{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Gastrula\" and experiment.platform = \"DNBSEQ\"", "rows": [[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.", null, "pubmed:38542412", null, "T1 1", "GSM7507236", null, "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", null, "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 \u03bcg 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\u00ae Catalog NO. DR08502  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "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 \u03bcg 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\u00ae Catalog NO. DR08502  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP445520", null, null, "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, null, null, 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", null, "China", "2023-06-23", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:38542412", null, "T1 2", "GSM7507237", null, "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", null, "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 \u03bcg 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\u00ae Catalog NO. DR08502  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "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 \u03bcg 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\u00ae Catalog NO. 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China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP445520", null, null, "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, null, null, 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", null, "China", "2023-06-23", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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. 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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.", null, null, null, "6 hpf embryos", "scRNA zf6hpf 2", null, "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", null, null, null, null, null, null, null, null, "scRNA 6 hpf", "scRNA 6 hpf rep2 cDNA", "scRNA 6 hpf rep2 cDNA", "scRNA seq of 6 hpf embryos", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP446710", null, "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, null, null, 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", null, "China", "2023-06-30", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, null, null, "6 hpf embryos", "scRNA zf6hpf 1", null, "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", null, null, null, null, null, null, null, null, "scRNA 6 hpf", "scRNA 6 hpf rep1 oligo", "scRNA 6 hpf rep1 oligo", "scRNA seq of 6 hpf embryos", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP446710", null, "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, null, null, 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", null, "China", "2023-06-30", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, null, null, "6 hpf embryos", "scRNA zf6hpf 1", null, "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", null, null, null, null, null, null, null, null, "scRNA 6 hpf", "scRNA 6 hpf rep1 cDNA", "scRNA 6 hpf rep1 cDNA", "scRNA seq of 6 hpf embryos", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP446710", null, "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, null, null, 8147068380, 5889045118, 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