run_metadata: 65315
This data as json
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| 65315 | SRR15036072 | SRX11347513 | SRS9393431 | SRP326822 | PRJNA743561 | Single cell imaging of T cell immunotherapy responses in vivo | GSE179401 | Transcriptome Analysis | T cell immunotherapies have revolutionized treatment for a subset of cancers. Yet a major hurdle has been the lack of facile and predicative preclinical animal models that permit dynamic visualization of T cell immune responses at single cell resolution in vivo. Here optically clear immunocompromised zebrafish were engrafted with fluorescent labelled human cancers along with chimeric antigen receptor T CAR T cells bispecific T cell engagers BiTEs and antibody peptide epitope conjugates APECs allowing real time single cell visualization of T cell based immunotherapies in vivo. This work uncovered important differences in the kinetics of T cell infiltration tumor cell engagement and killing between these immunotherapies and established early endpoint analysis to predict therapy responses. We also established EGFR targeted immunotherapies as a powerful approach to kill rhabdomyosarcoma muscle cancers providing strong preclinical rationale for assessing a wider array of T cell immunotherapies in this disease. Overall design: Blood Lineage analysis of zebrafish kidney marrow samples from WT rag2?/? and rag2?/? il2rga / immunocompromised zebrafish | pubmed:34415995 | rag2∆/∆ zebrafish kidney marrow animal 3 | GSM5416996 | source name:rag2∆/∆ zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta} | rag2∆/∆ zebrafish kidney marrow animal 3 | bcl2fastq2 v2.17.1 was used to convert BCL into FASTQ indrops pipeline https://github.com/indrops/indrops was used to demultiplex align sort and quantify the gene expression of barcoded cells. indrops sort output fastq.gz was uploaded Seurat was used for downstream analysis the preprocessing and analysis script is at https://github.com/qinqian/zebrafish indrop/. Genome build: GRCz10 Supplementary files format and content: indrop..counts.tsv.gz | rag2∆/∆ zebrafish kidney marrow | Extracted kidney marrow are dissociated into single cell suspension and subjected to indrop single cell sequencing | Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols | WT rag2∆/∆ and rag2∆/∆ il2rga / immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted | tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta} | GSM5416996 | GSM5416996: rag2∆/∆ zebrafish kidney marrow animal 3; Danio rerio; RNA Seq | GSM5416996 | 1 | Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM5416996 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP326822 | rag2_rep3_run1_ATTAGACG_L001.fastq.sorted.fastq.gz | fastq | 2222304640.0 | 37787809.0 | GSM5416996 r1 | 0:58.81 | A:645345287;C:476804005;G:443148112;T:656994972;N:12264 | 58 | 645345287 | 476804005 | 443148112 | 656994972 | 12264 | SRX11347513 | SRS9393431 | SRA1254398 | GEO | Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital | 1 | 0.84762 | 0.09206 | 0.81253 | 0.56514 | 61 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | trueseq | sc | single_cell_droplet | indrops | United States | 2021-07-03 | Juvenile | Juvenile | Multi-tissue | Multi-system |