run_metadata
2 rows where experiment.library_strategy = "OTHER", technology = "10x" and tissue_curation_coarse = "All anatomical structures"
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| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 60662 | 60662 | SRR12474621 | SRX8968761 | SRS7224498 | SRP278034 | PRJNA657343 | Satb2 acts as a gatekeeper for gene regulatory transitions during early embryonic development | PRJNA657343 | Other | Comprehensive integration of transcriptome genome wide occupancy and chromatin accessibility profiles in satb2 loss of function and gain of function systems to discover novel and evolutionary conserved molecular interplays between Satb2 and the genetic drivers of neurogenesis and neural crest development program. | scRNAseq FLAG SATB2 | scRNAseq FLAG SATB2 dome | strain:TU|isolate:Satb2 OE|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:4.5 hpf|dev stage:Dome|sex:not applicable|tissue:whole embryo|Replicate:replicate=FLAG SATB2 dome|BioSampleModel:Model organism or animal | scRNAseq FLAG SATB2 | scRNAseq FLAG SATB2 dome | scRNAseq FLAG SATB2 dome | 10x chromium 3 mRNA | OTHER | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 550 | SRP278034 | loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=scRNAseq FLAG SATB2 dome I1 sorted.fastq read2PairFiles=scRNAseq FLAG SATB2 dome R1 sorted.fastq read3PairFiles=scRNAseq FLAG SATB2 dome R2 sorted.fastq | scRNAseq_FLAG_SATB2_dome_I1_sorted.fastq scRNAseq_FLAG_SATB2_dome_R1_sorted.fastq scRNAseq_FLAG_SATB2_dome_R2_sorted.fastq | fastq fastq fastq | 47518418346.0 | 340198768.0 | scRNAseq FLAG SATB2 dome I1.fastq.gz | 0:8 1:30.68 2:101 | A:13016292601;C:10075463201;G:10532642161;T:13868229463;N:25790920 | 8 | 30 | 101 | 13016292601 | 10075463201 | 10532642161 | 13868229463 | 25790920 | SRX8968761 | SRS7224498 | SRA1114017 | IISER-PUNE|biology | IISER-PUNE | 1 | 0.92339 | 0.12479 | 0.81485 | 0.52987 | 101 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | India | 2020-09-01 | Blastula | Embryo | Whole Organism | All anatomical structures | ||||||||||||||||||||||||
| 72833 | 72833 | SRR23210472 | SRX19158411 | SRS16570832 | SRP418915 | PRJNA927004 | Differential Nodal level promotes mesendoderm cell fate segregation mediated by chromatin organization | GSE223636 | Other | Purpose: To investigate the mechanism of prechordal plate and anterior endoderm separation . Methods: Nodal injected explants injected with 10pg ndr2 mRNA constructed from lft1 mutants and ndr1 morphants were harvested at xxxhpf. Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics PN 1000075 according to the manufacturer's protocol for 10000 cells recovery. For single cell multiomics zebrafish embryos at 6 hpf were harvested. Libraries were prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics 4 rxns PN 1000285 according to the manufacturer's protocol for 10000 cells recovery. Results: A total of 10 614 single cell transcriptomes and 4 335 multiomics were collected post stringent quality control measures. Conclusions: A slight bias in Nodal signaling promotes a differential chromatin structure between prechordal plate and endoderm which drives a differential expression of those key regulators such as gsc and ripply1 in these two cell lineages and further regulates mesendoderm cell fate separation. Overall design: zebrafish Nodal explants constructed from lft1 mutants and ndr1 morphants were harvested at 6hpf for scRNA seq. Zebrafish embryos were harvested at 6hpf for single cell multiomics. | zebrafish embryo multiomics expression | GSM6969677 | source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:6hpf | zebrafish embryo multiomics expression | Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 using the 10x Genomics CellRanger pipeline version 6.1.2 and cellranger arc version 2.0.0 with default parameters. Assembly: GRCz11 Supplementary files format and content: tar archivr or gzip compressed files included filtered gene bc matrices and ATAC fragments post running CellRanger or cellranger arc pipeline. Library strategy: scMultiome GEX | zebrafish cells | 10pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage then were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 6hpf corresponding to embryonic developmental stage. | Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v3 10x Genomics PN 1000075 and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics 4 rxns PN 1000285 according to the manufacturer’s protocol for 10000 cells recovery. | Explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium | strain:AB|tissue:embryonic cells|age:6hpf | GSM6969677 | GSM6969677: zebrafish embryo multiomics expression; Danio rerio; OTHER | GSM6969677 r1 | GSM6969677 | 1 | Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics PN 1000075 and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics 4 rxns PN 1000285 according to the manufacturer's protocol for 10000 cells recovery. | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP418915 | loader:fastq load.py | 6-M-GEX-merge_S1_L001_R1_001.fastq.gz 6-M-GEX-merge_S1_L001_R2_001.fastq.gz | fastq fastq | 67059456600.0 | 223531522.0 | GSM6969677 r1 | 0:150 1:150 | A:20681044309;C:12370348813;G:11664316954;T:22341885756;N:1860768 | 150 | 150 | 20681044309 | 12370348813 | 11664316954 | 22341885756 | 1860768 | SRX19158411 | SRS16570832 | SRA1581154 | Institute of genetics, Zhejiang University | Institute of genetics, Zhejiang University | 2 | 0.45314 | 0.8745 | 0.16489 | 0.2261 | 0.99072 | 0.82641 | 0.79221 | 0.75799 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | unknown | other | unknown | sc | single_cell_droplet | 10x | China | 2023-01-24 | 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");;