metadata: run_metadata: 6 rows where devstage_curation = "Segmentation" and experiment.library

6 rows where devstage_curation = "Segmentation" 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.title	sample.alias	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.study_ref	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
51273	51273	SRR8663330	SRX5460027	SRS4433917	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 16hpf rep2	GSM3638671	source name:embryo\|tissue:embryo\|developmental stage:16 hpf\|strain:wild type AB fish	ZF 16hpf 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:16 hpf\|strain:wild type AB fish	GSM3638671	GSM3638671: ZF 16hpf rep2; Danio rerio; Bisulfite Seq	GSM3638671		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:GSM3638671	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP187415			25701246300.0	85670821.0	GSM3638671 r1	0:150 1:150	A:8976132831;C:3855344207;G:4201042226;T:8667517583;N:1209453	150	150	8976132831	3855344207	4201042226	8667517583	1209453	SRX5460027	SRS4433917	SRA855736	GEO	Sun Yat-sen University	2	0.00117	0.00107	0.00036	0.00034	0.99928	0.99941	0.73571	0.75206	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
51274	51274	SRR8663329	SRX5460026	SRS4433916	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 16hpf rep1	GSM3638670	source name:embryo\|tissue:embryo\|developmental stage:16 hpf\|strain:wild type AB fish	ZF 16hpf 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:16 hpf\|strain:wild type AB fish	GSM3638670	GSM3638670: ZF 16hpf rep1; Danio rerio; Bisulfite Seq	GSM3638670		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:GSM3638670	Bisulfite-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP187415			21585057600.0	71950192.0	GSM3638670 r1	0:150 1:150	A:7493903581;C:3312864799;G:3567558230;T:7209728977;N:1002013	150	150	7493903581	3312864799	3567558230	7209728977	1002013	SRX5460026	SRS4433916	SRA855736	GEO	Sun Yat-sen University	2	0.00125	0.00119	0.00039	0.00034	0.99945	0.99947	0.7551	0.76865	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown	China	2019-03-04	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
53394	53394	SRR9849857	SRX6604471	SRS5169414	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.				12h	cultivar:Danio rerio\|age:12hpf stage:segmentation\|sex:not determined\|tissue:not applicable\|BioSampleModel:Model organism or animal								circRNA 12h 2	12h 2	12h 2	circRNA sequence using embryo from zebrafish 12 hpf			RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP216580	12h-1_Clean_1.fq.gz 12h-1_Clean_2.fq.gz	fastq fastq	9760537114.0	32612820.0	12h 1 Clean 1.fq.gz	0:149.64 1:149.64	A:2537269193;C:2297094668;G:2379024620;T:2546216364;N:932269	149	149	2537269193	2297094668	2379024620	2546216364	932269	SRX6604471	SRS5169414	SRA927972	Guangxi Academy of Fishery Sciences\|Guangxi Academy of Fishery Sciences	Guangxi Academy of Fishery Sciences	2	0.75204	0.75144	0.34914	0.3456	0.79444	0.80298	0.47617	0.47647	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-07-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
53395	53395	SRR9849858	SRX6604470	SRS5169410	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.				16h	cultivar:Danio rerio\|age:16hpf stage:segmentation\|sex:not determined\|tissue:not applicable\|BioSampleModel:Model organism or animal								circRNA 16h 1	16h 1	16h 1	circRNA sequence using embryo from zebrafish 16 hpf			RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP216580	BN2-430_L3_56.R1.clean.fastq.gz BN2-430_L3_56.R2.clean.fastq.gz	fastq fastq	11290204500.0	37634015.0	BN2 430 L3 56.R1.clean.fastq.gz	0:150 1:150	A:2002607987;C:3409827596;G:3508023598;T:2368035468;N:1709851	150	150	2002607987	3409827596	3508023598	2368035468	1709851	SRX6604470	SRS5169410	SRA927972	Guangxi Academy of Fishery Sciences\|Guangxi Academy of Fishery Sciences	Guangxi Academy of Fishery Sciences	2	0.91788	0.9101	0.83385	0.81588	0.98462	0.9847	0.87183	0.87504	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-07-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
53397	53397	SRR9849860	SRX6604468	SRS5169414	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.				12h	cultivar:Danio rerio\|age:12hpf stage:segmentation\|sex:not determined\|tissue:not applicable\|BioSampleModel:Model organism or animal								circRNA 12h 1	12h 1	12h 1	circRNA sequence using embryo from zebrafish 12 hpf			RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP216580	BN2-429_L3_55.R1.clean.fastq.gz BN2-429_L3_55.R2.clean.fastq.gz	fastq fastq	9471315300.0	31571051.0	BN2 429 L3 55.R1.clean.fastq.gz	0:150 1:150	A:1671591116;C:2907243262;G:3000871353;T:1890180659;N:1428910	150	150	1671591116	2907243262	3000871353	1890180659	1428910	SRX6604468	SRS5169414	SRA927972	Guangxi Academy of Fishery Sciences\|Guangxi Academy of Fishery Sciences	Guangxi Academy of Fishery Sciences	2	0.76551	0.7596	0.58436	0.57204	0.9853	0.98567	0.95092	0.95274	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-07-27	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
53402	53402	SRR9849865	SRX6604463	SRS5169410	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.				16h	cultivar:Danio rerio\|age:16hpf stage:segmentation\|sex:not determined\|tissue:not applicable\|BioSampleModel:Model organism or animal								circRNA 16h 2	16h 2	16h 2	circRNA sequence using embryo from zebrafish 16 hpf			RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP216580	16h-1_Clean_1.fq.gz 16h-1_Clean_2.fq.gz	fastq fastq	13746008148.0	45914536.0	16h 1 Clean 1.fq.gz	0:149.69 1:149.69	A:3633911267;C:3175232398;G:3288410708;T:3647163703;N:1290072	149	149	3633911267	3175232398	3288410708	3647163703	1290072	SRX6604463	SRS5169410	SRA927972	Guangxi Academy of Fishery Sciences\|Guangxi Academy of Fishery Sciences	Guangxi Academy of Fishery Sciences	2	0.76446	0.76939	0.32701	0.32679	0.80537	0.8116	0.47029	0.4846	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-07-27	Segmentation	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");;