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62 rows where experiment.library_layout = "SINGLE", technology = "bulk" and tissue_curation_coarse = "Surface Structure"

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devstage_curation_coarse 4

devstage_curation 4

tissue_curation 3

tissue_curation_coarse 1

  • Surface Structure · 62 ✖

technology 1

  • bulk · 62 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

  • SINGLE · 62 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
36741 36741 SRR850608 SRX277695 SRS420758 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr18 danrer skin 42months rep5 GSM1141118   source name:total RNA extracted from skin|strain:TuAB|age:42 month|tissue:skin Nr18 danrer skin 42months rep5 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:42 month|tissue:skin GSM1141118 GSM1141118: Nr18 danrer skin 42months rep5; Danio rerio; RNA Seq GSM1141118 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141118 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr18_3.5y_l3_export.fq.gz fastq 3269418540.0 43018665.0 GSM1141118 r1 0:76 A:892486836;C:744426899;G:749230539;T:883114979;N:159287 76       892486836 744426899 749230539 883114979 159287 SRX277695 SRS420758 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91402   0.1106   0.73436   0.4911   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36742 36742 SRR850607 SRX277694 SRS420757 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr14 danrer skin 42months rep4 GSM1141117   source name:total RNA extracted from skin|strain:TuAB|age:42 month|tissue:skin Nr14 danrer skin 42months rep4 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:42 month|tissue:skin GSM1141117 GSM1141117: Nr14 danrer skin 42months rep4; Danio rerio; RNA Seq GSM1141117 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141117 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr14_3.5y_l2_export.fq.gz fastq 2300890044.0 30274869.0 GSM1141117 r1 0:76 A:631736236;C:525065199;G:510761115;T:633208038;N:119456 76       631736236 525065199 510761115 633208038 119456 SRX277694 SRS420757 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.90718   0.11607   0.71997   0.49141   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36743 36743 SRR850606 SRX277693 SRS420790 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr13 danrer skin 42months rep3 GSM1141116   source name:total RNA extracted from skin|strain:TuAB|age:42 month|tissue:skin Nr13 danrer skin 42months rep3 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:42 month|tissue:skin GSM1141116 GSM1141116: Nr13 danrer skin 42months rep3; Danio rerio; RNA Seq GSM1141116 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141116 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr13_3.5y_l1_export.fastq.gz fastq 3508110372.0 46159347.0 GSM1141116 r1 0:76 A:959986155;C:782258637;G:803256847;T:962450623;N:158110 76       959986155 782258637 803256847 962450623 158110 SRX277693 SRS420790 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.85747   0.12068   0.73819   0.4917   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36744 36744 SRR850605 SRX277692 SRS420789 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr12 danrer skin 42months rep2 GSM1141115   source name:total RNA extracted from skin|strain:TuAB|age:42 month|tissue:skin Nr12 danrer skin 42months rep2 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:42 month|tissue:skin GSM1141115 GSM1141115: Nr12 danrer skin 42months rep2; Danio rerio; RNA Seq GSM1141115 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141115 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr12_3.5y_l3_export.fq.gz fastq 3961243804.0 52121629.0 GSM1141115 r1 0:76 A:1092811778;C:874440215;G:892629531;T:1099367104;N:1995176 76       1092811778 874440215 892629531 1099367104 1995176 SRX277692 SRS420789 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.88854   0.12633   0.73746   0.53849   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36745 36745 SRR850604 SRX277691 SRS420788 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr11 danrer skin 42months rep1 GSM1141114   source name:total RNA extracted from skin|strain:TuAB|age:42 month|tissue:skin Nr11 danrer skin 42months rep1 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:42 month|tissue:skin GSM1141114 GSM1141114: Nr11 danrer skin 42months rep1; Danio rerio; RNA Seq GSM1141114 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141114 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr11_3.5y_l2_export.fq.gz fastq 3327777040.0 43786540.0 GSM1141114 r1 0:76 A:920364748;C:745739060;G:758842746;T:901558784;N:1271702 76       920364748 745739060 758842746 901558784 1271702 SRX277691 SRS420788 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.86781   0.11618   0.72888   0.50217   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36746 36746 SRR850603 SRX277690 SRS420756 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr76 danrer skin 24months rep6 GSM1141113   source name:total RNA extracted from skin|strain:TuAB|age:24 month|tissue:skin Nr76 danrer skin 24months rep6 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:24 month|tissue:skin GSM1141113 GSM1141113: Nr76 danrer skin 24months rep6; Danio rerio; RNA Seq GSM1141113 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141113 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr76_2y.fastq.gz fastq 2234765940.0 29404815.0 GSM1141113 r1 0:76 A:582794172;C:524083367;G:547601836;T:579473821;N:812744 76       582794172 524083367 547601836 579473821 812744 SRX277690 SRS420756 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.89808   0.07989   0.73511   0.47456   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36747 36747 SRR850602 SRX277689 SRS420755 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr75 danrer skin 24months rep5 GSM1141112   source name:total RNA extracted from skin|strain:TuAB|age:24 month|tissue:skin Nr75 danrer skin 24months rep5 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:24 month|tissue:skin GSM1141112 GSM1141112: Nr75 danrer skin 24months rep5; Danio rerio; RNA Seq GSM1141112 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141112 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr75_2y.fastq.gz fastq 1000606196.0 13165871.0 GSM1141112 r1 0:76 A:270569436;C:233353660;G:238144829;T:258045669;N:492602 76       270569436 233353660 238144829 258045669 492602 SRX277689 SRS420755 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.8949   0.07966   0.7293   0.47729   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36748 36748 SRR850601 SRX277688 SRS420754 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr73 danrer skin 24months rep4 GSM1141111   source name:total RNA extracted from skin|strain:TuAB|age:24 month|tissue:skin Nr73 danrer skin 24months rep4 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:24 month|tissue:skin GSM1141111 GSM1141111: Nr73 danrer skin 24months rep4; Danio rerio; RNA Seq GSM1141111 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141111 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr73_2y.fastq.gz fastq 2283103688.0 30040838.0 GSM1141111 r1 0:76 A:601138588;C:527906584;G:549863593;T:603391353;N:803570 76       601138588 527906584 549863593 603391353 803570 SRX277688 SRS420754 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.90138   0.08154   0.72598   0.49455   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36749 36749 SRR850600 SRX277687 SRS420787 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr72 danrer skin 24months rep3 GSM1141110   source name:total RNA extracted from skin|strain:TuAB|age:24 month|tissue:skin Nr72 danrer skin 24months rep3 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:24 month|tissue:skin GSM1141110 GSM1141110: Nr72 danrer skin 24months rep3; Danio rerio; RNA Seq GSM1141110 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141110 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr72_2y.fastq.gz fastq 1692545916.0 22270341.0 GSM1141110 r1 0:76 A:447927627;C:393400289;G:405212681;T:445305247;N:700072 76       447927627 393400289 405212681 445305247 700072 SRX277687 SRS420787 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.88704   0.08604   0.72833   0.47215   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36750 36750 SRR850599 SRX277686 SRS420786 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr71 danrer skin 24months rep2 GSM1141109   source name:total RNA extracted from skin|strain:TuAB|age:24 month|tissue:skin Nr71 danrer skin 24months rep2 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:24 month|tissue:skin GSM1141109 GSM1141109: Nr71 danrer skin 24months rep2; Danio rerio; RNA Seq GSM1141109 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141109 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr71_2y.fastq.gz fastq 1897129404.0 24962229.0 GSM1141109 r1 0:76 A:500740954;C:442627409;G:457159802;T:495689680;N:911559 76       500740954 442627409 457159802 495689680 911559 SRX277686 SRS420786 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.88731   0.07537   0.73628   0.4846   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36751 36751 SRR850598 SRX277685 SRS420785 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr70 danrer skin 24months rep1 GSM1141108   source name:total RNA extracted from skin|strain:TuAB|age:24 month|tissue:skin Nr70 danrer skin 24months rep1 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:24 month|tissue:skin GSM1141108 GSM1141108: Nr70 danrer skin 24months rep1; Danio rerio; RNA Seq GSM1141108 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141108 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr70_2y.fastq.gz fastq 2239190508.0 29463033.0 GSM1141108 r1 0:76 A:599665392;C:514113743;G:531871299;T:592730477;N:809597 76       599665392 514113743 531871299 592730477 809597 SRX277685 SRS420785 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.89167   0.09031   0.73515   0.49129   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36752 36752 SRR850597 SRX277684 SRS420784 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr30 danrer skin 5months rep9 GSM1141107   source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin Nr30 danrer skin 5months rep9 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:5 month|tissue:skin GSM1141107 GSM1141107: Nr30 danrer skin 5months rep9; Danio rerio; RNA Seq GSM1141107 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141107 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr30_5m.fastq.gz fastq 2502725752.0 32930602.0 GSM1141107 r1 0:76 A:684745428;C:570860380;G:565883575;T:679750149;N:1486220 76       684745428 570860380 565883575 679750149 1486220 SRX277684 SRS420784 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91789   0.10423   0.7263   0.4909   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36753 36753 SRR850596 SRX277683 SRS420783 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr29 danrer skin 5months rep8 GSM1141106   source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin Nr29 danrer skin 5months rep8 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:5 month|tissue:skin GSM1141106 GSM1141106: Nr29 danrer skin 5months rep8; Danio rerio; RNA Seq GSM1141106 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141106 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr29_5m.fastq.gz fastq 2012479468.0 26479993.0 GSM1141106 r1 0:76 A:558800574;C:450898608;G:447907004;T:553773824;N:1099458 76       558800574 450898608 447907004 553773824 1099458 SRX277683 SRS420783 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.9055   0.1197   0.7119   0.48553   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36754 36754 SRR850595 SRX277682 SRS420782 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr28 danrer skin 5months rep7 GSM1141105   source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin Nr28 danrer skin 5months rep7 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:5 month|tissue:skin GSM1141105 GSM1141105: Nr28 danrer skin 5months rep7; Danio rerio; RNA Seq GSM1141105 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141105 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr28_5m.fastq.gz fastq 2075098224.0 27303924.0 GSM1141105 r1 0:76 A:555062827;C:487427075;G:487360186;T:544381395;N:866741 76       555062827 487427075 487360186 544381395 866741 SRX277682 SRS420782 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91784   0.08866   0.73208   0.47793   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36755 36755 SRR850594 SRX277681 SRS420781 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr27 danrer skin 5months rep6 GSM1141104   source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin Nr27 danrer skin 5months rep6 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:5 month|tissue:skin GSM1141104 GSM1141104: Nr27 danrer skin 5months rep6; Danio rerio; RNA Seq GSM1141104 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141104 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr27_5m.fastq.gz fastq 2415354480.0 31780980.0 GSM1141104 r1 0:76 A:661012615;C:552471296;G:546304105;T:654315033;N:1251431 76       661012615 552471296 546304105 654315033 1251431 SRX277681 SRS420781 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91282   0.104   0.7236   0.48186   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36756 36756 SRR850593 SRX277680 SRS420780 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr26 danrer skin 5months rep5 GSM1141103   source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin Nr26 danrer skin 5months rep5 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:5 month|tissue:skin GSM1141103 GSM1141103: Nr26 danrer skin 5months rep5; Danio rerio; RNA Seq GSM1141103 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141103 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr26_5m_l8_export.fq.gz fastq 1866135464.0 24554414.0 GSM1141103 r1 0:76 A:495417130;C:442746432;G:436942898;T:490685510;N:343494 76       495417130 442746432 436942898 490685510 343494 SRX277680 SRS420780 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92443   0.08023   0.7288   0.48902   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36757 36757 SRR850592 SRX277679 SRS420778 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr25 danrer skin 5months rep4 GSM1141102   source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin Nr25 danrer skin 5months rep4 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:5 month|tissue:skin GSM1141102 GSM1141102: Nr25 danrer skin 5months rep4; Danio rerio; RNA Seq GSM1141102 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141102 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr25_5m_l7_export.fq.gz fastq 2146470508.0 28243033.0 GSM1141102 r1 0:76 A:583770580;C:491677255;G:491536604;T:579365742;N:120327 76       583770580 491677255 491536604 579365742 120327 SRX277679 SRS420778 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.89568   0.11303   0.71778   0.47882   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36758 36758 SRR850591 SRX277678 SRS420779 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr23 danrer skin 5months rep3 GSM1141101   source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin Nr23 danrer skin 5months rep3 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:5 month|tissue:skin GSM1141101 GSM1141101: Nr23 danrer skin 5months rep3; Danio rerio; RNA Seq GSM1141101 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141101 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr23_5m_l6_export.fq.gz fastq 2628691268.0 34588043.0 GSM1141101 r1 0:76 A:693944705;C:617538873;G:611502862;T:705582669;N:122159 76       693944705 617538873 611502862 705582669 122159 SRX277678 SRS420779 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92203   0.09747   0.71378   0.47796   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36759 36759 SRR850590 SRX277677 SRS420777 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr22 danrer skin 5months rep2 GSM1141100   source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin Nr22 danrer skin 5months rep2 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:5 month|tissue:skin GSM1141100 GSM1141100: Nr22 danrer skin 5months rep2; Danio rerio; RNA Seq GSM1141100 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141100 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr22_5m.fastq.gz fastq 3561382724.0 46860299.0 GSM1141100 r1 0:76 A:956105654;C:826498432;G:826128735;T:952426883;N:223020 76       956105654 826498432 826128735 952426883 223020 SRX277677 SRS420777 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.93192   0.09055   0.72876   0.52416   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
36760 36760 SRR850589 SRX277676 SRS420776 SRP022612 PRJNA203029 RNA seq of Danio rerio and Mus musculus skin for three different age groups GSE46916 Other Background: Comparison of temporal gene expression profiles. The RNA seq data comprises 3 age groups: 2 15 month and 30 month for mouse skin; 5 24 month and 42 month for zebrafish skin. Illumina 50bp single stranded single read RNA sequencing Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 15 samples for mouse: 5 biological replicates for 2 month 6 biological replicates for 15 month and 4 biological replicates for 30 month; 20 samples for zebrafish: 9 biological replicates for 5 month 6 biological replicates for 24 month and 5 biological replicates for 42 month   pubmed:26620638   Nr21 danrer skin 5months rep1 GSM1141099   source name:total RNA extracted from skin|strain:TuAB|age:5 month|tissue:skin Nr21 danrer skin 5months rep1 Illumina Casava software used for extraction of FASTQ files FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation Genome build: D. rerio: danRer7; M. musculus: mm9 Supplementary files format and content: Excel file include raw counts and RPKM values for each sample total RNA extracted from skin   D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.   strain:TuAB|age:5 month|tissue:skin GSM1141099 GSM1141099: Nr21 danrer skin 5months rep1; Danio rerio; RNA Seq GSM1141099 1   1 D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater Qiagen Hilden Germany at 80 °C. Total RNA was isolated with TRIzol Life Technologies Darmstadt Germany according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol Qiagen by subsequently adding 100 μl chloroform. Following phase separation the aqueous phase was transferred into a fresh tube then 0.16 volume NaAc 2 M pH 4.0 and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water GIBCO and stored at –80°C until use. D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA Seq sample prep kit Illumina San Diego CA USA following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit. GEO Accession:GSM1141099 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP022612     Nr21_5m_l4_export.fq.gz fastq 2709932304.0 35657004.0 GSM1141099 r1 0:76 A:730073083;C:631072920;G:619401848;T:729203191;N:181262 76       730073083 631072920 619401848 729203191 181262 SRX277676 SRS420776 SRA076297 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92839   0.10379   0.71392   0.4865   76   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk bulk bulk   Germany 2013-05-14 Adult Adult Skin Surface Structure
39771 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.   pubmed:28867488   Qkiac 3 GSM1838798   tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino Qkiac 3 Before mapping poly N read tails were trimmed reads ≤40 bases were removed and reads with quality mean ≤30 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°C 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 µg 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 ± 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   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 µg 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 ± 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   SRP061855     Sample6_CTTGTA.fastq.bz2 fastq 2507001849.0 49156899.0 GSM1838798 r1 0:51 A:683306529;C:570965534;G:570449436;T:679826815;N:2453535 51       683306529 570965534 570449436 679826815 2453535 SRX1125768 SRS1017739 SRA281148 GEO Plateforme transcriptome, Biologie, Ecole Normale Supérieure 1 0.92678   0.08779   0.72892   0.48795   51   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk bulk bulk   France 2015-07-30 Pharyngula Embryo Trunk Surface Structure
39772 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.   pubmed:28867488   Qkiac 2 GSM1838797   tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino Qkiac 2 Before mapping poly N read tails were trimmed reads ≤40 bases were removed and reads with quality mean ≤30 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°C 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 µg 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 ± 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   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 µg 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 ± 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   SRP061855     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       775475703 648531668 652753738 770730439 2780538 SRX1125767 SRS1017740 SRA281148 GEO Plateforme transcriptome, Biologie, Ecole Normale Supérieure 1 0.92802   0.08465   0.72744   0.48656   51   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk bulk bulk   France 2015-07-30 Pharyngula Embryo Trunk Surface Structure
39773 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.   pubmed:28867488   Qkiac 1 GSM1838796   tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino Qkiac 1 Before mapping poly N read tails were trimmed reads ≤40 bases were removed and reads with quality mean ≤30 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°C 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 µg 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 ± 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   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 µg 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 ± 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   SRP061855     Sample4_GCCAAT.fastq.bz2 fastq 2881827420.0 56506420.0 GSM1838796 r1 0:51 A:782512581;C:658453854;G:659856487;T:778195522;N:2808976 51       782512581 658453854 659856487 778195522 2808976 SRX1125766 SRS1017741 SRA281148 GEO Plateforme transcriptome, Biologie, Ecole Normale Supérieure 1 0.92629   0.08316   0.7276   0.47801   51   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk bulk bulk   France 2015-07-30 Pharyngula Embryo Trunk Surface Structure
39774 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.   pubmed:28867488   Control 3 GSM1838795   tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino Control 3 Before mapping poly N read tails were trimmed reads ≤40 bases were removed and reads with quality mean ≤30 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°C 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 µg 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 ± 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   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 µg 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 ± 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   SRP061855     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       707525221 599202602 597562199 705047589 2555171 SRX1125765 SRS1017742 SRA281148 GEO Plateforme transcriptome, Biologie, Ecole Normale Supérieure 1 0.9282   0.09007   0.72147   0.47387   51   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk bulk bulk   France 2015-07-30 Pharyngula Embryo Trunk Surface Structure
39775 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.   pubmed:28867488   Control 2 GSM1838794   tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino Control 2 Before mapping poly N read tails were trimmed reads ≤40 bases were removed and reads with quality mean ≤30 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°C 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 µg 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 ± 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   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 µg 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 ± 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   SRP061855     Sample2_TGACCA.fastq.bz2 fastq 2686989417.0 52686067.0 GSM1838794 r1 0:51 A:728607816;C:615847292;G:614033432;T:725881768;N:2619109 51       728607816 615847292 614033432 725881768 2619109 SRX1125764 SRS1017743 SRA281148 GEO Plateforme transcriptome, Biologie, Ecole Normale Supérieure 1 0.92483   0.09787   0.7203   0.45884   51   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk bulk bulk   France 2015-07-30 Pharyngula Embryo Trunk Surface Structure
39776 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.   pubmed:28867488   Control 1 GSM1838793   tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia+/+ or qkia+/ |injection:control morpholino Control 1 Before mapping poly N read tails were trimmed reads ≤40 bases were removed and reads with quality mean ≤30 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°C 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 µg 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 ± 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   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 µg 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 ± 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   SRP061855     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       788971393 671861209 669575375 787095383 2844715 SRX1125763 SRS1017744 SRA281148 GEO Plateforme transcriptome, Biologie, Ecole Normale Supérieure 1 0.92794   0.09884   0.71711   0.4721   51   B   usable mapping rate illumina hiseq_era unknown poly_a trueseq bulk bulk bulk   France 2015-07-30 Pharyngula Embryo Trunk Surface Structure
48110 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.         ptk7/+ 11   isolate:fish #11|age:21 dpf|sex:NA|tissue:trunk|genotype:ptk7/+|BioSampleModel:Model organism or animal                 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     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP141415   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     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   Canada 2018-05-16 Larval Larval Trunk Surface Structure
70891 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.   pubmed:35844027   Mtm1 KO DMSO treatment zebrafish rep4 GSM6434013   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     253867899 150713999 186967145 227898369 25212 SRX16888179 SRS14475663 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.84057   0.09126   0.81393   0.5072   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70892 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.   pubmed:35844027   Mtm1 KO DMSO treatment zebrafish rep3 GSM6434012   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     286773879 173045305 212203970 270527789 29017 SRX16888178 SRS14475662 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.85221   0.07868   0.802   0.517   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70893 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.   pubmed:35844027   Mtm1 KO DMSO treatment zebrafish rep2 GSM6434011   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     313998032 166431578 204849712 271283994 29200 SRX16888177 SRS14475661 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.76427   0.08867   0.8216   0.47678   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70894 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.   pubmed:35844027   Mtm1 KO DMSO treatment zebrafish rep1 GSM6434010   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     284740908 147201926 181724951 217238742 25457 SRX16888176 SRS14475660 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.76332   0.10117   0.82069   0.54485   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70895 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.   pubmed:35844027   HET DMSO treatment zebrafish rep5 GSM6434009   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     287361625 160168036 201822099 230293138 27038 SRX16888175 SRS14475659 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.79783   0.11832   0.81858   0.53184   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70896 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.   pubmed:35844027   HET DMSO treatment zebrafish rep4 GSM6434008   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     294008016 166492811 196902092 256969737 28172 SRX16888174 SRS14475658 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.80378   0.09051   0.81913   0.53428   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70897 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.   pubmed:35844027   HET DMSO treatment zebrafish rep3 GSM6434007   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     273539801 150455845 187644527 229287609 25702 SRX16888173 SRS14475657 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.8074   0.10306   0.816   0.55004   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70898 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.   pubmed:35844027   HET DMSO treatment zebrafish rep2 GSM6434006   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     281372378 156074885 192852640 236236763 26638 SRX16888172 SRS14475656 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.78328   0.10093   0.82483   0.50637   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70899 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.   pubmed:35844027   HET DMSO treatment zebrafish rep1 GSM6434005   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     272671962 152135239 192414605 226107225 25601 SRX16888171 SRS14475655 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.80999   0.10836   0.82087   0.54692   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70900 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.   pubmed:35844027   Mtm1 KO VPA treatment zebrafish rep5 GSM6434004   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     291725435 166577119 206636287 262343860 28811 SRX16888170 SRS14475654 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.82957   0.07535   0.80943   0.52892   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70901 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.   pubmed:35844027   Mtm1 KO VPA treatment zebrafish rep4 GSM6434003   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     287750544 163096141 204309196 256416158 27801 SRX16888169 SRS14475653 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.83046   0.10327   0.81109   0.53449   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70902 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.   pubmed:35844027   Mtm1 KO VPA treatment zebrafish rep3 GSM6434002   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     303836655 166378150 210423283 249170835 28517 SRX16888168 SRS14475652 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.80469   0.11617   0.81371   0.5335   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70903 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.   pubmed:35844027   Mtm1 KO VPA treatment zebrafish rep2 GSM6434001   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     298516548 149218718 188328193 220193538 26135 SRX16888167 SRS14475651 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.74816   0.1133   0.82012   0.54102   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70904 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.   pubmed:35844027   Mtm1 KO VPA treatment zebrafish rep1 GSM6434000   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     269574792 155617312 189177931 226602805 26000 SRX16888166 SRS14475650 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.82682   0.11442   0.81428   0.56002   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70905 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.   pubmed:35844027   HET VPA treatment zebrafish rep5 GSM6433999   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     291763235 163163197 196793555 250080362 27891 SRX16888165 SRS14475649 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.81103   0.09106   0.81397   0.55141   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70906 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.   pubmed:35844027   HET VPA treatment zebrafish rep4 GSM6433998   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     322076969 182902068 222775191 274412708 30664 SRX16888164 SRS14475648 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.8214   0.09555   0.81708   0.5555   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70907 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.   pubmed:35844027   HET VPA treatment zebrafish rep3 GSM6433997   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     298763838 164686057 208498185 241460289 28083 SRX16888163 SRS14475647 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.80018   0.11373   0.81438   0.36042   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70908 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.   pubmed:35844027   HET VPA treatment zebrafish rep2 GSM6433996   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     263283593 147216450 177773419 231843239 25315 SRX16888162 SRS14475646 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.81   0.08525   0.81335   0.54085   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70909 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.   pubmed:35844027   HET VPA treatment zebrafish rep1 GSM6433995   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     311986085 169749709 201471642 252412819 28669 SRX16888161 SRS14475645 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.71797   0.09744   0.81645   0.56605   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70910 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.   pubmed:35844027   Mtm1 KO TSA treatment zebrafish rep5 GSM6433994   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     289234513 155221667 194434609 228706315 26388 SRX16888160 SRS14475644 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.78415   0.11088   0.81355   0.51504   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70911 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.   pubmed:35844027   Mtm1 KO TSA treatment zebrafish rep4 GSM6433993   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     307372835 152869818 183626188 222699713 26506 SRX16888159 SRS14475643 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.71566   0.11015   0.82917   0.50431   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70912 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.   pubmed:35844027   Mtm1 KO TSA treatment zebrafish rep3 GSM6433992   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     294288974 166101496 195409922 252622316 27984 SRX16888158 SRS14475642 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.80995   0.0914   0.81389   0.54466   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70913 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.   pubmed:35844027   Mtm1 KO TSA treatment zebrafish rep2 GSM6433991   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     287151954 160498388 192579956 239765774 27424 SRX16888157 SRS14475641 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.8031   0.09849   0.81501   0.55513   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70914 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.   pubmed:35844027   Mtm1 KO TSA treatment zebrafish rep1 GSM6433990   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     328950780 180702054 217909263 275589304 31043 SRX16888156 SRS14475640 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.80451   0.09789   0.81533   0.55074   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70915 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.   pubmed:35844027   HET TSA treatment zebrafish rep4 GSM6433989   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     300989941 166218035 200751247 227578514 27023 SRX16888155 SRS14475639 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.65575   0.09506   0.83224   0.52894   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70916 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.   pubmed:35844027   HET TSA treatment zebrafish rep3 GSM6433988   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     386300445 167964779 205371083 261856684 31637 SRX16888154 SRS14475638 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.73302   0.10328   0.81466   0.55873   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70917 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.   pubmed:35844027   HET TSA treatment zebrafish rep2 GSM6433987   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     339449944 164483500 198328177 249377598 29077 SRX16888153 SRS14475637 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.73604   0.0885   0.82187   0.54577   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70918 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.   pubmed:35844027   HET TSA treatment zebrafish rep1 GSM6433986   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     303896452 155568953 193507200 229802351 27224 SRX16888152 SRS14475636 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.7587   0.1005   0.82071   0.54149   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70919 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.   pubmed:35844027   WT DMSO treatment zebrafish rep5 GSM6433985   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     308365583 164030703 197218474 243316551 28325 SRX16888151 SRS14475635 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.7904   0.09253   0.81886   0.57028   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70920 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.   pubmed:35844027   WT DMSO treatment zebrafish rep4 GSM6433984   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     304159499 157062642 192987191 232509378 26994 SRX16888150 SRS14475634 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.77072   0.08161   0.82294   0.56065   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70921 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.   pubmed:35844027   WT DMSO treatment zebrafish rep3 GSM6433983   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     288118744 154342074 181602972 228275755 26379 SRX16888149 SRS14475633 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.78952   0.07137   0.81941   0.55642   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70922 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.   pubmed:35844027   WT DMSO treatment zebrafish rep2 GSM6433982   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     314839314 161960932 199970507 238823895 27936 SRX16888148 SRS14475632 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.76878   0.08743   0.82304   0.57384   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
70923 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.   pubmed:35844027   WT DMSO treatment zebrafish rep1 GSM6433981   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   Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit Lexogen automated on an NGS workstation Agilent Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390172     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     351989460 174189591 216129629 255546296 30268 SRX16888147 SRS14475631 SRA1470408 Hospital for Sick Children Hospital for Sick Children 1 0.7455   0.08488   0.82611   0.57074   68   B   usable mapping rate illumina hiseq_era 3prime cdna_unspecified lexogen bulk bulk bulk   Canada 2022-08-05 Larval Larval Trunk Surface Structure
76470 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.   pubmed:37459514   Zebrafish scale 30mm replicate 2 GSM7498272   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 ‘aggregated’ transcript count for each gene as described by Martik et al. 2019. These aggregated transcript counts were then normalized using the formula: Zi=Ti−minT/maxT−minT 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   RNAqueous kit Ambion prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP445049     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       867694073 728518022 750424718 885367521 1419566 SRX20733648 SRS18024487 SRA1659604 Bronner, California Institute of Technology Bronner, California Institute of Technology 1 0.89607   0.08896   0.72612   0.4695   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2023-06-20 Undetermined Undetermined Scale Surface Structure
76471 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.   pubmed:37459514   Zebrafish scale 30mm replicate 1 GSM7498271   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 ‘aggregated’ transcript count for each gene as described by Martik et al. 2019. These aggregated transcript counts were then normalized using the formula: Zi=Ti−minT/maxT−minT 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   RNAqueous kit Ambion prepared according to the manufacturer's instructions. The libraries were built according to Illumina Standard Protocols.   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.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP445049     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       764903871 640842328 660536366 780092458 1264377 SRX20733647 SRS18024486 SRA1659604 Bronner, California Institute of Technology Bronner, California Institute of Technology 1 0.89576   0.08353   0.73594   0.45703   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2023-06-20 Undetermined Undetermined Scale Surface Structure

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