seq GSM6062266 r1 GSM6062266 1 Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP371883   loader:fastq load.py NT_2_R1.fastq.gz NT_2_R2.fastq.gz fastq fastq 12944530468.0 64081834.0 GSM6062266 r1 0:101 1:101 A:3642085778;C:2657512300;G:2804491849;T:3840293107;N:147434 101 101     3642085778 2657512300 2804491849 3840293107 147434 SRX14979861 SRS12729752 SRA1408865 Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.91453 0.86557 0.10035 0.0905 0.73261 0.7428 0.52684 0.51769 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter sc_generic bulk bulk   United States 2022-04-23 Undetermined Undetermined Skin Surface Structure
69557 69557 SRR18901601 SRX14979860 SRS12729751 SRP371883 PRJNA831276 Lipid droplets are a metabolic vulnerability in melanoma GSE201378 Transcriptome Analysis Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake an increased number of lipid droplets and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma   pubmed:37268606   sgNT 1 bulk RNAseq GSM6062265   source name:Skin|tissue:Skin|cell type:melanoma|genotype:WT sgNT 1 bulk RNAseq Sequencing reads underwent quality control with FASTQC 0.11.9 trimming with TRIMMOMATIC 14.0.1 and aligned using Salmon 1.4.0 to the danio rerio GRCz11. Data analysis was conducted in R version 4.0.5. Differential expression and normalized counts were calculated using DESeq2 1.30.1 using default parameters. Normalized counts derived from DESeq2 processing. Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11 Skin   Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.   tissue:Skin|cell type:melanoma|genotype:WT GSM6062265 GSM6062265: sgNT 1 bulk RNAseq; Danio rerio; RNA Seq GSM6062265 r1 GSM6062265 1 Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP371883   loader:fastq load.py NT_1_R1.fastq.gz NT_1_R2.fastq.gz fastq fastq 4065801864.0 20127732.0 GSM6062265 r1 0:101 1:101 A:1126164942;C:831186106;G:895618283;T:1212785857;N:46676 101 101     1126164942 831186106 895618283 1212785857 46676 SRX14979860 SRS12729751 SRA1408865 Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.92125 0.86236 0.09794 0.08896 0.73148 0.7457 0.52439 0.51074 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter sc_generic bulk bulk   United States 2022-04-23 Undetermined Undetermined 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");;