run_metadata: 56749
This data as json
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 56749 | SRR15813440 | SRX12105544 | SRS10085838 | SRP249509 | PRJNA606682 | CellOracle: Dissecting cell identity via network inference and in silico gene perturbation | GSE145298 | Other | Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method. | pubmed:36755098 | wt s3 | GSM5567814 | tissue:wt reference hpf 8|strain:WT|Stage:8 hpf|experiment:WT embryo | wt s3 | Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz | wt reference hpf 8 | 10x Genomcis Chromium single cell preparation | strain:WT|Stage:8 hpf|experiment:WT embryo | GSM5567814 | GSM5567814: wt s3; Danio rerio; RNA Seq | GSM5567814 | 1 | 10x Genomcis Chromium single cell preparation | GEO Accession:GSM5567814 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 550 | SRP249509 | assembly:GRCz11|intentional duplicate | wt_s3_possorted_genome_bam.bam | 10X Genomics bam file | 13357030950.0 | 148411455.0 | GSM5567814 r1 | 0:90 | A:3992336370;C:2912423812;G:3128958676;T:3318661163;N:4650929 | 90 | 3992336370 | 2912423812 | 3128958676 | 3318661163 | 4650929 | SRX12105544 | SRS10085838 | SRA1042742 | GEO | Washington University in St Louis | 1 | 0.9059 | 0.21809 | 0.82578 | 0.64796 | 90 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-09-08 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures |