run_metadata: 70841
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 70841 | SRR20668422 | SRX16690950 | SRS14321715 | SRP388388 | PRJNA862882 | An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish | GSE209884 | Transcriptome Analysis | Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo 15min neomycin 1hr post neo 3hr post neo 5hr post neo il10ra sib homeo il10ra sib 1hr il10ra sib 3hr il10ra mut homeo il10ra mut 1hr and il10ra mut 3hr Overall design: scRNA seq | pubmed:36127326 | 1hr post neomycin | GSM6404039 | source name:macrophage|age:5dpf|tissue:macrophage|genotype:1hr post neomycin|strain:Tgmpeg:GFP | 1hr post neomycin | Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 ensembl release 91 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell. | macrophage | Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry | age:5dpf|tissue:macrophage|genotype:1hr post neomycin|strain:Tgmpeg:GFP | GSM6404039 | GSM6404039: 1hr post neomycin; Danio rerio; RNA Seq | GSM6404039 r1 | GSM6404039 | 1 | Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP388388 | assembly:danRer10|intentional duplicate|dangling references:treat as unmapped | 1hr_possorted_genome_bam.bam | 10X Genomics bam file | 31569863871.0 | 346921581.0 | GSM6404039 r1 | 0:91 | A:9269126254;C:6667515682;G:7316895497;T:8315860639;N:465799 | 91 | 9269126254 | 6667515682 | 7316895497 | 8315860639 | 465799 | SRX16690950 | SRS14321715 | SRA1469295 | Stowers institute for medical research | Stowers institute for medical research | 1 | 0.93105 | 0.12507 | 0.81677 | 0.52209 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2022-07-27 | Larval | Larval | Blood | Hematopoietic System |