run_metadata: 56769
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 56769 | SRR15813420 | SRX12105524 | SRS10085818 | 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 | irx3a 3 | GSM5567794 | tissue:irx3a crispant|strain:irx3a crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo | irx3a 3 | 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 | irx3a crispant | 10x Genomcis Chromium single cell preparation | strain:irx3a crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo | GSM5567794 | GSM5567794: irx3a 3; Danio rerio; RNA Seq | GSM5567794 | 1 | 10x Genomcis Chromium single cell preparation | GEO Accession:GSM5567794 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 550 | SRP249509 | assembly:GRCz11|intentional duplicate | irx3a_3_possorted_genome_bam.bam | 10X Genomics bam file | 8702629560.0 | 96695884.0 | GSM5567794 r1 | 0:90 | A:2502778147;C:1869454970;G:2100874536;T:2226298889;N:3223018 | 90 | 2502778147 | 1869454970 | 2100874536 | 2226298889 | 3223018 | SRX12105524 | SRS10085818 | SRA1042742 | GEO | Washington University in St Louis | 1 | 0.93135 | 0.17699 | 0.83031 | 0.56065 | 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 |