run_metadata: 56754
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 56754 | SRR15813435 | SRX12105539 | SRS10085833 | 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 | tyr 5 | GSM5567809 | tissue:tyr crispant|strain:tyr crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo | tyr 5 | 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 | tyr crispant | 10x Genomcis Chromium single cell preparation | strain:tyr crispant generated from wild type|Stage:10 hpf|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo | GSM5567809 | GSM5567809: tyr 5; Danio rerio; RNA Seq | GSM5567809 | 1 | 10x Genomcis Chromium single cell preparation | GEO Accession:GSM5567809 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 550 | SRP249509 | assembly:GRCz11|intentional duplicate | tyr_5_possorted_genome_bam.bam | 10X Genomics bam file | 11100581280.0 | 123339792.0 | GSM5567809 r1 | 0:90 | A:3139119132;C:2435865589;G:2721973969;T:2802951898;N:670692 | 90 | 3139119132 | 2435865589 | 2721973969 | 2802951898 | 670692 | SRX12105539 | SRS10085833 | SRA1042742 | GEO | Washington University in St Louis | 1 | 0.93417 | 0.15847 | 0.83347 | 0.5442 | 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 |