{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", technology = \"bulk\" and tissue_curation_coarse = \"Surface Structure\"", "rows": [[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", null, "pubmed:26620638", null, "Nr18 danrer skin 42months rep5", "GSM1141118", null, "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:42 month|tissue:skin", "GSM1141118", "GSM1141118: Nr18 danrer skin 42months rep5; Danio rerio; RNA Seq", "GSM1141118 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141118", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "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, null, null, null, 892486836, 744426899, 749230539, 883114979, 159287, "SRX277695", "SRS420758", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.91402, null, 0.1106, null, 0.73436, null, 0.4911, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, "pubmed:26620638", null, "Nr14 danrer skin 42months rep4", "GSM1141117", null, "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:42 month|tissue:skin", "GSM1141117", "GSM1141117: Nr14 danrer skin 42months rep4; Danio rerio; RNA Seq", "GSM1141117 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141117", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "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, null, null, null, 631736236, 525065199, 510761115, 633208038, 119456, "SRX277694", "SRS420757", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.90718, null, 0.11607, null, 0.71997, null, 0.49141, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, "pubmed:26620638", null, "Nr13 danrer skin 42months rep3", "GSM1141116", null, "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:42 month|tissue:skin", "GSM1141116", "GSM1141116: Nr13 danrer skin 42months rep3; Danio rerio; RNA Seq", "GSM1141116 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "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, null, null, null, 959986155, 782258637, 803256847, 962450623, 158110, "SRX277693", "SRS420790", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.85747, null, 0.12068, null, 0.73819, null, 0.4917, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, "pubmed:26620638", null, "Nr12 danrer skin 42months rep2", "GSM1141115", null, "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:42 month|tissue:skin", "GSM1141115", "GSM1141115: Nr12 danrer skin 42months rep2; Danio rerio; RNA Seq", "GSM1141115 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "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, null, null, null, 1092811778, 874440215, 892629531, 1099367104, 1995176, "SRX277692", "SRS420789", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.88854, null, 0.12633, null, 0.73746, null, 0.53849, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, "pubmed:26620638", null, "Nr11 danrer skin 42months rep1", "GSM1141114", null, "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:42 month|tissue:skin", "GSM1141114", "GSM1141114: Nr11 danrer skin 42months rep1; Danio rerio; RNA Seq", "GSM1141114 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141114", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "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, null, null, null, 920364748, 745739060, 758842746, 901558784, 1271702, "SRX277691", "SRS420788", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.86781, null, 0.11618, null, 0.72888, null, 0.50217, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, "pubmed:26620638", null, "Nr76 danrer skin 24months rep6", "GSM1141113", null, "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:24 month|tissue:skin", "GSM1141113", "GSM1141113: Nr76 danrer skin 24months rep6; Danio rerio; RNA Seq", "GSM1141113 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141113", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr76_2y.fastq.gz", "fastq", 2234765940.0, 29404815.0, "GSM1141113 r1", "0:76", "A:582794172;C:524083367;G:547601836;T:579473821;N:812744", 76, null, null, null, 582794172, 524083367, 547601836, 579473821, 812744, "SRX277690", "SRS420756", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.89808, null, 0.07989, null, 0.73511, null, 0.47456, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, "pubmed:26620638", null, "Nr75 danrer skin 24months rep5", "GSM1141112", null, "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:24 month|tissue:skin", "GSM1141112", "GSM1141112: Nr75 danrer skin 24months rep5; Danio rerio; RNA Seq", "GSM1141112 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141112", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr75_2y.fastq.gz", "fastq", 1000606196.0, 13165871.0, "GSM1141112 r1", "0:76", "A:270569436;C:233353660;G:238144829;T:258045669;N:492602", 76, null, null, null, 270569436, 233353660, 238144829, 258045669, 492602, "SRX277689", "SRS420755", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.8949, null, 0.07966, null, 0.7293, null, 0.47729, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, "pubmed:26620638", null, "Nr73 danrer skin 24months rep4", "GSM1141111", null, "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:24 month|tissue:skin", "GSM1141111", "GSM1141111: Nr73 danrer skin 24months rep4; Danio rerio; RNA Seq", "GSM1141111 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141111", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr73_2y.fastq.gz", "fastq", 2283103688.0, 30040838.0, "GSM1141111 r1", "0:76", "A:601138588;C:527906584;G:549863593;T:603391353;N:803570", 76, null, null, null, 601138588, 527906584, 549863593, 603391353, 803570, "SRX277688", "SRS420754", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.90138, null, 0.08154, null, 0.72598, null, 0.49455, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, "pubmed:26620638", null, "Nr72 danrer skin 24months rep3", "GSM1141110", null, "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:24 month|tissue:skin", "GSM1141110", "GSM1141110: Nr72 danrer skin 24months rep3; Danio rerio; RNA Seq", "GSM1141110 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141110", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr72_2y.fastq.gz", "fastq", 1692545916.0, 22270341.0, "GSM1141110 r1", "0:76", "A:447927627;C:393400289;G:405212681;T:445305247;N:700072", 76, null, null, null, 447927627, 393400289, 405212681, 445305247, 700072, "SRX277687", "SRS420787", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.88704, null, 0.08604, null, 0.72833, null, 0.47215, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, "pubmed:26620638", null, "Nr71 danrer skin 24months rep2", "GSM1141109", null, "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:24 month|tissue:skin", "GSM1141109", "GSM1141109: Nr71 danrer skin 24months rep2; Danio rerio; RNA Seq", "GSM1141109 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141109", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr71_2y.fastq.gz", "fastq", 1897129404.0, 24962229.0, "GSM1141109 r1", "0:76", "A:500740954;C:442627409;G:457159802;T:495689680;N:911559", 76, null, null, null, 500740954, 442627409, 457159802, 495689680, 911559, "SRX277686", "SRS420786", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.88731, null, 0.07537, null, 0.73628, null, 0.4846, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, "pubmed:26620638", null, "Nr70 danrer skin 24months rep1", "GSM1141108", null, "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:24 month|tissue:skin", "GSM1141108", "GSM1141108: Nr70 danrer skin 24months rep1; Danio rerio; RNA Seq", "GSM1141108 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141108", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr70_2y.fastq.gz", "fastq", 2239190508.0, 29463033.0, "GSM1141108 r1", "0:76", "A:599665392;C:514113743;G:531871299;T:592730477;N:809597", 76, null, null, null, 599665392, 514113743, 531871299, 592730477, 809597, "SRX277685", "SRS420785", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.89167, null, 0.09031, null, 0.73515, null, 0.49129, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, "pubmed:26620638", null, "Nr30 danrer skin 5months rep9", "GSM1141107", null, "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:5 month|tissue:skin", "GSM1141107", "GSM1141107: Nr30 danrer skin 5months rep9; Danio rerio; RNA Seq", "GSM1141107 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141107", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr30_5m.fastq.gz", "fastq", 2502725752.0, 32930602.0, "GSM1141107 r1", "0:76", "A:684745428;C:570860380;G:565883575;T:679750149;N:1486220", 76, null, null, null, 684745428, 570860380, 565883575, 679750149, 1486220, "SRX277684", "SRS420784", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.91789, null, 0.10423, null, 0.7263, null, 0.4909, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, "pubmed:26620638", null, "Nr29 danrer skin 5months rep8", "GSM1141106", null, "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:5 month|tissue:skin", "GSM1141106", "GSM1141106: Nr29 danrer skin 5months rep8; Danio rerio; RNA Seq", "GSM1141106 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141106", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr29_5m.fastq.gz", "fastq", 2012479468.0, 26479993.0, "GSM1141106 r1", "0:76", "A:558800574;C:450898608;G:447907004;T:553773824;N:1099458", 76, null, null, null, 558800574, 450898608, 447907004, 553773824, 1099458, "SRX277683", "SRS420783", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.9055, null, 0.1197, null, 0.7119, null, 0.48553, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, "pubmed:26620638", null, "Nr28 danrer skin 5months rep7", "GSM1141105", null, "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:5 month|tissue:skin", "GSM1141105", "GSM1141105: Nr28 danrer skin 5months rep7; Danio rerio; RNA Seq", "GSM1141105 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141105", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr28_5m.fastq.gz", "fastq", 2075098224.0, 27303924.0, "GSM1141105 r1", "0:76", "A:555062827;C:487427075;G:487360186;T:544381395;N:866741", 76, null, null, null, 555062827, 487427075, 487360186, 544381395, 866741, "SRX277682", "SRS420782", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.91784, null, 0.08866, null, 0.73208, null, 0.47793, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, "pubmed:26620638", null, "Nr27 danrer skin 5months rep6", "GSM1141104", null, "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:5 month|tissue:skin", "GSM1141104", "GSM1141104: Nr27 danrer skin 5months rep6; Danio rerio; RNA Seq", "GSM1141104 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141104", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr27_5m.fastq.gz", "fastq", 2415354480.0, 31780980.0, "GSM1141104 r1", "0:76", "A:661012615;C:552471296;G:546304105;T:654315033;N:1251431", 76, null, null, null, 661012615, 552471296, 546304105, 654315033, 1251431, "SRX277681", "SRS420781", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.91282, null, 0.104, null, 0.7236, null, 0.48186, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, "pubmed:26620638", null, "Nr26 danrer skin 5months rep5", "GSM1141103", null, "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:5 month|tissue:skin", "GSM1141103", "GSM1141103: Nr26 danrer skin 5months rep5; Danio rerio; RNA Seq", "GSM1141103 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141103", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "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, null, null, null, 495417130, 442746432, 436942898, 490685510, 343494, "SRX277680", "SRS420780", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.92443, null, 0.08023, null, 0.7288, null, 0.48902, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, "pubmed:26620638", null, "Nr25 danrer skin 5months rep4", "GSM1141102", null, "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:5 month|tissue:skin", "GSM1141102", "GSM1141102: Nr25 danrer skin 5months rep4; Danio rerio; RNA Seq", "GSM1141102 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141102", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "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, null, null, null, 583770580, 491677255, 491536604, 579365742, 120327, "SRX277679", "SRS420778", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.89568, null, 0.11303, null, 0.71778, null, 0.47882, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, "pubmed:26620638", null, "Nr23 danrer skin 5months rep3", "GSM1141101", null, "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:5 month|tissue:skin", "GSM1141101", "GSM1141101: Nr23 danrer skin 5months rep3; Danio rerio; RNA Seq", "GSM1141101 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141101", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "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, null, null, null, 693944705, 617538873, 611502862, 705582669, 122159, "SRX277678", "SRS420779", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.92203, null, 0.09747, null, 0.71378, null, 0.47796, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, "pubmed:26620638", null, "Nr22 danrer skin 5months rep2", "GSM1141100", null, "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:5 month|tissue:skin", "GSM1141100", "GSM1141100: Nr22 danrer skin 5months rep2; Danio rerio; RNA Seq", "GSM1141100 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141100", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "Nr22_5m.fastq.gz", "fastq", 3561382724.0, 46860299.0, "GSM1141100 r1", "0:76", "A:956105654;C:826498432;G:826128735;T:952426883;N:223020", 76, null, null, null, 956105654, 826498432, 826128735, 952426883, 223020, "SRX277677", "SRS420777", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.93192, null, 0.09055, null, 0.72876, null, 0.52416, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [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", null, "pubmed:26620638", null, "Nr21 danrer skin 5months rep1", "GSM1141099", null, "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.\u00a0rerio: 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", null, "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", null, "strain:TuAB|age:5 month|tissue:skin", "GSM1141099", "GSM1141099: Nr21 danrer skin 5months rep1; Danio rerio; RNA Seq", "GSM1141099 1", null, "1", "D.\u00a0rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen  Hilden  Germany at 80 \u00b0C. Total RNA was isolated with TRIzol Life Technologies  Darmstadt  Germany according to the instructions of the manufacturer. M.\u00a0musculus: The isolated skin was homogenized in 500\u00a0\u03bcl QIAzol Qiagen by subsequently adding 100\u00a0\u03bcl chloroform. Following phase separation  the aqueous phase was transferred into a fresh tube  then 0.16 volume NaAc 2\u00a0M  pH\u00a04.0 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\u00a0\u03bcl water GIBCO and stored at \u201380\u00b0C until use. D.\u00a0rerio: 5\u00a0\u00b5g of total RNA was used for preparation of libraries using Illumina\u2019s mRNA Seq sample prep kit Illumina  San Diego  CA  USA following the manufacturer\u2019s instruction. M.\u00a0musculus: 2.5\u00a0\u00b5g of total RNA was used with Illumina\u2019s TruSeq RNA sample prep kit.", "GEO Accession:GSM1141099", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP022612", null, null, "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, null, null, null, 730073083, 631072920, 619401848, 729203191, 181262, "SRX277676", "SRS420776", "SRA076297", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.92839, null, 0.10379, null, 0.71392, null, 0.4865, null, 76, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "Germany", "2013-05-14", "Adult", "Adult", "Skin", "Surface Structure"], [39771, "SRR2136297", "SRX1125768", "SRS1017739", "SRP061855", "PRJNA291531", "Identification of qkia/c target genes", "GSE71573", "Transcriptome Analysis", "Quaking are RNA binding proteins  which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development  without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation  we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript  tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation  reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus  we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.", null, "pubmed:28867488", null, "Qkiac 3", "GSM1838798", null, "tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino", "Qkiac 3", "Before mapping  poly N read tails were trimmed  reads \u226440 bases were removed  and reads with quality mean \u226430 were discarded. To obtain the counts on the exon features  reads were then aligned against the genome using Bowtie version 0.12.9 with arguments  n 2  l 34  e 70  k 2   best. To obtain the counts on the gene features  reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression  Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features  we used the bowtie alignments  excluding the junction reads. HTSeq count was used with arguments: genomictype=exon  attributeid=Name  stranded=no  overlapmode=union  removeambiguouscases=false. To obtain the counts on the gene features  we used the STAR alignments  including the junction reads. HTSeq count was used with arguments: genomictype=exon  stranded=no  overlapmode=union  removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric.", "trunk", "Zebrafish trunks at 24 26hpf were dissected removal of head and yolk  flash frozen on dry ice and stored at  80\u00b0C until RNA extraction.", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "Embryos resulting from crossing between qkia+/  fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf  stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/  with control morpholino and double qkia/c loss of function embryos qkia /  with qkic morpholino.", "Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino", "GSM1838798", "GSM1838798: Qkiac 3; Danio rerio; RNA Seq", "GSM1838798", null, "1", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "GEO Accession:GSM1838798", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP061855", null, null, "Sample6_CTTGTA.fastq.bz2", "fastq", 2507001849.0, 49156899.0, "GSM1838798 r1", "0:51", "A:683306529;C:570965534;G:570449436;T:679826815;N:2453535", 51, null, null, null, 683306529, 570965534, 570449436, 679826815, 2453535, "SRX1125768", "SRS1017739", "SRA281148", "GEO", "Plateforme transcriptome, Biologie, Ecole Normale Sup\u00e9rieure", 1, 0.92678, null, 0.08779, null, 0.72892, null, 0.48795, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "France", "2015-07-30", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [39772, "SRR2136296", "SRX1125767", "SRS1017740", "SRP061855", "PRJNA291531", "Identification of qkia/c target genes", "GSE71573", "Transcriptome Analysis", "Quaking are RNA binding proteins  which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development  without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation  we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript  tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation  reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus  we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.", null, "pubmed:28867488", null, "Qkiac 2", "GSM1838797", null, "tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino", "Qkiac 2", "Before mapping  poly N read tails were trimmed  reads \u226440 bases were removed  and reads with quality mean \u226430 were discarded. To obtain the counts on the exon features  reads were then aligned against the genome using Bowtie version 0.12.9 with arguments  n 2  l 34  e 70  k 2   best. To obtain the counts on the gene features  reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression  Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features  we used the bowtie alignments  excluding the junction reads. HTSeq count was used with arguments: genomictype=exon  attributeid=Name  stranded=no  overlapmode=union  removeambiguouscases=false. To obtain the counts on the gene features  we used the STAR alignments  including the junction reads. HTSeq count was used with arguments: genomictype=exon  stranded=no  overlapmode=union  removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric.", "trunk", "Zebrafish trunks at 24 26hpf were dissected removal of head and yolk  flash frozen on dry ice and stored at  80\u00b0C until RNA extraction.", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "Embryos resulting from crossing between qkia+/  fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf  stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/  with control morpholino and double qkia/c loss of function embryos qkia /  with qkic morpholino.", "Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino", "GSM1838797", "GSM1838797: Qkiac 2; Danio rerio; RNA Seq", "GSM1838797", null, "1", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "GEO Accession:GSM1838797", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP061855", null, null, "Sample5_CAGATC.fastq.bz2", "fastq", 2850272086.0, 55887688.0, "GSM1838797 r1", "0:51.00", "A:775475703;C:648531668;G:652753738;T:770730439;N:2780538", 51, null, null, null, 775475703, 648531668, 652753738, 770730439, 2780538, "SRX1125767", "SRS1017740", "SRA281148", "GEO", "Plateforme transcriptome, Biologie, Ecole Normale Sup\u00e9rieure", 1, 0.92802, null, 0.08465, null, 0.72744, null, 0.48656, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "France", "2015-07-30", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [39773, "SRR2136295", "SRX1125766", "SRS1017741", "SRP061855", "PRJNA291531", "Identification of qkia/c target genes", "GSE71573", "Transcriptome Analysis", "Quaking are RNA binding proteins  which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development  without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation  we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript  tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation  reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus  we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.", null, "pubmed:28867488", null, "Qkiac 1", "GSM1838796", null, "tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino", "Qkiac 1", "Before mapping  poly N read tails were trimmed  reads \u226440 bases were removed  and reads with quality mean \u226430 were discarded. To obtain the counts on the exon features  reads were then aligned against the genome using Bowtie version 0.12.9 with arguments  n 2  l 34  e 70  k 2   best. To obtain the counts on the gene features  reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression  Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features  we used the bowtie alignments  excluding the junction reads. HTSeq count was used with arguments: genomictype=exon  attributeid=Name  stranded=no  overlapmode=union  removeambiguouscases=false. To obtain the counts on the gene features  we used the STAR alignments  including the junction reads. HTSeq count was used with arguments: genomictype=exon  stranded=no  overlapmode=union  removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric.", "trunk", "Zebrafish trunks at 24 26hpf were dissected removal of head and yolk  flash frozen on dry ice and stored at  80\u00b0C until RNA extraction.", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "Embryos resulting from crossing between qkia+/  fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf  stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/  with control morpholino and double qkia/c loss of function embryos qkia /  with qkic morpholino.", "Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino", "GSM1838796", "GSM1838796: Qkiac 1; Danio rerio; RNA Seq", "GSM1838796", null, "1", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "GEO Accession:GSM1838796", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP061855", null, null, "Sample4_GCCAAT.fastq.bz2", "fastq", 2881827420.0, 56506420.0, "GSM1838796 r1", "0:51", "A:782512581;C:658453854;G:659856487;T:778195522;N:2808976", 51, null, null, null, 782512581, 658453854, 659856487, 778195522, 2808976, "SRX1125766", "SRS1017741", "SRA281148", "GEO", "Plateforme transcriptome, Biologie, Ecole Normale Sup\u00e9rieure", 1, 0.92629, null, 0.08316, null, 0.7276, null, 0.47801, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "France", "2015-07-30", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [39774, "SRR2136294", "SRX1125765", "SRS1017742", "SRP061855", "PRJNA291531", "Identification of qkia/c target genes", "GSE71573", "Transcriptome Analysis", "Quaking are RNA binding proteins  which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development  without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation  we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript  tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation  reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus  we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.", null, "pubmed:28867488", null, "Control 3", "GSM1838795", null, "tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino", "Control 3", "Before mapping  poly N read tails were trimmed  reads \u226440 bases were removed  and reads with quality mean \u226430 were discarded. To obtain the counts on the exon features  reads were then aligned against the genome using Bowtie version 0.12.9 with arguments  n 2  l 34  e 70  k 2   best. To obtain the counts on the gene features  reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression  Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features  we used the bowtie alignments  excluding the junction reads. HTSeq count was used with arguments: genomictype=exon  attributeid=Name  stranded=no  overlapmode=union  removeambiguouscases=false. To obtain the counts on the gene features  we used the STAR alignments  including the junction reads. HTSeq count was used with arguments: genomictype=exon  stranded=no  overlapmode=union  removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric.", "trunk", "Zebrafish trunks at 24 26hpf were dissected removal of head and yolk  flash frozen on dry ice and stored at  80\u00b0C until RNA extraction.", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "Embryos resulting from crossing between qkia+/  fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf  stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/  with control morpholino and double qkia/c loss of function embryos qkia /  with qkic morpholino.", "Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino", "GSM1838795", "GSM1838795: Control 3; Danio rerio; RNA Seq", "GSM1838795", null, "1", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "GEO Accession:GSM1838795", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP061855", null, null, "Sample3_ACAGTG.fastq.bz2", "fastq", 2611892782.0, 51213584.0, "GSM1838795 r1", "0:51.00", "A:707525221;C:599202602;G:597562199;T:705047589;N:2555171", 51, null, null, null, 707525221, 599202602, 597562199, 705047589, 2555171, "SRX1125765", "SRS1017742", "SRA281148", "GEO", "Plateforme transcriptome, Biologie, Ecole Normale Sup\u00e9rieure", 1, 0.9282, null, 0.09007, null, 0.72147, null, 0.47387, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "France", "2015-07-30", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [39775, "SRR2136293", "SRX1125764", "SRS1017743", "SRP061855", "PRJNA291531", "Identification of qkia/c target genes", "GSE71573", "Transcriptome Analysis", "Quaking are RNA binding proteins  which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development  without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation  we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript  tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation  reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus  we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.", null, "pubmed:28867488", null, "Control 2", "GSM1838794", null, "tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino", "Control 2", "Before mapping  poly N read tails were trimmed  reads \u226440 bases were removed  and reads with quality mean \u226430 were discarded. To obtain the counts on the exon features  reads were then aligned against the genome using Bowtie version 0.12.9 with arguments  n 2  l 34  e 70  k 2   best. To obtain the counts on the gene features  reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression  Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features  we used the bowtie alignments  excluding the junction reads. HTSeq count was used with arguments: genomictype=exon  attributeid=Name  stranded=no  overlapmode=union  removeambiguouscases=false. To obtain the counts on the gene features  we used the STAR alignments  including the junction reads. HTSeq count was used with arguments: genomictype=exon  stranded=no  overlapmode=union  removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric.", "trunk", "Zebrafish trunks at 24 26hpf were dissected removal of head and yolk  flash frozen on dry ice and stored at  80\u00b0C until RNA extraction.", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "Embryos resulting from crossing between qkia+/  fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf  stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/  with control morpholino and double qkia/c loss of function embryos qkia /  with qkic morpholino.", "Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino", "GSM1838794", "GSM1838794: Control 2; Danio rerio; RNA Seq", "GSM1838794", null, "1", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "GEO Accession:GSM1838794", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP061855", null, null, "Sample2_TGACCA.fastq.bz2", "fastq", 2686989417.0, 52686067.0, "GSM1838794 r1", "0:51", "A:728607816;C:615847292;G:614033432;T:725881768;N:2619109", 51, null, null, null, 728607816, 615847292, 614033432, 725881768, 2619109, "SRX1125764", "SRS1017743", "SRA281148", "GEO", "Plateforme transcriptome, Biologie, Ecole Normale Sup\u00e9rieure", 1, 0.92483, null, 0.09787, null, 0.7203, null, 0.45884, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "France", "2015-07-30", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [39776, "SRR2136292", "SRX1125763", "SRS1017744", "SRP061855", "PRJNA291531", "Identification of qkia/c target genes", "GSE71573", "Transcriptome Analysis", "Quaking are RNA binding proteins  which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development  without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation  we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript  tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation  reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus  we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples.", null, "pubmed:28867488", null, "Control 1", "GSM1838793", null, "tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino", "Control 1", "Before mapping  poly N read tails were trimmed  reads \u226440 bases were removed  and reads with quality mean \u226430 were discarded. To obtain the counts on the exon features  reads were then aligned against the genome using Bowtie version 0.12.9 with arguments  n 2  l 34  e 70  k 2   best. To obtain the counts on the gene features  reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression  Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features  we used the bowtie alignments  excluding the junction reads. HTSeq count was used with arguments: genomictype=exon  attributeid=Name  stranded=no  overlapmode=union  removeambiguouscases=false. To obtain the counts on the gene features  we used the STAR alignments  including the junction reads. HTSeq count was used with arguments: genomictype=exon  stranded=no  overlapmode=union  removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled  disp.est.sharing.mode=maximum  disp.est.fit.type=parametric.", "trunk", "Zebrafish trunks at 24 26hpf were dissected removal of head and yolk  flash frozen on dry ice and stored at  80\u00b0C until RNA extraction.", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "Embryos resulting from crossing between qkia+/  fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf  stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/  with control morpholino and double qkia/c loss of function embryos qkia /  with qkic morpholino.", "Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino", "GSM1838793", "GSM1838793: Control 1; Danio rerio; RNA Seq", "GSM1838793", null, "1", "total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 \u00b5g of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238  \u00b1 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples.", "GEO Accession:GSM1838793", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP061855", null, null, "Sample1_CGATGT.fastq.bz2", "fastq", 2920348075.0, 57261727.0, "GSM1838793 r1", "0:51.00", "A:788971393;C:671861209;G:669575375;T:787095383;N:2844715", 51, null, null, null, 788971393, 671861209, 669575375, 787095383, 2844715, "SRX1125763", "SRS1017744", "SRA281148", "GEO", "Plateforme transcriptome, Biologie, Ecole Normale Sup\u00e9rieure", 1, 0.92794, null, 0.09884, null, 0.71711, null, 0.4721, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "France", "2015-07-30", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [48110, "SRR7049634", "SRX3981085", "SRS3205926", "SRP141415", "PRJNA451191", "RNA seq of zebrafish ptk7 mutants with severe spinal curvature and heterozygous straight siblings", "PRJNA451191", "Other", "To identify molecular mechanisms underlying scoliosis spine curvature  we performed next generation RNA sequencing on ptk7 mutant vs. ptk7/+ sibling fish  at an age correlating with severe scoliosis progression 1 cm length. Because the tissue of idiopathic scoliosis origin remains unknown  RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain.", null, null, null, null, "ptk7/+ 11", null, "isolate:fish #11|age:21 dpf|sex:NA|tissue:trunk|genotype:ptk7/+|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA sequencing of Danio rerio: scoliosis trunk", "ptk7 het 11", "ptk7 het 11", "Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP141415", null, "loader:fastq load.py", "Ptk7_het_straight_11_R2.fastq.gz Ptk7_het_straight_11_R1.fastq", "fastq fastq", 10112242392.0, 40127946.0, "Ptk7 het straight 11 R2.fastq.gz", "0:126 1:126", "A:2526420409;C:2531445826;G:2613534392;T:2439160326;N:1681439", 126, 126, null, null, 2526420409, 2531445826, 2613534392, 2439160326, 1681439, "SRX3981085", "SRS3205926", "SRA693409", "The Hospital for Sick Children|Developmental and Stem Cell Biology", "The Hospital for Sick Children", 2, 0.83476, 0.83453, 0.10235, 0.10313, 0.73614, 0.73799, 0.46442, 0.52808, 126, 126, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "bulk", "bulk", null, "Canada", "2018-05-16", "Larval", "Larval", "Trunk", "Surface Structure"], [70891, "SRR20869073", "SRX16888179", "SRS14475663", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  DMSO treatment  zebrafish  rep4", "GSM6434013", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:DMSO treatment", "Mtm1 KO  DMSO treatment  zebrafish  rep4", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:DMSO treatment", "GSM6434013", "GSM6434013: Mtm1 KO  DMSO treatment  zebrafish  rep4; Danio rerio; RNA Seq", "GSM6434013 r1", "GSM6434013", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1504_KY23_168_35_R1.fastq.gz", "fastq", 819472624.0, 12051068.0, "GSM6434013 r1", "0:68 1:0", "A:253867899;C:150713999;G:186967145;T:227898369;N:25212", 68, 0, null, null, 253867899, 150713999, 186967145, 227898369, 25212, "SRX16888179", "SRS14475663", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.84057, null, 0.09126, null, 0.81393, null, 0.5072, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70892, "SRR20869074", "SRX16888178", "SRS14475662", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  DMSO treatment  zebrafish  rep3", "GSM6434012", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:DMSO treatment", "Mtm1 KO  DMSO treatment  zebrafish  rep3", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:DMSO treatment", "GSM6434012", "GSM6434012: Mtm1 KO  DMSO treatment  zebrafish  rep3; Danio rerio; RNA Seq", "GSM6434012 r1", "GSM6434012", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1503_KY23_168_34_R1.fastq.gz", "fastq", 942579960.0, 13861470.0, "GSM6434012 r1", "0:68 1:0", "A:286773879;C:173045305;G:212203970;T:270527789;N:29017", 68, 0, null, null, 286773879, 173045305, 212203970, 270527789, 29017, "SRX16888178", "SRS14475662", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.85221, null, 0.07868, null, 0.802, null, 0.517, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70893, "SRR20869075", "SRX16888177", "SRS14475661", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  DMSO treatment  zebrafish  rep2", "GSM6434011", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:DMSO treatment", "Mtm1 KO  DMSO treatment  zebrafish  rep2", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:DMSO treatment", "GSM6434011", "GSM6434011: Mtm1 KO  DMSO treatment  zebrafish  rep2; Danio rerio; RNA Seq", "GSM6434011 r1", "GSM6434011", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1502_KY23_168_33_R1.fastq.gz", "fastq", 956592516.0, 14067537.0, "GSM6434011 r1", "0:68 1:0", "A:313998032;C:166431578;G:204849712;T:271283994;N:29200", 68, 0, null, null, 313998032, 166431578, 204849712, 271283994, 29200, "SRX16888177", "SRS14475661", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.76427, null, 0.08867, null, 0.8216, null, 0.47678, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70894, "SRR20869076", "SRX16888176", "SRS14475660", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  DMSO treatment  zebrafish  rep1", "GSM6434010", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:DMSO treatment", "Mtm1 KO  DMSO treatment  zebrafish  rep1", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:DMSO treatment", "GSM6434010", "GSM6434010: Mtm1 KO  DMSO treatment  zebrafish  rep1; Danio rerio; RNA Seq", "GSM6434010 r1", "GSM6434010", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1500_KY23_168_31_R1.fastq.gz", "fastq", 830931984.0, 12219588.0, "GSM6434010 r1", "0:68 1:0", "A:284740908;C:147201926;G:181724951;T:217238742;N:25457", 68, 0, null, null, 284740908, 147201926, 181724951, 217238742, 25457, "SRX16888176", "SRS14475660", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.76332, null, 0.10117, null, 0.82069, null, 0.54485, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70895, "SRR20869077", "SRX16888175", "SRS14475659", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  DMSO treatment  zebrafish  rep5", "GSM6434009", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:DMSO treatment", "HET  DMSO treatment  zebrafish  rep5", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:DMSO treatment", "GSM6434009", "GSM6434009: HET  DMSO treatment  zebrafish  rep5; Danio rerio; RNA Seq", "GSM6434009 r1", "GSM6434009", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1499_KY23_168_30_R1.fastq.gz", "fastq", 879671936.0, 12936352.0, "GSM6434009 r1", "0:68 1:0", "A:287361625;C:160168036;G:201822099;T:230293138;N:27038", 68, 0, null, null, 287361625, 160168036, 201822099, 230293138, 27038, "SRX16888175", "SRS14475659", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.79783, null, 0.11832, null, 0.81858, null, 0.53184, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70896, "SRR20869078", "SRX16888174", "SRS14475658", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  DMSO treatment  zebrafish  rep4", "GSM6434008", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:DMSO treatment", "HET  DMSO treatment  zebrafish  rep4", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:DMSO treatment", "GSM6434008", "GSM6434008: HET  DMSO treatment  zebrafish  rep4; Danio rerio; RNA Seq", "GSM6434008 r1", "GSM6434008", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1498_KY23_168_29_R1.fastq.gz", "fastq", 914400828.0, 13447071.0, "GSM6434008 r1", "0:68 1:0", "A:294008016;C:166492811;G:196902092;T:256969737;N:28172", 68, 0, null, null, 294008016, 166492811, 196902092, 256969737, 28172, "SRX16888174", "SRS14475658", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.80378, null, 0.09051, null, 0.81913, null, 0.53428, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70897, "SRR20869079", "SRX16888173", "SRS14475657", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  DMSO treatment  zebrafish  rep3", "GSM6434007", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:DMSO treatment", "HET  DMSO treatment  zebrafish  rep3", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:DMSO treatment", "GSM6434007", "GSM6434007: HET  DMSO treatment  zebrafish  rep3; Danio rerio; RNA Seq", "GSM6434007 r1", "GSM6434007", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1497_KY23_168_28_R1.fastq.gz", "fastq", 840953484.0, 12366963.0, "GSM6434007 r1", "0:68 1:0", "A:273539801;C:150455845;G:187644527;T:229287609;N:25702", 68, 0, null, null, 273539801, 150455845, 187644527, 229287609, 25702, "SRX16888173", "SRS14475657", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.8074, null, 0.10306, null, 0.816, null, 0.55004, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70898, "SRR20869080", "SRX16888172", "SRS14475656", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  DMSO treatment  zebrafish  rep2", "GSM6434006", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:DMSO treatment", "HET  DMSO treatment  zebrafish  rep2", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:DMSO treatment", "GSM6434006", "GSM6434006: HET  DMSO treatment  zebrafish  rep2; Danio rerio; RNA Seq", "GSM6434006 r1", "GSM6434006", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1496_KY23_168_27_R1.fastq.gz", "fastq", 866563304.0, 12743578.0, "GSM6434006 r1", "0:68 1:0", "A:281372378;C:156074885;G:192852640;T:236236763;N:26638", 68, 0, null, null, 281372378, 156074885, 192852640, 236236763, 26638, "SRX16888172", "SRS14475656", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.78328, null, 0.10093, null, 0.82483, null, 0.50637, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70899, "SRR20869081", "SRX16888171", "SRS14475655", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  DMSO treatment  zebrafish  rep1", "GSM6434005", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:DMSO treatment", "HET  DMSO treatment  zebrafish  rep1", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:DMSO treatment", "GSM6434005", "GSM6434005: HET  DMSO treatment  zebrafish  rep1; Danio rerio; RNA Seq", "GSM6434005 r1", "GSM6434005", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1495_KY23_168_26_R1.fastq.gz", "fastq", 843354632.0, 12402274.0, "GSM6434005 r1", "0:68 1:0", "A:272671962;C:152135239;G:192414605;T:226107225;N:25601", 68, 0, null, null, 272671962, 152135239, 192414605, 226107225, 25601, "SRX16888171", "SRS14475655", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.80999, null, 0.10836, null, 0.82087, null, 0.54692, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70900, "SRR20869082", "SRX16888170", "SRS14475654", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  VPA treatment  zebrafish  rep5", "GSM6434004", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:VPA treatment", "Mtm1 KO  VPA treatment  zebrafish  rep5", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:VPA treatment", "GSM6434004", "GSM6434004: Mtm1 KO  VPA treatment  zebrafish  rep5; Danio rerio; RNA Seq", "GSM6434004 r1", "GSM6434004", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1494_KY23_168_25_R1.fastq.gz", "fastq", 927311512.0, 13636934.0, "GSM6434004 r1", "0:68 1:0", "A:291725435;C:166577119;G:206636287;T:262343860;N:28811", 68, 0, null, null, 291725435, 166577119, 206636287, 262343860, 28811, "SRX16888170", "SRS14475654", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.82957, null, 0.07535, null, 0.80943, null, 0.52892, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70901, "SRR20869083", "SRX16888169", "SRS14475653", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  VPA treatment  zebrafish  rep4", "GSM6434003", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:VPA treatment", "Mtm1 KO  VPA treatment  zebrafish  rep4", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:VPA treatment", "GSM6434003", "GSM6434003: Mtm1 KO  VPA treatment  zebrafish  rep4; Danio rerio; RNA Seq", "GSM6434003 r1", "GSM6434003", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1493_KY23_168_24_R1.fastq.gz", "fastq", 911599840.0, 13405880.0, "GSM6434003 r1", "0:68 1:0", "A:287750544;C:163096141;G:204309196;T:256416158;N:27801", 68, 0, null, null, 287750544, 163096141, 204309196, 256416158, 27801, "SRX16888169", "SRS14475653", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.83046, null, 0.10327, null, 0.81109, null, 0.53449, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70902, "SRR20869084", "SRX16888168", "SRS14475652", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  VPA treatment  zebrafish  rep3", "GSM6434002", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:VPA treatment", "Mtm1 KO  VPA treatment  zebrafish  rep3", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:VPA treatment", "GSM6434002", "GSM6434002: Mtm1 KO  VPA treatment  zebrafish  rep3; Danio rerio; RNA Seq", "GSM6434002 r1", "GSM6434002", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1492_KY23_168_23_R1.fastq.gz", "fastq", 929837440.0, 13674080.0, "GSM6434002 r1", "0:68 1:0", "A:303836655;C:166378150;G:210423283;T:249170835;N:28517", 68, 0, null, null, 303836655, 166378150, 210423283, 249170835, 28517, "SRX16888168", "SRS14475652", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.80469, null, 0.11617, null, 0.81371, null, 0.5335, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70903, "SRR20869085", "SRX16888167", "SRS14475651", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  VPA treatment  zebrafish  rep2", "GSM6434001", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:VPA treatment", "Mtm1 KO  VPA treatment  zebrafish  rep2", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:VPA treatment", "GSM6434001", "GSM6434001: Mtm1 KO  VPA treatment  zebrafish  rep2; Danio rerio; RNA Seq", "GSM6434001 r1", "GSM6434001", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1491_KY23_168_22_R1.fastq.gz", "fastq", 856283132.0, 12592399.0, "GSM6434001 r1", "0:68 1:0", "A:298516548;C:149218718;G:188328193;T:220193538;N:26135", 68, 0, null, null, 298516548, 149218718, 188328193, 220193538, 26135, "SRX16888167", "SRS14475651", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.74816, null, 0.1133, null, 0.82012, null, 0.54102, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70904, "SRR20869086", "SRX16888166", "SRS14475650", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  VPA treatment  zebrafish  rep1", "GSM6434000", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:VPA treatment", "Mtm1 KO  VPA treatment  zebrafish  rep1", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:VPA treatment", "GSM6434000", "GSM6434000: Mtm1 KO  VPA treatment  zebrafish  rep1; Danio rerio; RNA Seq", "GSM6434000 r1", "GSM6434000", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1490_KY23_168_21_R1.fastq.gz", "fastq", 840998840.0, 12367630.0, "GSM6434000 r1", "0:68 1:0", "A:269574792;C:155617312;G:189177931;T:226602805;N:26000", 68, 0, null, null, 269574792, 155617312, 189177931, 226602805, 26000, "SRX16888166", "SRS14475650", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.82682, null, 0.11442, null, 0.81428, null, 0.56002, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70905, "SRR20869087", "SRX16888165", "SRS14475649", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  VPA treatment  zebrafish  rep5", "GSM6433999", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:VPA treatment", "HET  VPA treatment  zebrafish  rep5", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:VPA treatment", "GSM6433999", "GSM6433999: HET  VPA treatment  zebrafish  rep5; Danio rerio; RNA Seq", "GSM6433999 r1", "GSM6433999", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1489_KY23_168_20_R1.fastq.gz", "fastq", 901828240.0, 13262180.0, "GSM6433999 r1", "0:68 1:0", "A:291763235;C:163163197;G:196793555;T:250080362;N:27891", 68, 0, null, null, 291763235, 163163197, 196793555, 250080362, 27891, "SRX16888165", "SRS14475649", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.81103, null, 0.09106, null, 0.81397, null, 0.55141, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70906, "SRR20869088", "SRX16888164", "SRS14475648", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  VPA treatment  zebrafish  rep4", "GSM6433998", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:VPA treatment", "HET  VPA treatment  zebrafish  rep4", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:VPA treatment", "GSM6433998", "GSM6433998: HET  VPA treatment  zebrafish  rep4; Danio rerio; RNA Seq", "GSM6433998 r1", "GSM6433998", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1488_KY23_168_19_R1.fastq.gz", "fastq", 1002197600.0, 14738200.0, "GSM6433998 r1", "0:68 1:0", "A:322076969;C:182902068;G:222775191;T:274412708;N:30664", 68, 0, null, null, 322076969, 182902068, 222775191, 274412708, 30664, "SRX16888164", "SRS14475648", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.8214, null, 0.09555, null, 0.81708, null, 0.5555, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70907, "SRR20869089", "SRX16888163", "SRS14475647", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  VPA treatment  zebrafish  rep3", "GSM6433997", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:VPA treatment", "HET  VPA treatment  zebrafish  rep3", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:VPA treatment", "GSM6433997", "GSM6433997: HET  VPA treatment  zebrafish  rep3; Danio rerio; RNA Seq", "GSM6433997 r1", "GSM6433997", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1487_KY23_168_18_R1.fastq.gz", "fastq", 913436452.0, 13432889.0, "GSM6433997 r1", "0:68 1:0", "A:298763838;C:164686057;G:208498185;T:241460289;N:28083", 68, 0, null, null, 298763838, 164686057, 208498185, 241460289, 28083, "SRX16888163", "SRS14475647", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.80018, null, 0.11373, null, 0.81438, null, 0.36042, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70908, "SRR20869090", "SRX16888162", "SRS14475646", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  VPA treatment  zebrafish  rep2", "GSM6433996", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:VPA treatment", "HET  VPA treatment  zebrafish  rep2", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:VPA treatment", "GSM6433996", "GSM6433996: HET  VPA treatment  zebrafish  rep2; Danio rerio; RNA Seq", "GSM6433996 r1", "GSM6433996", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1486_KY23_168_17_R1.fastq.gz", "fastq", 820142016.0, 12060912.0, "GSM6433996 r1", "0:68 1:0", "A:263283593;C:147216450;G:177773419;T:231843239;N:25315", 68, 0, null, null, 263283593, 147216450, 177773419, 231843239, 25315, "SRX16888162", "SRS14475646", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.81, null, 0.08525, null, 0.81335, null, 0.54085, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70909, "SRR20869091", "SRX16888161", "SRS14475645", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  VPA treatment  zebrafish  rep1", "GSM6433995", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:VPA treatment", "HET  VPA treatment  zebrafish  rep1", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:VPA treatment", "GSM6433995", "GSM6433995: HET  VPA treatment  zebrafish  rep1; Danio rerio; RNA Seq", "GSM6433995 r1", "GSM6433995", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1485_KY23_168_16_R1.fastq.gz", "fastq", 935648924.0, 13759543.0, "GSM6433995 r1", "0:68 1:0", "A:311986085;C:169749709;G:201471642;T:252412819;N:28669", 68, 0, null, null, 311986085, 169749709, 201471642, 252412819, 28669, "SRX16888161", "SRS14475645", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.71797, null, 0.09744, null, 0.81645, null, 0.56605, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70910, "SRR20869092", "SRX16888160", "SRS14475644", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  TSA treatment  zebrafish  rep5", "GSM6433994", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:TSA treatment", "Mtm1 KO  TSA treatment  zebrafish  rep5", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:TSA treatment", "GSM6433994", "GSM6433994: Mtm1 KO  TSA treatment  zebrafish  rep5; Danio rerio; RNA Seq", "GSM6433994 r1", "GSM6433994", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1484_KY23_168_15_R1.fastq.gz", "fastq", 867623492.0, 12759169.0, "GSM6433994 r1", "0:68 1:0", "A:289234513;C:155221667;G:194434609;T:228706315;N:26388", 68, 0, null, null, 289234513, 155221667, 194434609, 228706315, 26388, "SRX16888160", "SRS14475644", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.78415, null, 0.11088, null, 0.81355, null, 0.51504, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70911, "SRR20869093", "SRX16888159", "SRS14475643", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  TSA treatment  zebrafish  rep4", "GSM6433993", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:TSA treatment", "Mtm1 KO  TSA treatment  zebrafish  rep4", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:TSA treatment", "GSM6433993", "GSM6433993: Mtm1 KO  TSA treatment  zebrafish  rep4; Danio rerio; RNA Seq", "GSM6433993 r1", "GSM6433993", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1483_KY23_168_14_R1.fastq.gz", "fastq", 866595060.0, 12744045.0, "GSM6433993 r1", "0:68 1:0", "A:307372835;C:152869818;G:183626188;T:222699713;N:26506", 68, 0, null, null, 307372835, 152869818, 183626188, 222699713, 26506, "SRX16888159", "SRS14475643", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.71566, null, 0.11015, null, 0.82917, null, 0.50431, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70912, "SRR20869094", "SRX16888158", "SRS14475642", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  TSA treatment  zebrafish  rep3", "GSM6433992", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:TSA treatment", "Mtm1 KO  TSA treatment  zebrafish  rep3", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:TSA treatment", "GSM6433992", "GSM6433992: Mtm1 KO  TSA treatment  zebrafish  rep3; Danio rerio; RNA Seq", "GSM6433992 r1", "GSM6433992", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1482_KY23_168_13_R1.fastq.gz", "fastq", 908450692.0, 13359569.0, "GSM6433992 r1", "0:68 1:0", "A:294288974;C:166101496;G:195409922;T:252622316;N:27984", 68, 0, null, null, 294288974, 166101496, 195409922, 252622316, 27984, "SRX16888158", "SRS14475642", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.80995, null, 0.0914, null, 0.81389, null, 0.54466, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70913, "SRR20869095", "SRX16888157", "SRS14475641", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  TSA treatment  zebrafish  rep2", "GSM6433991", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:TSA treatment", "Mtm1 KO  TSA treatment  zebrafish  rep2", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:TSA treatment", "GSM6433991", "GSM6433991: Mtm1 KO  TSA treatment  zebrafish  rep2; Danio rerio; RNA Seq", "GSM6433991 r1", "GSM6433991", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1481_KY23_168_12_R1.fastq.gz", "fastq", 880023496.0, 12941522.0, "GSM6433991 r1", "0:68 1:0", "A:287151954;C:160498388;G:192579956;T:239765774;N:27424", 68, 0, null, null, 287151954, 160498388, 192579956, 239765774, 27424, "SRX16888157", "SRS14475641", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.8031, null, 0.09849, null, 0.81501, null, 0.55513, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70914, "SRR20869096", "SRX16888156", "SRS14475640", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "Mtm1 KO  TSA treatment  zebrafish  rep1", "GSM6433990", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:TSA treatment", "Mtm1 KO  TSA treatment  zebrafish  rep1", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:Mtm1 KO|treatment:TSA treatment", "GSM6433990", "GSM6433990: Mtm1 KO  TSA treatment  zebrafish  rep1; Danio rerio; RNA Seq", "GSM6433990 r1", "GSM6433990", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1480_KY23_168_11_R1.fastq.gz", "fastq", 1003182444.0, 14752683.0, "GSM6433990 r1", "0:68 1:0", "A:328950780;C:180702054;G:217909263;T:275589304;N:31043", 68, 0, null, null, 328950780, 180702054, 217909263, 275589304, 31043, "SRX16888156", "SRS14475640", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.80451, null, 0.09789, null, 0.81533, null, 0.55074, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70915, "SRR20869097", "SRX16888155", "SRS14475639", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  TSA treatment  zebrafish  rep4", "GSM6433989", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:TSA treatment", "HET  TSA treatment  zebrafish  rep4", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:TSA treatment", "GSM6433989", "GSM6433989: HET  TSA treatment  zebrafish  rep4; Danio rerio; RNA Seq", "GSM6433989 r1", "GSM6433989", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1479_KY23_168_10_R1.fastq.gz", "fastq", 895564760.0, 13170070.0, "GSM6433989 r1", "0:68 1:0", "A:300989941;C:166218035;G:200751247;T:227578514;N:27023", 68, 0, null, null, 300989941, 166218035, 200751247, 227578514, 27023, "SRX16888155", "SRS14475639", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.65575, null, 0.09506, null, 0.83224, null, 0.52894, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70916, "SRR20869098", "SRX16888154", "SRS14475638", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  TSA treatment  zebrafish  rep3", "GSM6433988", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:TSA treatment", "HET  TSA treatment  zebrafish  rep3", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:TSA treatment", "GSM6433988", "GSM6433988: HET  TSA treatment  zebrafish  rep3; Danio rerio; RNA Seq", "GSM6433988 r1", "GSM6433988", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1477_KY23_168_8_R1.fastq.gz", "fastq", 1021524628.0, 15022421.0, "GSM6433988 r1", "0:68 1:0", "A:386300445;C:167964779;G:205371083;T:261856684;N:31637", 68, 0, null, null, 386300445, 167964779, 205371083, 261856684, 31637, "SRX16888154", "SRS14475638", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.73302, null, 0.10328, null, 0.81466, null, 0.55873, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70917, "SRR20869099", "SRX16888153", "SRS14475637", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  TSA treatment  zebrafish  rep2", "GSM6433987", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:TSA treatment", "HET  TSA treatment  zebrafish  rep2", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:TSA treatment", "GSM6433987", "GSM6433987: HET  TSA treatment  zebrafish  rep2; Danio rerio; RNA Seq", "GSM6433987 r1", "GSM6433987", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1476_KY23_168_7_R1.fastq.gz", "fastq", 951668296.0, 13995122.0, "GSM6433987 r1", "0:68 1:0", "A:339449944;C:164483500;G:198328177;T:249377598;N:29077", 68, 0, null, null, 339449944, 164483500, 198328177, 249377598, 29077, "SRX16888153", "SRS14475637", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.73604, null, 0.0885, null, 0.82187, null, 0.54577, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70918, "SRR20869100", "SRX16888152", "SRS14475636", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "HET  TSA treatment  zebrafish  rep1", "GSM6433986", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:HET|treatment:TSA treatment", "HET  TSA treatment  zebrafish  rep1", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:HET|treatment:TSA treatment", "GSM6433986", "GSM6433986: HET  TSA treatment  zebrafish  rep1; Danio rerio; RNA Seq", "GSM6433986 r1", "GSM6433986", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1475_KY23_168_6_R1.fastq.gz", "fastq", 882802180.0, 12982385.0, "GSM6433986 r1", "0:68 1:0", "A:303896452;C:155568953;G:193507200;T:229802351;N:27224", 68, 0, null, null, 303896452, 155568953, 193507200, 229802351, 27224, "SRX16888152", "SRS14475636", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.7587, null, 0.1005, null, 0.82071, null, 0.54149, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70919, "SRR20869101", "SRX16888151", "SRS14475635", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "WT  DMSO treatment  zebrafish  rep5", "GSM6433985", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:WT|treatment:DMSO treatment", "WT  DMSO treatment  zebrafish  rep5", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:WT|treatment:DMSO treatment", "GSM6433985", "GSM6433985: WT  DMSO treatment  zebrafish  rep5; Danio rerio; RNA Seq", "GSM6433985 r1", "GSM6433985", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1474_KY23_168_5_R1.fastq.gz", "fastq", 912959636.0, 13425877.0, "GSM6433985 r1", "0:68 1:0", "A:308365583;C:164030703;G:197218474;T:243316551;N:28325", 68, 0, null, null, 308365583, 164030703, 197218474, 243316551, 28325, "SRX16888151", "SRS14475635", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.7904, null, 0.09253, null, 0.81886, null, 0.57028, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70920, "SRR20869102", "SRX16888150", "SRS14475634", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "WT  DMSO treatment  zebrafish  rep4", "GSM6433984", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:WT|treatment:DMSO treatment", "WT  DMSO treatment  zebrafish  rep4", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:WT|treatment:DMSO treatment", "GSM6433984", "GSM6433984: WT  DMSO treatment  zebrafish  rep4; Danio rerio; RNA Seq", "GSM6433984 r1", "GSM6433984", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1473_KY23_168_4_R1.fastq.gz", "fastq", 886745704.0, 13040378.0, "GSM6433984 r1", "0:68 1:0", "A:304159499;C:157062642;G:192987191;T:232509378;N:26994", 68, 0, null, null, 304159499, 157062642, 192987191, 232509378, 26994, "SRX16888150", "SRS14475634", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.77072, null, 0.08161, null, 0.82294, null, 0.56065, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70921, "SRR20869103", "SRX16888149", "SRS14475633", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "WT  DMSO treatment  zebrafish  rep3", "GSM6433983", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:WT|treatment:DMSO treatment", "WT  DMSO treatment  zebrafish  rep3", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:WT|treatment:DMSO treatment", "GSM6433983", "GSM6433983: WT  DMSO treatment  zebrafish  rep3; Danio rerio; RNA Seq", "GSM6433983 r1", "GSM6433983", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1472_KY23_168_3_R1.fastq.gz", "fastq", 852365924.0, 12534793.0, "GSM6433983 r1", "0:68 1:0", "A:288118744;C:154342074;G:181602972;T:228275755;N:26379", 68, 0, null, null, 288118744, 154342074, 181602972, 228275755, 26379, "SRX16888149", "SRS14475633", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.78952, null, 0.07137, null, 0.81941, null, 0.55642, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70922, "SRR20869104", "SRX16888148", "SRS14475632", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "WT  DMSO treatment  zebrafish  rep2", "GSM6433982", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:WT|treatment:DMSO treatment", "WT  DMSO treatment  zebrafish  rep2", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:WT|treatment:DMSO treatment", "GSM6433982", "GSM6433982: WT  DMSO treatment  zebrafish  rep2; Danio rerio; RNA Seq", "GSM6433982 r1", "GSM6433982", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1471_KY23_168_2_R1.fastq.gz", "fastq", 915622584.0, 13465038.0, "GSM6433982 r1", "0:68 1:0", "A:314839314;C:161960932;G:199970507;T:238823895;N:27936", 68, 0, null, null, 314839314, 161960932, 199970507, 238823895, 27936, "SRX16888148", "SRS14475632", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.76878, null, 0.08743, null, 0.82304, null, 0.57384, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [70923, "SRR20869105", "SRX16888147", "SRS14475631", "SRP390172", "PRJNA866536", "X linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition", "GSE210642", "Other", "X linked myotubular myopathy XLMTM is a fatal neuromuscular disorder caused by loss of function mutations in MTM1 . At present  there are no directed therapies for XLMTM  and incomplete understanding of disease pathomechanisms. To address these knowledge gaps  we performed a drug screen in mtm1 mutant zebrafish andidentified four positive hits  including valproic acid  which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model  and showed that valproic acid ameliorates the murine phenotype. Overall design: Zebrafish: At 1 dpf  embryos from single pair in crossings of mtm1+/zf711 adults were divided equally into three chemical treatment groups: DMSO  sodium valproate VPA  or trichostatin A. For tissue collection  the posterior section of larvae and fin fold tissues was dissected and snap frozen on dry ice at 4 dpf. A total of n=6 10 larvae per pool per condition with 5 biological replicates were used for RNA extraction.  Mice: Bulk RNA sequencing was performed on RNA extracts from tibialis anterior muscle from 35 dpf Mtm1KO and WT mice  either treated with PBS or valproic acid VPA starting at 21 days.", null, "pubmed:35844027", null, "WT  DMSO treatment  zebrafish  rep1", "GSM6433981", null, "source name:posterior half of larvae|tissue:posterior half of larvae|genotype:WT|treatment:DMSO treatment", "WT  DMSO treatment  zebrafish  rep1", "Sequencing reads were aligned to the mouseGRCm38 /zebrafish genomeGRCz9 using STAR. Read quality was assessed with FastQC  and adaptors were trimmed from reads using Cutadapt. STAR gene level counts ReadsPerGene.out.tab files were used for differential expression with DESeq2 package Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38 Supplementary files format and content: tab delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.", "posterior half of larvae", null, "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer\u2019s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3\u2019 mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "tissue:posterior half of larvae|genotype:WT|treatment:DMSO treatment", "GSM6433981", "GSM6433981: WT  DMSO treatment  zebrafish  rep1; Danio rerio; RNA Seq", "GSM6433981 r1", "GSM6433981", "1", "Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer's protocol Zebrafish: RNA libraries were generated using the QuantSeq three prime mRNA sequencing kit Lexogen automated on an NGS workstation Agilent   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP390172", null, null, "WL1470_KY23_168_1_R1.fastq.gz", "fastq", 997885244.0, 14674783.0, "GSM6433981 r1", "0:68 1:0", "A:351989460;C:174189591;G:216129629;T:255546296;N:30268", 68, 0, null, null, 351989460, 174189591, 216129629, 255546296, 30268, "SRX16888147", "SRS14475631", "SRA1470408", "Hospital for Sick Children", "Hospital for Sick Children", 1, 0.7455, null, 0.08488, null, 0.82611, null, 0.57074, null, 68, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "bulk", "bulk", null, "Canada", "2022-08-05", "Larval", "Larval", "Trunk", "Surface Structure"], [76470, "SRR24976460", "SRX20733648", "SRS18024487", "SRP445049", "PRJNA985650", "Ancient vertebrate dermal armor evolved from trunk neural crest", "GSE235280", "Other", "Bone is an evolutionary novelty of vertebrates  likely to have first emerged as part of ancestral dermal armor that consisted of osteogenic and odontogenic components. Whether these early vertebrate structures arose from mesoderm or neural crest cells has been a matter of considerable debate. To examine the developmental origin of the bony part of the dermal armor  we have performed in vivo lineage tracing in the sterlet sturgeon  a representative of non teleost ray finned fish that has retained an extensive postcranial dermal skeleton. The results definitively show that sterlet trunk neural crest cells give rise to osteoblasts of the scutes. Transcriptional profiling further reveals neural crest gene signature in sterlet scutes as well as bichir scales. Finally  histological and microCT analysis of ray finned fish dermal armor show that their scales and scutes are formed by bone  dentin and hypermineralized covering tissues  in various combinations  that resemble those of the first armored vertebrates. Taken together  our results support a primitive skeletogenic role for the neural crest along the entire body axis  that was later progressively restricted to the cranial region during vertebrate evolution. Thus  the neural crest was a crucial evolutionary innovation driving the origin and diversification of dermal armor along the entire body axis. Overall design: To investigate the expression profiles of the dermal armor  we performed bulk RNA sequencing of sterlet sturgeon scutes  scales of the Senegal bichir  and zebrafish scales.", null, "pubmed:37459514", null, "Zebrafish scale 30mm  replicate 2", "GSM7498272", null, "source name:cells of elasmoid scale|tissue:cells of elasmoid scale|genotype:WT|measure:30 mm|geo loc name:missing|collection date:missing", "Zebrafish scale 30mm  replicate 2", "In brief  every sterlet/bichir protein sequence was queried locally against the zebrafish proteome  following which regions with the longest alignment were matched to the respective zebrafish proteins. Using this alignment based approach  proteins with highest alignment percentage score were identified as orthologues. Sterlet/bichir scute/scale RNA sequencing libraries were aligned to the sterlet/bichir sequences  while the zebrafish scale RNA sequencing libraries were aligned to the zebrafish sequences using Bowtie23. Transcript counts were calculated using featureCounts and differential gene expression analysis was performed using DESeq2. Using zebrafish gene annotations as a reference  we added the transcript counts for duplicated orthologues found in the sterlet/bichir genome to calculate an \u2018aggregated\u2019 transcript count for each gene as described by Martik et al.  2019. These aggregated transcript counts were then normalized using the formula: Zi=Ti\u2212minT/maxT\u2212minT whereZiis the normalized transcript count andTiis the absolute transcript count. A subset of genes previously identified as being part of the neural crest gene regulatory network was then isolated from the count matrix and plotted as a heatmap using ComplexHeatmap package in Rstudio. Assembly: Sterlet sturgeon Genome assembly ASM1064508v1/ Senegal bichir Genome assembly ASM1683550v1/ zebrafish Genome assembly GRCz11 Supplementary files format and content: tab delimited text files that includes featurecounts values for each sample", "cells of elasmoid scale", null, "RNAqueous kit Ambion  prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols.", null, "tissue:cells of elasmoid scale|genotype:WT|measure:30 mm", "GSM7498272", "GSM7498272: Zebrafish scale 30mm  replicate 2; Danio rerio; RNA Seq", "GSM7498272 r1", "GSM7498272", "1", "RNAqueous kit Ambion  prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP445049", null, null, "DR_scale_2.fastq.gz", "fastq", 3233423900.0, 64668478.0, "GSM7498272 r1", "0:50", "A:867694073;C:728518022;G:750424718;T:885367521;N:1419566", 50, null, null, null, 867694073, 728518022, 750424718, 885367521, 1419566, "SRX20733648", "SRS18024487", "SRA1659604", "Bronner, California Institute of Technology", "Bronner, California Institute of Technology", 1, 0.89607, null, 0.08896, null, 0.72612, null, 0.4695, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-20", "Undetermined", "Undetermined", "Scale", "Surface Structure"], [76471, "SRR24976461", "SRX20733647", "SRS18024486", "SRP445049", "PRJNA985650", "Ancient vertebrate dermal armor evolved from trunk neural crest", "GSE235280", "Other", "Bone is an evolutionary novelty of vertebrates  likely to have first emerged as part of ancestral dermal armor that consisted of osteogenic and odontogenic components. Whether these early vertebrate structures arose from mesoderm or neural crest cells has been a matter of considerable debate. To examine the developmental origin of the bony part of the dermal armor  we have performed in vivo lineage tracing in the sterlet sturgeon  a representative of non teleost ray finned fish that has retained an extensive postcranial dermal skeleton. The results definitively show that sterlet trunk neural crest cells give rise to osteoblasts of the scutes. Transcriptional profiling further reveals neural crest gene signature in sterlet scutes as well as bichir scales. Finally  histological and microCT analysis of ray finned fish dermal armor show that their scales and scutes are formed by bone  dentin and hypermineralized covering tissues  in various combinations  that resemble those of the first armored vertebrates. Taken together  our results support a primitive skeletogenic role for the neural crest along the entire body axis  that was later progressively restricted to the cranial region during vertebrate evolution. Thus  the neural crest was a crucial evolutionary innovation driving the origin and diversification of dermal armor along the entire body axis. Overall design: To investigate the expression profiles of the dermal armor  we performed bulk RNA sequencing of sterlet sturgeon scutes  scales of the Senegal bichir  and zebrafish scales.", null, "pubmed:37459514", null, "Zebrafish scale 30mm  replicate 1", "GSM7498271", null, "source name:cells of elasmoid scale|tissue:cells of elasmoid scale|genotype:WT|measure:30 mm|geo loc name:missing|collection date:missing", "Zebrafish scale 30mm  replicate 1", "In brief  every sterlet/bichir protein sequence was queried locally against the zebrafish proteome  following which regions with the longest alignment were matched to the respective zebrafish proteins. Using this alignment based approach  proteins with highest alignment percentage score were identified as orthologues. Sterlet/bichir scute/scale RNA sequencing libraries were aligned to the sterlet/bichir sequences  while the zebrafish scale RNA sequencing libraries were aligned to the zebrafish sequences using Bowtie23. Transcript counts were calculated using featureCounts and differential gene expression analysis was performed using DESeq2. Using zebrafish gene annotations as a reference  we added the transcript counts for duplicated orthologues found in the sterlet/bichir genome to calculate an \u2018aggregated\u2019 transcript count for each gene as described by Martik et al.  2019. These aggregated transcript counts were then normalized using the formula: Zi=Ti\u2212minT/maxT\u2212minT whereZiis the normalized transcript count andTiis the absolute transcript count. A subset of genes previously identified as being part of the neural crest gene regulatory network was then isolated from the count matrix and plotted as a heatmap using ComplexHeatmap package in Rstudio. Assembly: Sterlet sturgeon Genome assembly ASM1064508v1/ Senegal bichir Genome assembly ASM1683550v1/ zebrafish Genome assembly GRCz11 Supplementary files format and content: tab delimited text files that includes featurecounts values for each sample", "cells of elasmoid scale", null, "RNAqueous kit Ambion  prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols.", null, "tissue:cells of elasmoid scale|genotype:WT|measure:30 mm", "GSM7498271", "GSM7498271: Zebrafish scale 30mm  replicate 1; Danio rerio; RNA Seq", "GSM7498271 r1", "GSM7498271", "1", "RNAqueous kit Ambion  prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP445049", null, null, "DR_scale_1.fastq.gz", "fastq", 2847639400.0, 56952788.0, "GSM7498271 r1", "0:50", "A:764903871;C:640842328;G:660536366;T:780092458;N:1264377", 50, null, null, null, 764903871, 640842328, 660536366, 780092458, 1264377, "SRX20733647", "SRS18024486", "SRA1659604", "Bronner, California Institute of Technology", "Bronner, California Institute of Technology", 1, 0.89576, null, 0.08353, null, 0.73594, null, 0.45703, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-06-20", "Undetermined", "Undetermined", "Scale", "Surface Structure"]], "truncated": false, "filtered_table_rows_count": 62, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", 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