run_metadata: 54763
This data as json
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| 54763 | SRR10151722 | SRX6877421 | SRS5413203 | SRP222763 | PRJNA572587 | Characterization of T cells from the larval zebrafish tail via single cell RNAseq | GSE137770 | Transcriptome Analysis | We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed. | pubmed:32427565 | lckgfp s163 | GSM4087284 | source name:Danio rerio tail|line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf | lckgfp s163 | STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt | Danio rerio tail | Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+ | Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018 | line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf | GSM4087284 | GSM4087284: lckgfp s163; Danio rerio; RNA Seq | GSM4087284 | 1 | Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018 | GEO Accession:GSM4087284 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP222763 | lckgfp_s163_R1.fastq.gz lckgfp_s163_R2.fastq.gz | fastq fastq | 277914000.0 | 1389570.0 | GSM4087284 r1 | 0:100 1:100 | A:82409899;C:58251309;G:57339795;T:79911604;N:1393 | 100 | 100 | 82409899 | 58251309 | 57339795 | 79911604 | 1393 | SRX6877421 | SRS5413203 | SRA965286 | GEO | Stanford University | 2 | 0.76932 | 0.77938 | 0.13303 | 0.13733 | 0.9707 | 0.97092 | 0.62097 | 0.53929 | 100 | 100 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | nextera | sc | single_cell_plate | smartseq | United States | 2019-09-20 | Larval | Larval | Tail | Multi-system |