metadata: run_metadata: 2 rows where technology = "matqseq" and tissue

2 rows where technology = "matqseq" and tissue_curation = "Trunk"

descending

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
64989	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		MZdnmt3aa 2 dpf RNAseq	GSM5396122		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		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® 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® PolyA mRNA Magnetic Isolation Module New England Biolabs for mRNA isolation. Strand specific RNA seq libraries were constructed using the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® New England Biolabs. The libraries with adapters were sequenced on the Novaseq 6000 Illumina with 2 × 150 bp paired end reads. RNA extraction mRNA isolation library preparation and sequencing were performed by Rhelixa Inc. Tokyo Japan.		tissue:whole body\|developmental stage:2 dpf zygotic dnmt3aa /	GSM5396122	GSM5396122: MZdnmt3aa 2 dpf RNAseq; Danio rerio; ssRNA seq	GSM5396122		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® 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® PolyA mRNA Magnetic Isolation Module New England Biolabs for mRNA isolation. Strand specific RNA seq libraries were constructed using the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® New England Biolabs. The libraries with adapters were sequenced on the Novaseq 6000 Illumina with 2 × 150 bp paired end reads. RNA extraction mRNA isolation library preparation and sequencing were performed by Rhelixa Inc. Tokyo Japan.	GEO Accession:GSM5396122	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP325103		loader:fastq load.py	dnmt8_1.fq.gz dnmt8_2.fq.gz	fastq fastq	12590413200.0	41968044.0	GSM5396122 r1	0:150 1:150	A:3330832240;C:2968653740;G:2998592350;T:3292140438;N:194432	150	150			3330832240	2968653740	2998592350	3292140438	194432	SRX11199251	SRS9254366	SRA1249386	GEO	Hiroshima University	2	0.95709	0.95762	0.07343	0.07107	0.68333	0.68243	0.46557	0.46424	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	matqseq		Japan	2021-06-22	Hatching	Embryo	Trunk	Surface Structure
64990	64990	SRR14882119	SRX11199250	SRS9254365	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		WT 2 dpf RNAseq	GSM5396121		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		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® 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® PolyA mRNA Magnetic Isolation Module New England Biolabs for mRNA isolation. Strand specific RNA seq libraries were constructed using the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® New England Biolabs. The libraries with adapters were sequenced on the Novaseq 6000 Illumina with 2 × 150 bp paired end reads. RNA extraction mRNA isolation library preparation and sequencing were performed by Rhelixa Inc. Tokyo Japan.		tissue:whole body\|developmental stage:2 dpf type	GSM5396121	GSM5396121: WT 2 dpf RNAseq; Danio rerio; ssRNA seq	GSM5396121		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® 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® PolyA mRNA Magnetic Isolation Module New England Biolabs for mRNA isolation. Strand specific RNA seq libraries were constructed using the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® New England Biolabs. The libraries with adapters were sequenced on the Novaseq 6000 Illumina with 2 × 150 bp paired end reads. RNA extraction mRNA isolation library preparation and sequencing were performed by Rhelixa Inc. Tokyo Japan.	GEO Accession:GSM5396121	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP325103		loader:fastq load.py	wt_1.fq.gz wt_2.fq.gz	fastq fastq	12662226000.0	42207420.0	GSM5396121 r1	0:150 1:150	A:3366552752;C:2968190763;G:3005399900;T:3321888610;N:193975	150	150			3366552752	2968190763	3005399900	3321888610	193975	SRX11199250	SRS9254365	SRA1249386	GEO	Hiroshima University	2	0.95626	0.95695	0.05987	0.05848	0.68099	0.68	0.47385	0.47125	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	matqseq		Japan	2021-06-22	Hatching	Embryo	Trunk	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");;