metadata: run_metadata: 6 rows where devstage_curation = "Gastrula" and experiment.platform = "DNBSEQ"

6 rows where devstage_curation = "Gastrula" and experiment.platform = "DNBSEQ"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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
76527	76527	SRR25007132	SRX20762488	SRS18050782	SRP445520	PRJNA986875	Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish	GSE235668	Transcriptome Analysis	Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target.	pubmed:38542412	T1 1	GSM7507236	source name:Embryos\|tissue:Embryos\|genotype:WT\|developmental stage:10hpf\|geo loc name:missing\|collection date:missing	T1 1	The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	Embryos	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.	tissue:Embryos\|genotype:WT\|developmental stage:10hpf	GSM7507236	GSM7507236: T1 1; Danio rerio; RNA Seq	GSM7507236 r1	GSM7507236	1	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP445520		T1_1.R1.fq.gz T1_1.R2.fq.gz	fastq fastq	13484033700.0	44946779.0	GSM7507236 r1	0:150 1:150	A:3415746428;C:3329088326;G:3392039530;T:3347088129;N:71287	150	150	3415746428	3329088326	3392039530	3347088129	71287	SRX20762488	SRS18050782	SRA1661372	henan normal university	henan normal university	2	0.40423	0.57514	0.07655	0.11873	0.80308	0.77092	0.46754	0.46803	150	150	B	B	mate1-mate2 similar by mapping diff	bgi	bgi	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	China	2023-06-23	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
76528	76528	SRR25007133	SRX20762487	SRS18050781	SRP445520	PRJNA986875	Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish	GSE235668	Transcriptome Analysis	Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues but their identification and organogenesis related function have not elucidated. In this study high throughput sequencing was performed at three different organogenesis stages of zebrafish embryos which were important for zebrafish muscle development. The three stages were 10 hpf T1 24 hpf T2 hpf and 36 hpf T3. Overall design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA seq during three key organogenesis stages 10 24 36hpf. Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target.	pubmed:38542412	T1 2	GSM7507237	source name:Embryos\|tissue:Embryos\|genotype:WT\|developmental stage:10hpf\|geo loc name:missing\|collection date:missing	T1 2	The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules The library products corresponding to 200 500 bps were enriched quantified and finally sequenced on DNBSEQ T7 sequencer MGI Tech Co. Ltd. China with PE150 model. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample	Embryos	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.	tissue:Embryos\|genotype:WT\|developmental stage:10hpf	GSM7507237	GSM7507237: T1 2; Danio rerio; RNA Seq	GSM7507237 r1	GSM7507237	1	Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagentInvitrogen cat. NO 15596026 following the methods by Chomczynski et al DOI:10.1006/abio.1987.9999. 2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo off rRNA Depletion Kit Catalog NO. MRZG12324 Illumina and KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP445520		T1_2.R1.fq.gz T1_2.R2.fq.gz	fastq fastq	13733190600.0	45777302.0	GSM7507237 r1	0:150 1:150	A:3445382955;C:3412918499;G:3490188153;T:3384626806;N:74187	150	150	3445382955	3412918499	3490188153	3384626806	74187	SRX20762487	SRS18050781	SRA1661372	henan normal university	henan normal university	2	0.43011	0.59623	0.08158	0.13068	0.80288	0.77544	0.47026	0.47364	150	150	B	B	mate1-mate2 similar by mapping diff	bgi	bgi	unknown	rrna_depletion	trueseq	bulk	unknown	unknown	China	2023-06-23	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
76532	76532	SRR25081951	SRX20835391	SRS18112575	SRP446710	PRJNA987386	Single nucleus chromatin landscapes during zebrafish early embryogenesis	PRJNA987386	Other	Vertebrate embryogenesis is a remarkable process during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis regulatory elements CREs and gene expression within the hierarchy of cell fate decisions. Here we employed single nucleus ATAC seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis including 3.3 hpf 5.25 hpf 6 hpf 10 hpf 12 hpf 18 hpf and 24 hpf obtained 51 620 high quality nuclei and 23 clusters. Furthermore by integrating snATAC seq data with single cell RNA seq data we described the dynamics of chromatin accessibility and gene expression across developmental time points which validates the accuracy of the chromatin landscape data. Together our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis.		6 hpf embryos	scRNA zf6hpf 2	strain:AB/Wild type\|isolate:scRNA zf6hpf 2\|breed:not collected\|cultivar:not collected\|ecotype:not determined\|age:embryo\|dev stage:6 hpf\|collection date:2021 08 08\|geo loc name:China: Wuhan\|sex:not determined\|tissue:embryo\|BioSampleModel:Model organism or animal							scRNA 6 hpf	scRNA 6 hpf rep2 oligo	scRNA 6 hpf rep2 oligo	scRNA seq of 6 hpf embryos		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP446710	CNGB Experiment ID:CNX0591993	DP8450003515BR_L01_5_1.fq.gz DP8450003515BR_L01_5_2.fq.gz	fastq fastq	14588474300.0	291769486.0	DP8450003515BR L01 5 1.fq.gz	0:20 1:30	A:3813233297;C:3660627848;G:3388591530;T:3724524333;N:1497292	20	30	3813233297	3660627848	3388591530	3724524333	1497292	SRX20835391	SRS18112575	SRA1664681	BGI Research, Shenzhen	BGI Research, Shenzhen CNGB Nucleotide Sequence Archive (CNSA) BGI-Shenzhen	2	0.00464	0.0003	0.00396	0.00028	0.9978	0.99995	0.39694	0.5	20	30	T	T	mates < 9% mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-06-30	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
76533	76533	SRR25081952	SRX20835390	SRS18112575	SRP446710	PRJNA987386	Single nucleus chromatin landscapes during zebrafish early embryogenesis	PRJNA987386	Other	Vertebrate embryogenesis is a remarkable process during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis regulatory elements CREs and gene expression within the hierarchy of cell fate decisions. Here we employed single nucleus ATAC seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis including 3.3 hpf 5.25 hpf 6 hpf 10 hpf 12 hpf 18 hpf and 24 hpf obtained 51 620 high quality nuclei and 23 clusters. Furthermore by integrating snATAC seq data with single cell RNA seq data we described the dynamics of chromatin accessibility and gene expression across developmental time points which validates the accuracy of the chromatin landscape data. Together our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis.		6 hpf embryos	scRNA zf6hpf 2	strain:AB/Wild type\|isolate:scRNA zf6hpf 2\|breed:not collected\|cultivar:not collected\|ecotype:not determined\|age:embryo\|dev stage:6 hpf\|collection date:2021 08 08\|geo loc name:China: Wuhan\|sex:not determined\|tissue:embryo\|BioSampleModel:Model organism or animal							scRNA 6 hpf	scRNA 6 hpf rep2 cDNA	scRNA 6 hpf rep2 cDNA	scRNA seq of 6 hpf embryos		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP446710	CNGB Experiment ID:CNX0591991	E100036348_L01_5_1.fq.gz E100036348_L01_5_2.fq.gz	fastq fastq	55097250780.0	423825006.0	E100036348 L01 5 1.fq.gz	0:30 1:100	A:16194629059;C:11467532715;G:12387290556;T:15046756280;N:1042170	30	100	16194629059	11467532715	12387290556	15046756280	1042170	SRX20835390	SRS18112575	SRA1664681	BGI Research, Shenzhen	BGI Research, Shenzhen CNGB Nucleotide Sequence Archive (CNSA) BGI-Shenzhen	2	0.00035	0.58961	0.00033	0.06118	0.99993	0.82564	0.33333	0.62483	30	100	T	B	mate1 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-06-30	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
76534	76534	SRR25081953	SRX20835389	SRS18112574	SRP446710	PRJNA987386	Single nucleus chromatin landscapes during zebrafish early embryogenesis	PRJNA987386	Other	Vertebrate embryogenesis is a remarkable process during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis regulatory elements CREs and gene expression within the hierarchy of cell fate decisions. Here we employed single nucleus ATAC seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis including 3.3 hpf 5.25 hpf 6 hpf 10 hpf 12 hpf 18 hpf and 24 hpf obtained 51 620 high quality nuclei and 23 clusters. Furthermore by integrating snATAC seq data with single cell RNA seq data we described the dynamics of chromatin accessibility and gene expression across developmental time points which validates the accuracy of the chromatin landscape data. Together our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis.		6 hpf embryos	scRNA zf6hpf 1	strain:AB/Wild type\|isolate:scRNA zf6hpf 1\|breed:not collected\|cultivar:not collected\|ecotype:not determined\|age:embryo\|dev stage:6 hpf\|collection date:2021 08 08\|geo loc name:China: Wuhan\|sex:not determined\|tissue:embryo\|BioSampleModel:Model organism or animal							scRNA 6 hpf	scRNA 6 hpf rep1 oligo	scRNA 6 hpf rep1 oligo	scRNA seq of 6 hpf embryos		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP446710	CNGB Experiment ID:CNX0591992	DP8450003515BR_L01_4_2.fq.gz DP8450003515BR_L01_4_1.fq.gz	fastq fastq	11338346750.0	226766935.0	DP8450003515BR L01 4 1.fq.gz	0:20 1:30	A:2978703558;C:2824119061;G:2623216087;T:2911128054;N:1179990	20	30	2978703558	2824119061	2623216087	2911128054	1179990	SRX20835389	SRS18112574	SRA1664681	BGI Research, Shenzhen	BGI Research, Shenzhen CNGB Nucleotide Sequence Archive (CNSA) BGI-Shenzhen	2	0.00475	0.00048	0.0041	0.00042	0.99799	0.99979	0.472	0.4	20	30	T	T	mates < 9% mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-06-30	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
76535	76535	SRR25081954	SRX20835388	SRS18112574	SRP446710	PRJNA987386	Single nucleus chromatin landscapes during zebrafish early embryogenesis	PRJNA987386	Other	Vertebrate embryogenesis is a remarkable process during which numerous cell types of different lineages arise within a short time frame. An overwhelming challenge to understand this process is the lack of dynamic chromatin accessibility information to correlate cis regulatory elements CREs and gene expression within the hierarchy of cell fate decisions. Here we employed single nucleus ATAC seq to generate a chromatin accessibility dataset on the first day of zebrafish embryogenesis including 3.3 hpf 5.25 hpf 6 hpf 10 hpf 12 hpf 18 hpf and 24 hpf obtained 51 620 high quality nuclei and 23 clusters. Furthermore by integrating snATAC seq data with single cell RNA seq data we described the dynamics of chromatin accessibility and gene expression across developmental time points which validates the accuracy of the chromatin landscape data. Together our data could serve as a fundamental resource for revealing the epigenetic regulatory mechanisms of zebrafish embryogenesis.		6 hpf embryos	scRNA zf6hpf 1	strain:AB/Wild type\|isolate:scRNA zf6hpf 1\|breed:not collected\|cultivar:not collected\|ecotype:not determined\|age:embryo\|dev stage:6 hpf\|collection date:2021 08 08\|geo loc name:China: Wuhan\|sex:not determined\|tissue:embryo\|BioSampleModel:Model organism or animal							scRNA 6 hpf	scRNA 6 hpf rep1 cDNA	scRNA 6 hpf rep1 cDNA	scRNA seq of 6 hpf embryos		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP446710	CNGB Experiment ID:CNX0591990	E100036348_L01_6_1.fq.gz E100036348_L01_6_2.fq.gz	fastq fastq	28127062860.0	216362022.0	E100036348 L01 6 1.fq.gz	0:30 1:100	A:8147068380;C:5889045118;G:6317467122;T:7772966880;N:515360	30	100	8147068380	5889045118	6317467122	7772966880	515360	SRX20835388	SRS18112574	SRA1664681	BGI Research, Shenzhen	BGI Research, Shenzhen CNGB Nucleotide Sequence Archive (CNSA) BGI-Shenzhen	2	0.00014	0.82035	0.00012	0.07422	0.99995	0.81412	1.0	0.68234	30	100	T	B	mate1 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	China	2023-06-30	Gastrula	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");;