run_metadata: 56747
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 56747 | SRR15813442 | SRX12105546 | SRS10085840 | 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 s5 | GSM5567816 | tissue:wt reference hpf 10|strain:WT|Stage:10 hpf|experiment:WT embryo | wt s5 | 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 10 | 10x Genomcis Chromium single cell preparation | strain:WT|Stage:10 hpf|experiment:WT embryo | GSM5567816 | GSM5567816: wt s5; Danio rerio; RNA Seq | GSM5567816 | 1 | 10x Genomcis Chromium single cell preparation | GEO Accession:GSM5567816 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 550 | SRP249509 | assembly:GRCz11|intentional duplicate | wt_s5_possorted_genome_bam.bam | 10X Genomics bam file | 7404734700.0 | 82274830.0 | GSM5567816 r1 | 0:90 | A:2195721377;C:1607643736;G:1735950843;T:1863072717;N:2346027 | 90 | 2195721377 | 1607643736 | 1735950843 | 1863072717 | 2346027 | SRX12105546 | SRS10085840 | SRA1042742 | GEO | Washington University in St Louis | 1 | 0.91448 | 0.23763 | 0.80933 | 0.63338 | 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 |