run_metadata: 56762
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 56762 | SRR15813427 | SRX12105531 | SRS10085825 | 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 | noto 3 | GSM5567801 | tissue:noto crispant|strain:noto crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo | noto 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 | noto crispant | 10x Genomcis Chromium single cell preparation | strain:noto crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo | GSM5567801 | GSM5567801: noto 3; Danio rerio; RNA Seq | GSM5567801 | 1 | 10x Genomcis Chromium single cell preparation | GEO Accession:GSM5567801 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 550 | SRP249509 | assembly:GRCz11|intentional duplicate | noto_3_possorted_genome_bam.bam | 10X Genomics bam file | 9696476250.0 | 107738625.0 | GSM5567801 r1 | 0:90 | A:2759552091;C:2046867650;G:2381514508;T:2503080064;N:5461937 | 90 | 2759552091 | 2046867650 | 2381514508 | 2503080064 | 5461937 | SRX12105531 | SRS10085825 | SRA1042742 | GEO | Washington University in St Louis | 1 | 0.88572 | 0.24263 | 0.83228 | 0.5118 | 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 |