run_metadata: 56773
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 56773 | SRR15813416 | SRX12105520 | SRS10085816 | 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 | flh mut 1 | GSM5567790 | tissue:flh mutant|strain:floating head mutant n1/n1|Stage:10 hpf|experiment:Mutant embryos were generated by crossing heterozygous and selecting mutants based on their morphology at 10 hpf. | flh mut 1 | 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 | flh mutant | 10x Genomcis Chromium single cell preparation | strain:floating head mutant n1/n1|Stage:10 hpf|experiment:Mutant embryos were generated by crossing heterozygous and selecting mutants based on their morphology at 10 hpf. | GSM5567790 | GSM5567790: flh mut 1; Danio rerio; RNA Seq | GSM5567790 | 1 | 10x Genomcis Chromium single cell preparation | GEO Accession:GSM5567790 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 550 | SRP249509 | assembly:GRCz11|intentional duplicate | flh_mut_1_possorted_genome_bam.bam | 10X Genomics bam file | 20399851800.0 | 226665020.0 | GSM5567790 r1 | 0:90 | A:6026150068;C:4212547690;G:4691267625;T:5463467796;N:6418621 | 90 | 6026150068 | 4212547690 | 4691267625 | 5463467796 | 6418621 | SRX12105520 | SRS10085816 | SRA1042742 | GEO | Washington University in St Louis | 1 | 0.91268 | 0.26785 | 0.81288 | 0.49462 | 90 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-09-08 | Gastrula | Embryo | Head | Nervous System |