run_metadata: 56746
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 56746 | SRR15813443 | SRX12105547 | SRS10085839 | 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 s6 | GSM5567817 | tissue:wt reference hpf 10|strain:WT|Stage:10 hpf|experiment:WT embryo | wt s6 | 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 | GSM5567817 | GSM5567817: wt s6; Danio rerio; RNA Seq | GSM5567817 | 1 | 10x Genomcis Chromium single cell preparation | GEO Accession:GSM5567817 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 550 | SRP249509 | assembly:GRCz11|intentional duplicate | wt_s6_possorted_genome_bam.bam | 10X Genomics bam file | 10559763630.0 | 117330707.0 | GSM5567817 r1 | 0:90 | A:3140440043;C:2269672250;G:2444938588;T:2701186457;N:3526292 | 90 | 3140440043 | 2269672250 | 2444938588 | 2701186457 | 3526292 | SRX12105547 | SRS10085839 | SRA1042742 | GEO | Washington University in St Louis | 1 | 0.91901 | 0.24752 | 0.80736 | 0.6329 | 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 |