run_metadata
4 rows where experiment.platform = "DNBSEQ", technology = "generic-scrnaseq-only" and tissue_curation_coarse = "All anatomical structures"
This data as json, CSV (advanced)
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 |
Advanced export
JSON shape: default, array, newline-delimited
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");;