run_metadata
7 rows where experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL", technology = "10x" and tissue_curation_coarse = "Embryo Imprecise"
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 33864 | 33864 | SRR30779425 | SRX26181412 | SRS22725400 | SRP534298 | PRJNA1164307 | Time resolved single cell Multiomic zebrafish atlas | PRJNA1164307 | Other | During development dynamic interplay between transcription factors chromatin and genes termed gene regulatory network GRN shapes the cell fate determination along the developmental trajectory. Recent advances in joint measurement of chromatin accessibility and gene expression enabled the genome wide identification of regulatory relationships. Here we assess the dynamics of the gene regulatory network in zebrafish development using joint single cell ATAC and single cell RNA sequencing. We discovered some key regulatory modules that exhibit cell type and time dependent activity suggesting that the role of transcription factors vary over cell type and timepoints. With time resolved GRNs combined with linear modeling framework we performed a systematic in silico knock out simulation using CellOracle. This in silico knock out simulation revealed that the role of transcription factors is shared between mesodermal and neuro ectodermal lineages in the early timepoints but later commit significantly to either lineages. Together we provide a dataset and a framework to systematically dissect the role of transcription factors during the zebrafish embryonic development. | TDR126 | TDR126 10hpf EKW NA none 10xmultiome | strain:EKW|dev stage:Bud stage 10 hpf|collection date:2023 11 22|geo loc name:USA: San Francisco|sex:N/A|tissue:organism|BioSampleModel:Model organism or animal | TDR126 10hpf RNA | TDR126 10hpf RNA EKW NA none 10xmultiome | TDR126 10hpf RNA EKW NA none 10xmultiome | 10x multiome nuc seq | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP534298 | TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L001_I1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L001_I2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L001_R1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L001_R2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L002_I1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L002_I2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L002_R1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L002_R2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L003_I1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L003_I2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L003_R1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L003_R2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L004_I1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L004_I2_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L004_R1_001.fastq.gz TDR126_10hpf_RNA_EKW_NA_none_10xmultiome_S4_L004_R2_001.fastq.gz | fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq | TDR126 10hpf RNA EKW NA none 10xmultiome S4 L001 I1 001.fastq.gz | SRX26181412 | SRA1977819 | Chan Zuckerberg Biohub San Francisco|Computational Biology | Chan Zuckerberg Biohub San Francisco | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2024-09-23 | Gastrula | Embryo | Undetermined | Embryo Imprecise | ||||||||||||||||||||||||||||||||||||||||||||||
| 33865 | 33865 | SRR30779427 | SRX26181410 | SRS22725399 | SRP534298 | PRJNA1164307 | Time resolved single cell Multiomic zebrafish atlas | PRJNA1164307 | Other | During development dynamic interplay between transcription factors chromatin and genes termed gene regulatory network GRN shapes the cell fate determination along the developmental trajectory. Recent advances in joint measurement of chromatin accessibility and gene expression enabled the genome wide identification of regulatory relationships. Here we assess the dynamics of the gene regulatory network in zebrafish development using joint single cell ATAC and single cell RNA sequencing. We discovered some key regulatory modules that exhibit cell type and time dependent activity suggesting that the role of transcription factors vary over cell type and timepoints. With time resolved GRNs combined with linear modeling framework we performed a systematic in silico knock out simulation using CellOracle. This in silico knock out simulation revealed that the role of transcription factors is shared between mesodermal and neuro ectodermal lineages in the early timepoints but later commit significantly to either lineages. Together we provide a dataset and a framework to systematically dissect the role of transcription factors during the zebrafish embryonic development. | TDR125 | TDR125 19hpf EKW NA none 10xmultiome | strain:EKW|dev stage:20 somites 19 hpf|collection date:2023 09 13|geo loc name:USA: San Francisco|sex:N/A|tissue:organism|BioSampleModel:Model organism or animal | TDR125 19hpf RNA | TDR125 19hpf RNA EKW NA none 10xmultiome | TDR125 19hpf RNA EKW NA none 10xmultiome | 10x multiome nuc seq | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP534298 | TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L001_I1_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L001_I2_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L001_R1_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L001_R2_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L002_I1_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L002_I2_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L002_R1_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L002_R2_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L003_I1_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L003_I2_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L003_R1_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L003_R2_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L004_I1_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L004_I2_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L004_R1_001.fastq.gz TDR125_19hpf_RNA_EKW_NA_none_10xmultiome_S3_L004_R2_001.fastq.gz | fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq | TDR125 19hpf RNA EKW NA none 10xmultiome S3 L001 I1 001.fastq.gz | SRX26181410 | SRA1977819 | Chan Zuckerberg Biohub San Francisco|Computational Biology | Chan Zuckerberg Biohub San Francisco | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2024-09-23 | Segmentation | Embryo | Undetermined | Embryo Imprecise | ||||||||||||||||||||||||||||||||||||||||||||||
| 33866 | 33866 | SRR30779429 | SRX26181408 | SRS22725395 | SRP534298 | PRJNA1164307 | Time resolved single cell Multiomic zebrafish atlas | PRJNA1164307 | Other | During development dynamic interplay between transcription factors chromatin and genes termed gene regulatory network GRN shapes the cell fate determination along the developmental trajectory. Recent advances in joint measurement of chromatin accessibility and gene expression enabled the genome wide identification of regulatory relationships. Here we assess the dynamics of the gene regulatory network in zebrafish development using joint single cell ATAC and single cell RNA sequencing. We discovered some key regulatory modules that exhibit cell type and time dependent activity suggesting that the role of transcription factors vary over cell type and timepoints. With time resolved GRNs combined with linear modeling framework we performed a systematic in silico knock out simulation using CellOracle. This in silico knock out simulation revealed that the role of transcription factors is shared between mesodermal and neuro ectodermal lineages in the early timepoints but later commit significantly to either lineages. Together we provide a dataset and a framework to systematically dissect the role of transcription factors during the zebrafish embryonic development. | TDR124 | TDR124 24hpf EKW NA none 10xmultiome | strain:EKW|dev stage:30 somites 24 hpf|collection date:2023 08 17|geo loc name:USA: San Francisco|sex:N/A|tissue:organism|BioSampleModel:Model organism or animal | TDR124 24hpf RNA | TDR124 24hpf RNA EKW NA none 10xmultiome | TDR124 24hpf RNA EKW NA none 10xmultiome | 10x multiome nuc seq | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP534298 | TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L001_I1_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L001_I2_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L001_R1_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L001_R2_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L002_I1_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L002_I2_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L002_R1_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L002_R2_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L003_I1_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L003_I2_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L003_R1_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L003_R2_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L004_I1_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L004_I2_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L004_R1_001.fastq.gz TDR124_24hpf_RNA_EKW_NA_none_10xmultiome_S2_L004_R2_001.fastq.gz | fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq | TDR124 24hpf RNA EKW NA none 10xmultiome S2 L001 I1 001.fastq.gz | SRX26181408 | SRA1977819 | Chan Zuckerberg Biohub San Francisco|Computational Biology | Chan Zuckerberg Biohub San Francisco | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2024-09-23 | Multi-stage | Embryo | Undetermined | Embryo Imprecise | ||||||||||||||||||||||||||||||||||||||||||||||
| 33867 | 33867 | SRR30779430 | SRX26181407 | SRS22725398 | SRP534298 | PRJNA1164307 | Time resolved single cell Multiomic zebrafish atlas | PRJNA1164307 | Other | During development dynamic interplay between transcription factors chromatin and genes termed gene regulatory network GRN shapes the cell fate determination along the developmental trajectory. Recent advances in joint measurement of chromatin accessibility and gene expression enabled the genome wide identification of regulatory relationships. Here we assess the dynamics of the gene regulatory network in zebrafish development using joint single cell ATAC and single cell RNA sequencing. We discovered some key regulatory modules that exhibit cell type and time dependent activity suggesting that the role of transcription factors vary over cell type and timepoints. With time resolved GRNs combined with linear modeling framework we performed a systematic in silico knock out simulation using CellOracle. This in silico knock out simulation revealed that the role of transcription factors is shared between mesodermal and neuro ectodermal lineages in the early timepoints but later commit significantly to either lineages. Together we provide a dataset and a framework to systematically dissect the role of transcription factors during the zebrafish embryonic development. | TDR119 | TDR119 16hpf EKW NA none 10xmultiome | strain:EKW|dev stage:15 somites 16 hpf|collection date:2023 06 30|geo loc name:USA: San Francisco|sex:N/A|tissue:organism|BioSampleModel:Model organism or animal | TDR119 16hpf RNA | TDR119 16hpf RNA EKW NA none 10xmultiome | TDR119 16hpf RNA EKW NA none 10xmultiome | 10x multiome nuc seq | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP534298 | TDR119_16hpf_RNA_EKW_NA_none_10xmultiome_S2_L001_I1_001.fastq.gz TDR119_16hpf_RNA_EKW_NA_none_10xmultiome_S2_L001_I2_001.fastq.gz TDR119_16hpf_RNA_EKW_NA_none_10xmultiome_S2_L001_R1_001.fastq.gz TDR119_16hpf_RNA_EKW_NA_none_10xmultiome_S2_L001_R2_001.fastq.gz TDR119_16hpf_RNA_EKW_NA_none_10xmultiome_S2_L002_I1_001.fastq.gz TDR119_16hpf_RNA_EKW_NA_none_10xmultiome_S2_L002_I2_001.fastq.gz TDR119_16hpf_RNA_EKW_NA_none_10xmultiome_S2_L002_R1_001.fastq.gz TDR119_16hpf_RNA_EKW_NA_none_10xmultiome_S2_L002_R2_001.fastq.gz | fastq fastq fastq fastq fastq fastq fastq fastq | 137611060524.0 | 997181598.0 | TDR119 16hpf RNA EKW NA none 10xmultiome S2 L001 I1 001.fastq.gz | 0:10 1:10 2:28 3:90 | A:26107486444;C:20041229894;G:22171622563;T:21408164549;N:17840370 | 10 | 10 | 28 | 90 | 26107486444 | 20041229894 | 22171622563 | 21408164549 | 17840370 | SRX26181407 | SRS22725398 | SRA1977819 | Chan Zuckerberg Biohub San Francisco|Computational Biology | Chan Zuckerberg Biohub San Francisco | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2024-09-24 | Segmentation | Embryo | Undetermined | Embryo Imprecise | ||||||||||||||||||||||||||||||
| 33868 | 33868 | SRR30779433 | SRX26181405 | SRS22725397 | SRP534298 | PRJNA1164307 | Time resolved single cell Multiomic zebrafish atlas | PRJNA1164307 | Other | During development dynamic interplay between transcription factors chromatin and genes termed gene regulatory network GRN shapes the cell fate determination along the developmental trajectory. Recent advances in joint measurement of chromatin accessibility and gene expression enabled the genome wide identification of regulatory relationships. Here we assess the dynamics of the gene regulatory network in zebrafish development using joint single cell ATAC and single cell RNA sequencing. We discovered some key regulatory modules that exhibit cell type and time dependent activity suggesting that the role of transcription factors vary over cell type and timepoints. With time resolved GRNs combined with linear modeling framework we performed a systematic in silico knock out simulation using CellOracle. This in silico knock out simulation revealed that the role of transcription factors is shared between mesodermal and neuro ectodermal lineages in the early timepoints but later commit significantly to either lineages. Together we provide a dataset and a framework to systematically dissect the role of transcription factors during the zebrafish embryonic development. | TDR128 | TDR128 14hpf EKW NA none 10xmultiome | strain:EKW|dev stage:10 somites 14 hpf|collection date:2023 11 22|geo loc name:USA: San Francisco|sex:N/A|tissue:organism|BioSampleModel:Model organism or animal | TDR128 14hpf RNA | TDR128 14hpf RNA EKW NA none 10xmultiome | TDR128 14hpf RNA EKW NA none 10xmultiome | 10x multiome nuc seq | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP534298 | TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L001_I1_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L001_I2_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L001_R1_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L001_R2_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L002_I1_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L002_I2_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L002_R1_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L002_R2_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L003_I1_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L003_I2_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L003_R1_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L003_R2_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L004_I1_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L004_I2_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L004_R1_001.fastq.gz TDR128_14hpf_RNA_EKW_NA_none_10xmultiome_S6_L004_R2_001.fastq.gz | fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq | TDR128 14hpf RNA EKW NA none 10xmultiome S6 L001 I1 001.fastq.gz | SRX26181405 | SRA1977819 | Chan Zuckerberg Biohub San Francisco|Computational Biology | Chan Zuckerberg Biohub San Francisco | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2024-09-23 | Segmentation | Embryo | Undetermined | Embryo Imprecise | ||||||||||||||||||||||||||||||||||||||||||||||
| 33869 | 33869 | SRR30779435 | SRX26181403 | SRS22725396 | SRP534298 | PRJNA1164307 | Time resolved single cell Multiomic zebrafish atlas | PRJNA1164307 | Other | During development dynamic interplay between transcription factors chromatin and genes termed gene regulatory network GRN shapes the cell fate determination along the developmental trajectory. Recent advances in joint measurement of chromatin accessibility and gene expression enabled the genome wide identification of regulatory relationships. Here we assess the dynamics of the gene regulatory network in zebrafish development using joint single cell ATAC and single cell RNA sequencing. We discovered some key regulatory modules that exhibit cell type and time dependent activity suggesting that the role of transcription factors vary over cell type and timepoints. With time resolved GRNs combined with linear modeling framework we performed a systematic in silico knock out simulation using CellOracle. This in silico knock out simulation revealed that the role of transcription factors is shared between mesodermal and neuro ectodermal lineages in the early timepoints but later commit significantly to either lineages. Together we provide a dataset and a framework to systematically dissect the role of transcription factors during the zebrafish embryonic development. | TDR127 | TDR127 12hpf EKW NA none 10xmultiome | strain:EKW|dev stage:5 somites 12 hpf|collection date:2023 11 22|geo loc name:USA: San Francisco|sex:N/A|tissue:organism|BioSampleModel:Model organism or animal | TDR127 12hpf RNA | TDR127 12hpf RNA EKW NA none 10xmultiome | TDR127 12hpf RNA EKW NA none 10xmultiome | 10x multiome nuc seq | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP534298 | TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L001_I1_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L001_I2_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L001_R1_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L001_R2_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L002_I1_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L002_I2_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L002_R1_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L002_R2_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L003_I1_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L003_I2_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L003_R1_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L003_R2_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L004_I1_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L004_I2_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L004_R1_001.fastq.gz TDR127_12hpf_RNA_EKW_NA_none_10xmultiome_S5_L004_R2_001.fastq.gz | fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq | TDR127 12hpf RNA EKW NA none 10xmultiome S5 L001 I1 001.fastq.gz | SRX26181403 | SRA1977819 | Chan Zuckerberg Biohub San Francisco|Computational Biology | Chan Zuckerberg Biohub San Francisco | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2024-09-23 | Segmentation | Embryo | Undetermined | Embryo Imprecise | ||||||||||||||||||||||||||||||||||||||||||||||
| 33870 | 33870 | SRR30779437 | SRX26181400 | SRS22725394 | SRP534298 | PRJNA1164307 | Time resolved single cell Multiomic zebrafish atlas | PRJNA1164307 | Other | During development dynamic interplay between transcription factors chromatin and genes termed gene regulatory network GRN shapes the cell fate determination along the developmental trajectory. Recent advances in joint measurement of chromatin accessibility and gene expression enabled the genome wide identification of regulatory relationships. Here we assess the dynamics of the gene regulatory network in zebrafish development using joint single cell ATAC and single cell RNA sequencing. We discovered some key regulatory modules that exhibit cell type and time dependent activity suggesting that the role of transcription factors vary over cell type and timepoints. With time resolved GRNs combined with linear modeling framework we performed a systematic in silico knock out simulation using CellOracle. This in silico knock out simulation revealed that the role of transcription factors is shared between mesodermal and neuro ectodermal lineages in the early timepoints but later commit significantly to either lineages. Together we provide a dataset and a framework to systematically dissect the role of transcription factors during the zebrafish embryonic development. | TDR118 | TDR118 16hpf EKW NA none 10xmultiome | strain:EKW|dev stage:15 somites 16 hpf|collection date:2023 06 23|geo loc name:USA: San Francisco|sex:N/A|tissue:organism|BioSampleModel:Model organism or animal | TDR118 16hpf RNA | TDR118 16hpf RNA EKW NA none 10xmultiome | TDR118 16hpf RNA EKW NA none 10xmultiome | 10x multiome nuc seq | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP534298 | TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L001_I1_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L001_I2_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L001_R1_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L001_R2_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L002_I1_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L002_I2_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L002_R1_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L002_R2_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L003_I1_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L003_I2_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L003_R1_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L003_R2_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L004_I1_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L004_I2_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L004_R1_001.fastq.gz TDR118_16hpf_RNA_EKW_NA_none_10xmultiome_S1_L004_R2_001.fastq.gz | fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq | TDR118 16hpf RNA EKW NA none 10xmultiome S1 L001 I1 001.fastq.gz | SRX26181400 | SRA1977819 | Chan Zuckerberg Biohub San Francisco|Computational Biology | Chan Zuckerberg Biohub San Francisco | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2024-09-23 | Segmentation | Embryo | Undetermined | Embryo Imprecise |
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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");;