{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where technology = \"matqseq\" and tissue_curation = \"Trunk\"", "rows": [[64989, "SRR14882120", "SRX11199251", "SRS9254366", "SRP325103", "PRJNA740017", "Identification of transcription termination defects at DNA hypomethylated transcription termination sites in DNA methyltransferase 3a deficient vertebrates [RNA Seq]", "GSE178688", "Transcriptome Analysis", "CpG methylation in genomic DNA is well known as a repressive epigenetic marker in eukaryotic transcription  and hypermethylation of the promoter region is correlated with silencing of gene expression. In contrast to the promoter region  the function of DNA methylation at transcription termination remains to be elucidated. A recent study has revealed that mouse DNA methyltransferase 3a Dnmt3a mainly functions in de novo methylation in the promoter and gene body regions including transcription termination sites TTSs during development. To investigate the relationship between DNA methylation overlapping the TTSs and transcription termination  we employed two strategies: informatic analysis using already deposited datasets of Dnmt3a /  mouse cells and the zebrafish model system. Bioinformatic analysis using methylome and transcriptome data showed that hypomethylated differentially methylated regions overlapping the TTSs were associated with increased transcript counts and chimeric transcripts downstream of TTSs in Dnmt3a /  Agouti related protein neurons  but not in Dnmt3a /  ES cells and MEFs. We experimentally detected increased read through and chimeric transcripts downstream of hypomethylated TTSs in zebrafish maternal zygotic Dnmt3aa /  mutants. This study is the first to identify transcription termination defects in DNA hypomethylated TTSs in Dnmt3a /  vertebrates. Overall design: Analyzing transcriptional profiles by RNA seq in WT and MZdnmt3aa / .", "parent bioproject:PRJNA740013", "pubmed:36034642", null, "MZdnmt3aa 2 dpf RNAseq", "GSM5396122", null, "source name:2 dpf larvae|tissue:whole body|developmental stage:2 dpf zygotic dnmt3aa / ", "MZdnmt3aa 2 dpf RNAseq", "The FASTQ format sequence reads were trimmed of adaptors and low quality bases were filtered using Trim Galore version 0.6.4 with Cutadapt version 1.18 or 2.10 and FastQC version 0.11.8 or 0.11.9. post trimming  the reads were aligned to the zebrafish genome danRer10 using HISAT2 version 2.1.0. Alignment of datasets was performed using the strand specific option. Aligned files .bam were sorted and indexed using Samtools version 1.9. In addition  the strand specific aligned files were generated using Samtools version 1.9. Read coverage was normalized with 1 bin size by counts per million mapped reads CPM using the bamCoverage tool from the DeepTools version 3.3.2 and visualized using the IGV version 2.7.2. Genome build: danRer10 Supplementary files format and content: bigWig", "2 dpf larvae", null, "Tissue lysates were prepared from 30 pooled 2 dpf WT and MZdnmt3aa /  mutant larvae by homogenization using TissueLyser LT QIAGEN with zirconia beads for 10 s at 50 Hz. RNA was extracted from the lysate using the PureLink\u00ae RNA Mini Kit Thermo Fisher Scientific. RNA quality of all samples was RNA Integrity Number RIN > 9.0  using the 4150 TapeStation System Agilent. Total RNA was treated using the NEBNext\u00ae PolyA mRNA Magnetic Isolation Module New England Biolabs for mRNA isolation. Strand specific RNA seq libraries were constructed using the NEBNext\u00ae UltraTM Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs. The libraries with adapters were sequenced on the Novaseq 6000 Illumina with 2 \u00d7 150 bp paired end reads. RNA extraction  mRNA isolation  library preparation  and sequencing were performed by Rhelixa Inc. Tokyo  Japan.", null, "tissue:whole body|developmental stage:2 dpf zygotic dnmt3aa / ", "GSM5396122", "GSM5396122: MZdnmt3aa 2 dpf RNAseq; Danio rerio; ssRNA seq", "GSM5396122", null, "1", "Tissue lysates were prepared from 30 pooled 2 dpf WT and MZdnmt3aa /  mutant larvae by homogenization using TissueLyser LT QIAGEN with zirconia beads for 10 s at 50 Hz. RNA was extracted from the lysate using the PureLink\u00ae RNA Mini Kit Thermo Fisher Scientific. RNA quality of all samples was RNA Integrity Number RIN > 9.0  using the 4150 TapeStation System Agilent. Total RNA was treated using the NEBNext\u00ae PolyA mRNA Magnetic Isolation Module New England Biolabs for mRNA isolation. Strand specific RNA seq libraries were constructed using the NEBNext\u00ae UltraTM Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs. The libraries with adapters were sequenced on the Novaseq 6000 Illumina with 2 \u00d7 150 bp paired end reads. RNA extraction  mRNA isolation  library preparation  and sequencing were performed by Rhelixa Inc. 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In contrast to the promoter region  the function of DNA methylation at transcription termination remains to be elucidated. A recent study has revealed that mouse DNA methyltransferase 3a Dnmt3a mainly functions in de novo methylation in the promoter and gene body regions including transcription termination sites TTSs during development. To investigate the relationship between DNA methylation overlapping the TTSs and transcription termination  we employed two strategies: informatic analysis using already deposited datasets of Dnmt3a /  mouse cells and the zebrafish model system. Bioinformatic analysis using methylome and transcriptome data showed that hypomethylated differentially methylated regions overlapping the TTSs were associated with increased transcript counts and chimeric transcripts downstream of TTSs in Dnmt3a /  Agouti related protein neurons  but not in Dnmt3a /  ES cells and MEFs. We experimentally detected increased read through and chimeric transcripts downstream of hypomethylated TTSs in zebrafish maternal zygotic Dnmt3aa /  mutants. This study is the first to identify transcription termination defects in DNA hypomethylated TTSs in Dnmt3a /  vertebrates. Overall design: Analyzing transcriptional profiles by RNA seq in WT and MZdnmt3aa / .", "parent bioproject:PRJNA740013", "pubmed:36034642", null, "WT 2 dpf RNAseq", "GSM5396121", null, "source name:2 dpf larvae|tissue:whole body|developmental stage:2 dpf type", "WT 2 dpf RNAseq", "The FASTQ format sequence reads were trimmed of adaptors and low quality bases were filtered using Trim Galore version 0.6.4 with Cutadapt version 1.18 or 2.10 and FastQC version 0.11.8 or 0.11.9. post trimming  the reads were aligned to the zebrafish genome danRer10 using HISAT2 version 2.1.0. Alignment of datasets was performed using the strand specific option. Aligned files .bam were sorted and indexed using Samtools version 1.9. In addition  the strand specific aligned files were generated using Samtools version 1.9. Read coverage was normalized with 1 bin size by counts per million mapped reads CPM using the bamCoverage tool from the DeepTools version 3.3.2 and visualized using the IGV version 2.7.2. Genome build: danRer10 Supplementary files format and content: bigWig", "2 dpf larvae", null, "Tissue lysates were prepared from 30 pooled 2 dpf WT and MZdnmt3aa /  mutant larvae by homogenization using TissueLyser LT QIAGEN with zirconia beads for 10 s at 50 Hz. RNA was extracted from the lysate using the PureLink\u00ae RNA Mini Kit Thermo Fisher Scientific. RNA quality of all samples was RNA Integrity Number RIN > 9.0  using the 4150 TapeStation System Agilent. Total RNA was treated using the NEBNext\u00ae PolyA mRNA Magnetic Isolation Module New England Biolabs for mRNA isolation. Strand specific RNA seq libraries were constructed using the NEBNext\u00ae UltraTM Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs. The libraries with adapters were sequenced on the Novaseq 6000 Illumina with 2 \u00d7 150 bp paired end reads. RNA extraction  mRNA isolation  library preparation  and sequencing were performed by Rhelixa Inc. Tokyo  Japan.", null, "tissue:whole body|developmental stage:2 dpf type", "GSM5396121", "GSM5396121: WT 2 dpf RNAseq; Danio rerio; ssRNA seq", "GSM5396121", null, "1", "Tissue lysates were prepared from 30 pooled 2 dpf WT and MZdnmt3aa /  mutant larvae by homogenization using TissueLyser LT QIAGEN with zirconia beads for 10 s at 50 Hz. RNA was extracted from the lysate using the PureLink\u00ae RNA Mini Kit Thermo Fisher Scientific. RNA quality of all samples was RNA Integrity Number RIN > 9.0  using the 4150 TapeStation System Agilent. Total RNA was treated using the NEBNext\u00ae PolyA mRNA Magnetic Isolation Module New England Biolabs for mRNA isolation. Strand specific RNA seq libraries were constructed using the NEBNext\u00ae UltraTM Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs. The libraries with adapters were sequenced on the Novaseq 6000 Illumina with 2 \u00d7 150 bp paired end reads. RNA extraction  mRNA isolation  library preparation  and sequencing were performed by Rhelixa Inc. 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[submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"technology\" = :p0 and \"tissue_curation\" = :p1 order by rowid limit 101", "params": {"p0": "matqseq", "p1": "Trunk"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?technology=matqseq&tissue_curation=Trunk", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=matqseq&tissue_curation=Trunk&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?technology=matqseq&tissue_curation=Trunk", "results": [{"value": "TRANSCRIPTOMIC", "label": 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