metadata: run_metadata: 4 rows where devstage_curation = "Blastula" and experiment.library

4 rows where devstage_curation = "Blastula" and experiment.library_selection = "RANDOM"

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.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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
8089	8089	ERR034126	ERX012652	ERS032267	ERP000635	PRJEB2512	The Zebrafish transcriptome during early development	KI-BN-JKE-DRERIO-RNASEQ-2011	Transcriptome Analysis	Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.			RNA extracted from zebrafish embryo at 512 cell stage	zebrafish embryo 512 cell	SAMEA791632	Department of Biosciences and Nutrition, Karolinska Institutet, Sweden	ENA first public:2011 06 09\|ENA last update:2018 03 08\|External Id:SAMEA791632\|INSDC center alias:KI BN\|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden\|INSDC first public:2011 06 09T11:04:10Z\|INSDC last update:2018 03 08T15:26:39Z\|INSDC status:public\|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 512cell\|common name:zebrafish\|sample name:KI BN JKE DRERIO RNASEQ 2011 512cell\|sex:mixed\|strain:Tuebingen								Transcriptome profiling of early zebrafish development	KI BN JKE DRERIO RNASEQ 2011 512cell	JKE Drerio rna seq	Transcriptome profiling of 512 cell stage of zebrafish embryos.	Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.		RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP000635	AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development	ENA FIRST PUBLIC:2011 06 09\|ENA LAST UPDATE:2018 11 16	KI-BN-JKE-DRERIO-RNASEQ-2011-512cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-512cell_QV.qual.gz	SOLiD_native SOLiD_native	3918756250.0	78375125.0	KI BN JKE DRERIO RNASEQ 2011 512cell	0:50		50							ERX012652	ERS032267	ERA029959	KI-BN\|Department of Biosciences and Nutrition	Department of Biosciences and Nutrition, Karolinska Institutet, Sweden	1	0.63824		0.09111		0.91969		0.73496		50		B		usable mapping rate	legacy	early	unknown	random_priming	unknown	bulk	unknown	unknown	Sweden	2011-06-09	Blastula	Embryo	Embryo Imprecise	All anatomical structures
51281	51281	SRR8663322	SRX5460019	SRS4433909	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466		ZF 4hpf rep2	GSM3638663		source name:embryo\|tissue:embryo\|developmental stage:4 hpf\|strain:wild type AB fish	ZF 4hpf rep2	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:4 hpf\|strain:wild type AB fish	GSM3638663	GSM3638663: ZF 4hpf rep2; Danio rerio; Bisulfite Seq	GSM3638663		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638663	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP187415					14505809700.0	48352699.0	GSM3638663 r1	0:150 1:150	A:4877194269;C:2388898572;G:2560124505;T:4676340810;N:3251544	150	150	4877194269	2388898572	2560124505	4676340810	3251544	SRX5460019	SRS4433909	SRA855736	GEO	Sun Yat-sen University	2	0.00065	0.00045	0.00027	0.00016	0.99928	0.99945	0.46376	0.54166	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Blastula	Embryo	Embryo Imprecise	All anatomical structures
51282	51282	SRR8663321	SRX5460018	SRS4433908	SRP187415	PRJNA525392	Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]	GSE127779	Other	We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.	parent bioproject:PRJNA525389	pubmed:35513466		ZF 4hpf rep1	GSM3638662		source name:embryo\|tissue:embryo\|developmental stage:4 hpf\|strain:wild type AB fish	ZF 4hpf rep1	Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites	embryo	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.	tissue:embryo\|developmental stage:4 hpf\|strain:wild type AB fish	GSM3638662	GSM3638662: ZF 4hpf rep1; Danio rerio; Bisulfite Seq	GSM3638662		1	For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.	GEO Accession:GSM3638662	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP187415					13666257000.0	45554190.0	GSM3638662 r1	0:150 1:150	A:4616947793;C:2221382014;G:2373430205;T:4451384606;N:3112382	150	150	4616947793	2221382014	2373430205	4451384606	3112382	SRX5460018	SRS4433908	SRA855736	GEO	Sun Yat-sen University	2	0.00094	0.00054	0.00044	0.00022	0.99928	0.99939	0.38888	0.50943	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Blastula	Embryo	Embryo Imprecise	All anatomical structures
53398	53398	SRR9849861	SRX6604467	SRS5169413	SRP216580	PRJNA556992	Global identification of circular RNAs during zebrafish embryogenesis	PRJNA556992	Other	Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.					4h		cultivar:Danio rerio\|age:4hpf stage:bastula\|sex:not determined\|tissue:not applicable\|BioSampleModel:Model organism or animal								circRNA 4h 1	4h 1	4h 1	circRNA sequence using embryo from zebrafish 4 hpf			RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP216580			BN2-427_L3_53.R1.clean.fastq.gz BN2-427_L3_53.R2.clean.fastq.gz	fastq fastq	10733190600.0	35777302.0	BN2 427 L3 53.R1.clean.fastq.gz	0:150 1:150	A:1899542444;C:3199739789;G:3296303811;T:2336021248;N:1583308	150	150	1899542444	3199739789	3296303811	2336021248	1583308	SRX6604467	SRS5169413	SRA927972	Guangxi Academy of Fishery Sciences\|Guangxi Academy of Fishery Sciences	Guangxi Academy of Fishery Sciences	2	0.84333	0.8387	0.65527	0.64575	0.97634	0.97737	0.70606	0.63009	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-07-27	Blastula	Embryo	Embryo Imprecise	All anatomical structures

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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");;