run_metadata: 54740
This data as json
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| 54740 | SRR10151937 | SRX6877444 | SRS5413226 | 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 s378 | GSM4087499 | source name:Danio rerio tail|line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf | lckgfp s378 | 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 | GSM4087499 | GSM4087499: lckgfp s378; Danio rerio; RNA Seq | GSM4087499 | 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:GSM4087499 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP222763 | lckgfp_s378_R1.fastq.gz lckgfp_s378_R2.fastq.gz | fastq fastq | 337111400.0 | 1685557.0 | GSM4087499 r1 | 0:100 1:100 | A:98638322;C:70570254;G:69961020;T:97940105;N:1699 | 100 | 100 | 98638322 | 70570254 | 69961020 | 97940105 | 1699 | SRX6877444 | SRS5413226 | SRA965286 | GEO | Stanford University | 2 | 0.87386 | 0.87621 | 0.19517 | 0.19574 | 0.97443 | 0.97463 | 0.60077 | 0.60132 | 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 |