{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where technology = \"indrops\" and tissue_curation_coarse = \"Multi-system\"", "rows": [[32781, "SRR29411985", "SRX24925451", "SRS21630866", "SRP513930", "PRJNA1124008", "Cell state transitions are decoupled from cell division during early embryo development [II]", "GSE269848", "Other", "Paper abstract: As tissues develop  cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation  we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. However  in the absence of cell division  differentiation slows down in some cell types  and cells exhibit global stress responses. While differentiation is robust to blocking cell division  the proportions of cells across cell states are not but show evidence of partial compensation. This work clarifies our understanding of the role of cell division in development and showcases the utility of combining embryo wide perturbations with single cell RNA sequencing to uncover the role of common biological processes across multiple tissues. Overall design: Design of experiment for this particular dataset: Forty tails from zebrafish embryos at 24  38 hpf and 48 hpf were collected. Cells were dissociated from these tails and multi seq tags were added to the cells for each time point. Cells from all time points were pooled and single cell sequencing was performed using Indrops. Four gene expression GEX libraries were prepared for transcriptomic information and four multiseq tag libraries TAG were prepared for reading out the multiseq tags. We provide the raw data .fastq files  processed data   both raw counts.tsv.gz and filtered by total UMI counts filtered.h5ad files and the entire filtered data post removing doublets as all data.h5ad. We also provide counts for multi seq tags example  TAG 1.counts.csv. Information about pooling libraries and library indices is provided in Pooling Samples.xlsx. Only 24 hpf data was used for Kukreja et. al. 2024 and hence the cell state information we provide in the all data.h5ad is only for 24 hpf.", null, "pubmed:37546736", null, "24  38 hpf and 48 hpf tails", "GSM8328864", null, "source name:embryo tail|tissue:embryo tail|geo loc name:missing|collection date:missing", "24  38 hpf and 48 hpf tails", "Reads were mapped onto the Zebrafish genome as described in Kukreja et al. 2024 manuscript. Multi seq barcodes for each sample were identified using a custom pipeline available here: https://github.com/AllonKleinLab/klunctions/. Barcode abundance was used to manually remove multiplet populations as well as assign cells to their appropriate sample. Data from only 24 hpf tails were used for the manuscript. We provide 8 FASTQ files 2 lanes x 4 reads per lane. The read files from an inDrops run have the following content: * R1 001.fastq.gz : contains the three prime UTR cDNA read * R2 001.fastq.gz : contains the first half of the cell barcode * R3 001.fastq.gz : contains the library index for demultiplexing libraries * R4 001.fastq.gz : contains the second half of the barcode and the UMI.  All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis github.com/indrops. Single cell transcriptomes were barcoded using inDrops Klein et al  Cell 2015. Standard transcriptome RNA seq libraries were processed as reported in Zilionis et al. Nature Protocol 2016 using inDrops v3 protocol. The transcriptome libraries were sequenced on reads Illumina NextSeq 500. Libraries used standard Illumina sequencing primers and 61 cycles for Read1  14 cycles for Read2  8 cycles each for IndexRead1 and IndexRead2. Raw fastq files was processed using inDrops.py pipeline github.com/indrops/indrops. Sequenced reads were mapped to a zebrafish reference transcriptome built from the zebrafish GRCz10 genome assembly Assembly Accession: GCF 000002035.5 using bowtie version 1.1.143. To obtain the final counts matrix used for data analysis  total count filters were applied as described in Kukreja et. al. 2024  method section \"Single cell RNA seq Data preprocessing\" Assembly: GRCz10 genome assembly Assembly Accession: GCF 000002035.5 Supplementary files format and content: Raw counts for transcriptome tsv.gz: cell barcode  gene names  and raw counts for all cells Supplementary files format and content: Raw counts for multi seq tags csv.gz: cell barcode  tag sequence  and raw counts for all cells Supplementary files format and content: Filtered barcodes filtered.h5ad: cell barcode  and associated metadata for all cells Library strategy: inDrops v3 scRNA seq", "embryo tail", null, "Forty zebrafish tail samples collected at 24  38 hpf and 48 hpf  were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly  the tails were dissociated with a mixture of DNaseI 20\u00b5g/mL  Collagenase/Dispase 8 mg/mL  and 0.25% Trypsin EDTA at 30.5\u00b0C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled  washed with 1% BSA + PBS  and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.", null, "tissue:embryo tail", "GSM8328864", "GSM8328864: 24  38 hpf and 48 hpf tails; Danio rerio; OTHER", "GSM8328864 r1", "GSM8328864", "1", "Forty zebrafish tail samples collected at 24  38 hpf and 48 hpf  were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly  the tails were dissociated with a mixture of DNaseI 20\u00b5g/mL  Collagenase/Dispase 8 mg/mL  and 0.25% Trypsin EDTA at 30.5\u00b0C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled  washed with 1% BSA + PBS  and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP513930", null, null, "Undetermined_S0_L002_R1_001.fastq.gz Undetermined_S0_L002_R2_001.fastq.gz Undetermined_S0_L002_R3_001.fastq.gz Undetermined_S0_L002_R4_001.fastq.gz", "fastq fastq fastq fastq", 58603546956.0, 505202991.0, "GSM8328864 r1", "0:86 1:8 2:8 3:14", "A:13191204330;C:9162028793;G:9431065581;T:11662090182;N:1068340", 86, 8, 8, 14, 13191204330, 9162028793, 9431065581, 11662090182, 1068340, "SRX24925451", "SRS21630866", "SRA1899240", "Harvard University", "Harvard University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "other", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2024-06-14", "Multi-stage", "Embryo", "Tail", "Multi-system"], [32782, "SRR29411986", "SRX24925451", "SRS21630866", "SRP513930", "PRJNA1124008", "Cell state transitions are decoupled from cell division during early embryo development [II]", "GSE269848", "Other", "Paper abstract: As tissues develop  cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation  we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. However  in the absence of cell division  differentiation slows down in some cell types  and cells exhibit global stress responses. While differentiation is robust to blocking cell division  the proportions of cells across cell states are not but show evidence of partial compensation. This work clarifies our understanding of the role of cell division in development and showcases the utility of combining embryo wide perturbations with single cell RNA sequencing to uncover the role of common biological processes across multiple tissues. Overall design: Design of experiment for this particular dataset: Forty tails from zebrafish embryos at 24  38 hpf and 48 hpf were collected. Cells were dissociated from these tails and multi seq tags were added to the cells for each time point. Cells from all time points were pooled and single cell sequencing was performed using Indrops. Four gene expression GEX libraries were prepared for transcriptomic information and four multiseq tag libraries TAG were prepared for reading out the multiseq tags. We provide the raw data .fastq files  processed data   both raw counts.tsv.gz and filtered by total UMI counts filtered.h5ad files and the entire filtered data post removing doublets as all data.h5ad. We also provide counts for multi seq tags example  TAG 1.counts.csv. Information about pooling libraries and library indices is provided in Pooling Samples.xlsx. Only 24 hpf data was used for Kukreja et. al. 2024 and hence the cell state information we provide in the all data.h5ad is only for 24 hpf.", null, "pubmed:37546736", null, "24  38 hpf and 48 hpf tails", "GSM8328864", null, "source name:embryo tail|tissue:embryo tail|geo loc name:missing|collection date:missing", "24  38 hpf and 48 hpf tails", "Reads were mapped onto the Zebrafish genome as described in Kukreja et al. 2024 manuscript. Multi seq barcodes for each sample were identified using a custom pipeline available here: https://github.com/AllonKleinLab/klunctions/. Barcode abundance was used to manually remove multiplet populations as well as assign cells to their appropriate sample. Data from only 24 hpf tails were used for the manuscript. We provide 8 FASTQ files 2 lanes x 4 reads per lane. The read files from an inDrops run have the following content: * R1 001.fastq.gz : contains the three prime UTR cDNA read * R2 001.fastq.gz : contains the first half of the cell barcode * R3 001.fastq.gz : contains the library index for demultiplexing libraries * R4 001.fastq.gz : contains the second half of the barcode and the UMI.  All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis github.com/indrops. Single cell transcriptomes were barcoded using inDrops Klein et al  Cell 2015. Standard transcriptome RNA seq libraries were processed as reported in Zilionis et al. Nature Protocol 2016 using inDrops v3 protocol. The transcriptome libraries were sequenced on reads Illumina NextSeq 500. Libraries used standard Illumina sequencing primers and 61 cycles for Read1  14 cycles for Read2  8 cycles each for IndexRead1 and IndexRead2. Raw fastq files was processed using inDrops.py pipeline github.com/indrops/indrops. Sequenced reads were mapped to a zebrafish reference transcriptome built from the zebrafish GRCz10 genome assembly Assembly Accession: GCF 000002035.5 using bowtie version 1.1.143. To obtain the final counts matrix used for data analysis  total count filters were applied as described in Kukreja et. al. 2024  method section \"Single cell RNA seq Data preprocessing\" Assembly: GRCz10 genome assembly Assembly Accession: GCF 000002035.5 Supplementary files format and content: Raw counts for transcriptome tsv.gz: cell barcode  gene names  and raw counts for all cells Supplementary files format and content: Raw counts for multi seq tags csv.gz: cell barcode  tag sequence  and raw counts for all cells Supplementary files format and content: Filtered barcodes filtered.h5ad: cell barcode  and associated metadata for all cells Library strategy: inDrops v3 scRNA seq", "embryo tail", null, "Forty zebrafish tail samples collected at 24  38 hpf and 48 hpf  were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly  the tails were dissociated with a mixture of DNaseI 20\u00b5g/mL  Collagenase/Dispase 8 mg/mL  and 0.25% Trypsin EDTA at 30.5\u00b0C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled  washed with 1% BSA + PBS  and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.", null, "tissue:embryo tail", "GSM8328864", "GSM8328864: 24  38 hpf and 48 hpf tails; Danio rerio; OTHER", "GSM8328864 r1", "GSM8328864", "1", "Forty zebrafish tail samples collected at 24  38 hpf and 48 hpf  were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly  the tails were dissociated with a mixture of DNaseI 20\u00b5g/mL  Collagenase/Dispase 8 mg/mL  and 0.25% Trypsin EDTA at 30.5\u00b0C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled  washed with 1% BSA + PBS  and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP513930", null, null, "Undetermined_S0_L001_R1_001.fastq.gz Undetermined_S0_L001_R2_001.fastq.gz Undetermined_S0_L001_R3_001.fastq.gz Undetermined_S0_L001_R4_001.fastq.gz", "fastq fastq fastq fastq", 44072422880.0, 379934680.0, "GSM8328864 r2", "0:86 1:8 2:8 3:14", "A:9919784228;C:6894965731;G:7094749745;T:8764100624;N:782152", 86, 8, 8, 14, 9919784228, 6894965731, 7094749745, 8764100624, 782152, "SRX24925451", "SRS21630866", "SRA1899240", "Harvard University", "Harvard University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "other", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2024-06-14", "Multi-stage", "Embryo", "Tail", "Multi-system"], [65304, "SRR15036083", "SRX11347516", "SRS9393434", "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", null, "pubmed:34415995", null, "rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 3", "GSM5416999", null, "source name:rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "rag2\u2206/\u2206  il2rga /  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\u2206/\u2206  il2rga /  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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "GSM5416999", "GSM5416999: rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 3; Danio rerio; RNA Seq", "GSM5416999", null, "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:GSM5416999", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "rag2il2rga_rep3_run1_TACTCCTT_L001.fastq.sorted.fastq.gz", "fastq", 1540876806.0, 26201226.0, "GSM5416999 r1", "0:58.81", "A:453086964;C:337301672;G:300857192;T:449622475;N:8503", 58, null, null, null, 453086964, 337301672, 300857192, 449622475, 8503, "SRX11347516", "SRS9393434", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.80729, null, 0.07332, null, 0.82055, null, 0.60511, null, 61, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65305, "SRR15036084", "SRX11347516", "SRS9393434", "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", null, "pubmed:34415995", null, "rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 3", "GSM5416999", null, "source name:rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "rag2\u2206/\u2206  il2rga /  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\u2206/\u2206  il2rga /  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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "GSM5416999", "GSM5416999: rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 3; Danio rerio; RNA Seq", "GSM5416999", null, "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:GSM5416999", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "rag2il2rga_rep3_run1_TACTCCTT_L002.fastq.sorted.fastq.gz", "fastq", 1464761387.0, 24907711.0, "GSM5416999 r2", "0:58.81", "A:430310565;C:320135615;G:286001024;T:428308829;N:5354", 58, null, null, null, 430310565, 320135615, 286001024, 428308829, 5354, "SRX11347516", "SRS9393434", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.80697, null, 0.07529, null, 0.81921, null, 0.60121, null, 61, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65306, "SRR15036085", "SRX11347516", "SRS9393434", "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", null, "pubmed:34415995", null, "rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 3", "GSM5416999", null, "source name:rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "rag2\u2206/\u2206  il2rga /  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\u2206/\u2206  il2rga /  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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "GSM5416999", "GSM5416999: rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 3; Danio rerio; RNA Seq", "GSM5416999", null, "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:GSM5416999", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "rag2il2rga_rep3_run1_TACTCCTT_L003.fastq.sorted.fastq.gz", "fastq", 1559071690.0, 26477894.0, "GSM5416999 r3", "0:58.88", "A:457962961;C:341679675;G:304164183;T:455257776;N:7095", 58, null, null, null, 457962961, 341679675, 304164183, 455257776, 7095, "SRX11347516", "SRS9393434", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.80662, null, 0.07406, null, 0.82154, null, 0.56588, null, 61, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65307, "SRR15036086", "SRX11347516", "SRS9393434", "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", null, "pubmed:34415995", null, "rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 3", "GSM5416999", null, "source name:rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "rag2\u2206/\u2206  il2rga /  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/. 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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", null, "pubmed:34415995", null, "rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 2", "GSM5416998", null, "source name:rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 2", "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\u2206/\u2206  il2rga /  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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "GSM5416998", "GSM5416998: rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 2; Danio rerio; RNA Seq", "GSM5416998", null, "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:GSM5416998", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "rag2il2rga_rep2_run1_TATGCAGT_L001.fastq.sorted.fastq.gz", "fastq", 1198566764.0, 20263317.0, "GSM5416998 r1", "0:59.15", "A:348615404;C:279444276;G:237318155;T:333180819;N:8110", 59, null, null, null, 348615404, 279444276, 237318155, 333180819, 8110, "SRX11347515", "SRS9393433", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.78095, null, 0.05246, null, 0.83422, null, 0.60686, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65309, "SRR15036080", "SRX11347515", "SRS9393433", "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", null, "pubmed:34415995", null, "rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 2", "GSM5416998", null, "source name:rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 2", "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\u2206/\u2206  il2rga /  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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "GSM5416998", "GSM5416998: rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 2; Danio rerio; RNA Seq", "GSM5416998", null, "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:GSM5416998", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "rag2il2rga_rep2_run1_TATGCAGT_L002.fastq.sorted.fastq.gz", "fastq", 1150642006.0, 19454469.0, "GSM5416998 r2", "0:59.15", "A:334924475;C:266975981;G:228180514;T:320550327;N:10709", 59, null, null, null, 334924475, 266975981, 228180514, 320550327, 10709, "SRX11347515", "SRS9393433", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.78751, null, 0.05418, null, 0.83471, null, 0.61606, null, 61, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65310, "SRR15036081", "SRX11347515", "SRS9393433", "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", null, "pubmed:34415995", null, "rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 2", "GSM5416998", null, "source name:rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 2", "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\u2206/\u2206  il2rga /  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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "GSM5416998", "GSM5416998: rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 2; Danio rerio; RNA Seq", "GSM5416998", null, "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:GSM5416998", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "rag2il2rga_rep2_run1_TATGCAGT_L003.fastq.sorted.fastq.gz", "fastq", 1224804533.0, 20697063.0, "GSM5416998 r3", "0:59.18", "A:356526291;C:284995125;G:242763299;T:340516650;N:3168", 59, null, null, null, 356526291, 284995125, 242763299, 340516650, 3168, "SRX11347515", "SRS9393433", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.78411, null, 0.05285, null, 0.83447, null, 0.56902, null, 61, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65311, "SRR15036082", "SRX11347515", "SRS9393433", "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", null, "pubmed:34415995", null, "rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 2", "GSM5416998", null, "source name:rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 2", "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\u2206/\u2206  il2rga /  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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "GSM5416998", "GSM5416998: rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 2; Danio rerio; RNA Seq", "GSM5416998", null, "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:GSM5416998", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "rag2il2rga_rep2_run1_TATGCAGT_L004.fastq.sorted.fastq.gz", "fastq", 1183829432.0, 20014508.0, "GSM5416998 r4", "0:59.15", "A:345040424;C:274431327;G:234489457;T:329861445;N:6779", 59, null, null, null, 345040424, 274431327, 234489457, 329861445, 6779, "SRX11347515", "SRS9393433", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.78584, null, 0.05337, null, 0.83457, null, 0.61081, null, 61, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65312, "SRR15036076", "SRX11347514", "SRS9393432", "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", null, "pubmed:34415995", null, "rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 1", "GSM5416997", null, "source name:rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 1", "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\u2206/\u2206  il2rga /  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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "GSM5416997", "GSM5416997: rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 1; Danio rerio; RNA Seq", "GSM5416997", null, "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. 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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", null, "pubmed:34415995", null, "rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 1", "GSM5416997", null, "source name:rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 1", "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\u2206/\u2206  il2rga /  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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "GSM5416997", "GSM5416997: rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 1; Danio rerio; RNA Seq", "GSM5416997", null, "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:GSM5416997", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "rag2il2rga_rep1_run1_CTCCTTAC_L003.fastq.sorted.fastq.gz", "fastq", 1224788809.0, 23016551.0, "GSM5416997 r2", "0:53.21", "A:384419718;C:254006293;G:219689014;T:366669699;N:4085", 53, null, null, null, 384419718, 254006293, 219689014, 366669699, 4085, "SRX11347514", "SRS9393432", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.75456, null, 0.06946, null, 0.84082, null, 0.58125, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65314, "SRR15036078", "SRX11347514", "SRS9393432", "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", null, "pubmed:34415995", null, "rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 1", "GSM5416997", null, "source name:rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 1", "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\u2206/\u2206  il2rga /  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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ", "GSM5416997", "GSM5416997: rag2\u2206/\u2206  il2rga /  zebrafish kidney marrow animal 1; Danio rerio; RNA Seq", "GSM5416997", null, "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:GSM5416997", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "rag2il2rga_rep1_run1_CTCCTTAC_L004.fastq.sorted.fastq.gz", "fastq", 1160912686.0, 21817834.0, "GSM5416997 r3", "0:53.21", "A:364837636;C:239223801;G:207638568;T:349212231;N:450", 53, null, null, null, 364837636, 239223801, 207638568, 349212231, 450, "SRX11347514", "SRS9393432", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.75964, null, 0.07051, null, 0.84122, null, 0.59786, null, 61, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [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", null, "pubmed:34415995", null, "rag2\u2206/\u2206 zebrafish kidney marrow animal 3", "GSM5416996", null, "source name:rag2\u2206/\u2206 zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}", "rag2\u2206/\u2206 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\u2206/\u2206 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\u2206/\u2206 and rag2\u2206/\u2206  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\u2206/\u2206 zebrafish kidney marrow animal 3; Danio rerio; RNA Seq", "GSM5416996", null, "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", null, "SRP326822", null, null, "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, null, null, null, 645345287, 476804005, 443148112, 656994972, 12264, "SRX11347513", "SRS9393431", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.84762, null, 0.09206, null, 0.81253, null, 0.56514, null, 61, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65316, "SRR15036073", "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", null, "pubmed:34415995", null, "rag2\u2206/\u2206 zebrafish kidney marrow animal 3", "GSM5416996", null, "source name:rag2\u2206/\u2206 zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}", "rag2\u2206/\u2206 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\u2206/\u2206 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\u2206/\u2206 and rag2\u2206/\u2206  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\u2206/\u2206 zebrafish kidney marrow animal 3; Danio rerio; RNA Seq", "GSM5416996", null, "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", null, "SRP326822", null, null, "rag2_rep3_run1_ATTAGACG_L002.fastq.sorted.fastq.gz", "fastq", 2107657788.0, 35841044.0, "GSM5416996 r2", "0:58.81", "A:611831337;C:451383668;G:420138423;T:624296408;N:7952", 58, null, null, null, 611831337, 451383668, 420138423, 624296408, 7952, "SRX11347513", "SRS9393431", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.84465, null, 0.09069, null, 0.81207, null, 0.56951, null, 61, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65317, "SRR15036074", "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", null, "pubmed:34415995", null, "rag2\u2206/\u2206 zebrafish kidney marrow animal 3", "GSM5416996", null, "source name:rag2\u2206/\u2206 zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}", "rag2\u2206/\u2206 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\u2206/\u2206 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\u2206/\u2206 and rag2\u2206/\u2206  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\u2206/\u2206 zebrafish kidney marrow animal 3; Danio rerio; RNA Seq", "GSM5416996", null, "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", null, "SRP326822", null, null, "rag2_rep3_run1_ATTAGACG_L003.fastq.sorted.fastq.gz", "fastq", 2244797132.0, 38112752.0, "GSM5416996 r3", "0:58.90", "A:651287231;C:482208798;G:447299624;T:663990887;N:10592", 58, null, null, null, 651287231, 482208798, 447299624, 663990887, 10592, "SRX11347513", "SRS9393431", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.84552, null, 0.09016, null, 0.81349, null, 0.56434, null, 61, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65318, "SRR15036075", "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", null, "pubmed:34415995", null, "rag2\u2206/\u2206 zebrafish kidney marrow animal 3", "GSM5416996", null, "source name:rag2\u2206/\u2206 zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}", "rag2\u2206/\u2206 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\u2206/\u2206 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\u2206/\u2206 and rag2\u2206/\u2206  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\u2206/\u2206 zebrafish kidney marrow animal 3; Danio rerio; RNA Seq", "GSM5416996", null, "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. 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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", null, "pubmed:34415995", null, "rag2\u2206/\u2206 zebrafish kidney marrow animal 2", "GSM5416995", null, "source name:rag2\u2206/\u2206 zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}", "rag2\u2206/\u2206 zebrafish kidney marrow animal 2", "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/. 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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", null, "pubmed:34415995", null, "rag2\u2206/\u2206 zebrafish kidney marrow animal 2", "GSM5416995", null, "source name:rag2\u2206/\u2206 zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}", "rag2\u2206/\u2206 zebrafish kidney marrow animal 2", "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\u2206/\u2206 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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}", "GSM5416995", "GSM5416995: rag2\u2206/\u2206 zebrafish kidney marrow animal 2; Danio rerio; RNA Seq", "GSM5416995", null, "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:GSM5416995", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "rag2_rep2_run1_AGAGGATA_L002.fastq.sorted.fastq.gz", "fastq", 1720282118.0, 29036996.0, "GSM5416995 r2", "0:59.24", "A:490612069;C:411469635;G:321613090;T:496571770;N:15554", 59, null, null, null, 490612069, 411469635, 321613090, 496571770, 15554, "SRX11347512", "SRS9393430", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.81467, null, 0.08996, null, 0.82879, null, 0.5598, null, 61, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65321, "SRR15036070", "SRX11347512", "SRS9393430", "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", null, "pubmed:34415995", null, "rag2\u2206/\u2206 zebrafish kidney marrow animal 2", "GSM5416995", null, "source name:rag2\u2206/\u2206 zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}", "rag2\u2206/\u2206 zebrafish kidney marrow animal 2", "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\u2206/\u2206 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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}", "GSM5416995", "GSM5416995: rag2\u2206/\u2206 zebrafish kidney marrow animal 2; Danio rerio; RNA Seq", "GSM5416995", null, "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:GSM5416995", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "rag2_rep2_run1_AGAGGATA_L003.fastq.sorted.fastq.gz", "fastq", 1819680197.0, 30703341.0, "GSM5416995 r3", "0:59.27", "A:518979591;C:436620699;G:340176627;T:523898644;N:4636", 59, null, null, null, 518979591, 436620699, 340176627, 523898644, 4636, "SRX11347512", "SRS9393430", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.81176, null, 0.08863, null, 0.82929, null, 0.57421, null, 61, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65322, "SRR15036071", "SRX11347512", "SRS9393430", "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", null, "pubmed:34415995", null, "rag2\u2206/\u2206 zebrafish kidney marrow animal 2", "GSM5416995", null, "source name:rag2\u2206/\u2206 zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}", "rag2\u2206/\u2206 zebrafish kidney marrow animal 2", "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\u2206/\u2206 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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}", "GSM5416995", "GSM5416995: rag2\u2206/\u2206 zebrafish kidney marrow animal 2; Danio rerio; RNA Seq", "GSM5416995", null, "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:GSM5416995", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "rag2_rep2_run1_AGAGGATA_L004.fastq.sorted.fastq.gz", "fastq", 1763566037.0, 29766811.0, "GSM5416995 r4", "0:59.25", "A:503631253;C:421409855;G:329457720;T:509057252;N:9957", 59, null, null, null, 503631253, 421409855, 329457720, 509057252, 9957, "SRX11347512", "SRS9393430", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.81558, null, 0.08928, null, 0.82804, null, 0.57087, null, 61, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65323, "SRR15036065", "SRX11347511", "SRS9393429", "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", null, "pubmed:34415995", null, "rag2\u2206/\u2206 zebrafish kidney marrow animal 1", "GSM5416994", null, "source name:rag2\u2206/\u2206 zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}", "rag2\u2206/\u2206 zebrafish kidney marrow animal 1", "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\u2206/\u2206 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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}", "GSM5416994", "GSM5416994: rag2\u2206/\u2206 zebrafish kidney marrow animal 1; Danio rerio; RNA Seq", "GSM5416994", null, "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:GSM5416994", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "rag2_rep1_run1_ATAGAGAG_L001.fastq.sorted.fastq.gz", "fastq", 699126466.0, 13170718.0, "GSM5416994 r1", "0:53.08", "A:218468551;C:153721094;G:124232493;T:202701592;N:2736", 53, null, null, null, 218468551, 153721094, 124232493, 202701592, 2736, "SRX11347511", "SRS9393429", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.68917, null, 0.06168, null, 0.85117, null, 0.58413, null, 25, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65324, "SRR15036066", "SRX11347511", "SRS9393429", "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", null, "pubmed:34415995", null, "rag2\u2206/\u2206 zebrafish kidney marrow animal 1", "GSM5416994", null, "source name:rag2\u2206/\u2206 zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}", "rag2\u2206/\u2206 zebrafish kidney marrow animal 1", "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\u2206/\u2206 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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}", "GSM5416994", "GSM5416994: rag2\u2206/\u2206 zebrafish kidney marrow animal 1; Danio rerio; RNA Seq", "GSM5416994", null, "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:GSM5416994", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "rag2_rep1_run1_ATAGAGAG_L003.fastq.sorted.fastq.gz", "fastq", 697028972.0, 13133712.0, "GSM5416994 r2", "0:53.07", "A:217845323;C:152574316;G:124291442;T:202315510;N:2381", 53, null, null, null, 217845323, 152574316, 124291442, 202315510, 2381, "SRX11347511", "SRS9393429", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.69486, null, 0.06113, null, 0.85251, null, 0.59868, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65325, "SRR15036067", "SRX11347511", "SRS9393429", "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", null, "pubmed:34415995", null, "rag2\u2206/\u2206 zebrafish kidney marrow animal 1", "GSM5416994", null, "source name:rag2\u2206/\u2206 zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}", "rag2\u2206/\u2206 zebrafish kidney marrow animal 1", "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\u2206/\u2206 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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}", "GSM5416994", "GSM5416994: rag2\u2206/\u2206 zebrafish kidney marrow animal 1; Danio rerio; RNA Seq", "GSM5416994", null, "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:GSM5416994", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "rag2_rep1_run1_ATAGAGAG_L004.fastq.sorted.fastq.gz", "fastq", 653515768.0, 12306908.0, "GSM5416994 r3", "0:53.10", "A:205055005;C:141133606;G:116472911;T:190854009;N:237", 53, null, null, null, 205055005, 141133606, 116472911, 190854009, 237, "SRX11347511", "SRS9393429", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.70594, null, 0.06468, null, 0.84999, null, 0.5849, null, 34, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65326, "SRR15036061", "SRX11347510", "SRS9393426", "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", null, "pubmed:34415995", null, "WT zebrafish kidney marrow sample animal 3", "GSM5416993", null, "source name:WT zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "WT zebrafish kidney marrow sample 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", "WT 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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "GSM5416993", "GSM5416993: WT zebrafish kidney marrow sample animal 3; Danio rerio; RNA Seq", "GSM5416993", null, "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. 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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", null, "pubmed:34415995", null, "WT zebrafish kidney marrow sample animal 3", "GSM5416993", null, "source name:WT zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "WT zebrafish kidney marrow sample 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", "WT 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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "GSM5416993", "GSM5416993: WT zebrafish kidney marrow sample animal 3; Danio rerio; RNA Seq", "GSM5416993", null, "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:GSM5416993", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "WT_rep3_run1_CTAGTCGA_L002.fastq.sorted.fastq.gz", "fastq", 2429257160.0, 41334915.0, "GSM5416993 r2", "0:58.77", "A:698209332;C:500659631;G:479258250;T:751121127;N:8820", 58, null, null, null, 698209332, 500659631, 479258250, 751121127, 8820, "SRX11347510", "SRS9393426", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.84518, null, 0.10802, null, 0.8127, null, 0.51482, null, 61, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65328, "SRR15036063", "SRX11347510", "SRS9393426", "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", null, "pubmed:34415995", null, "WT zebrafish kidney marrow sample animal 3", "GSM5416993", null, "source name:WT zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "WT zebrafish kidney marrow sample 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", "WT 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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "GSM5416993", "GSM5416993: WT zebrafish kidney marrow sample animal 3; Danio rerio; RNA Seq", "GSM5416993", null, "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:GSM5416993", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "WT_rep3_run1_CTAGTCGA_L003.fastq.sorted.fastq.gz", "fastq", 2585471590.0, 43915493.0, "GSM5416993 r3", "0:58.87", "A:742309784;C:534972384;G:510339526;T:797838293;N:11603", 58, null, null, null, 742309784, 534972384, 510339526, 797838293, 11603, "SRX11347510", "SRS9393426", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.8468, null, 0.10719, null, 0.81235, null, 0.52285, null, 61, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65329, "SRR15036064", "SRX11347510", "SRS9393426", "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", null, "pubmed:34415995", null, "WT zebrafish kidney marrow sample animal 3", "GSM5416993", null, "source name:WT zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "WT zebrafish kidney marrow sample 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", "WT 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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "GSM5416993", "GSM5416993: WT zebrafish kidney marrow sample animal 3; Danio rerio; RNA Seq", "GSM5416993", null, "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:GSM5416993", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "WT_rep3_run1_CTAGTCGA_L004.fastq.sorted.fastq.gz", "fastq", 2487233731.0, 42318406.0, "GSM5416993 r4", "0:58.77", "A:714440946;C:513072299;G:490202831;T:769509072;N:8583", 58, null, null, null, 714440946, 513072299, 490202831, 769509072, 8583, "SRX11347510", "SRS9393426", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.8486, null, 0.10677, null, 0.81314, null, 0.52091, null, 61, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65330, "SRR15036057", "SRX11347509", "SRS9393428", "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", null, "pubmed:34415995", null, "WT zebrafish kidney marrow sample animal 2", "GSM5416992", null, "source name:WT zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "WT zebrafish kidney marrow sample animal 2", "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", "WT 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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "GSM5416992", "GSM5416992: WT zebrafish kidney marrow sample animal 2; Danio rerio; RNA Seq", "GSM5416992", null, "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:GSM5416992", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "WT_rep2_run1_CGGAGAGA_L001.fastq.sorted.fastq.gz", "fastq", 1086949202.0, 18378765.0, "GSM5416992 r1", "0:59.14", "A:314483956;C:239809718;G:209071648;T:323576758;N:7122", 59, null, null, null, 314483956, 239809718, 209071648, 323576758, 7122, "SRX11347509", "SRS9393428", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.79795, null, 0.09375, null, 0.82522, null, 0.53498, null, 61, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65331, "SRR15036058", "SRX11347509", "SRS9393428", "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", null, "pubmed:34415995", null, "WT zebrafish kidney marrow sample animal 2", "GSM5416992", null, "source name:WT zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "WT zebrafish kidney marrow sample animal 2", "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", "WT 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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "GSM5416992", "GSM5416992: WT zebrafish kidney marrow sample animal 2; Danio rerio; RNA Seq", "GSM5416992", null, "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:GSM5416992", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "WT_rep2_run1_CGGAGAGA_L002.fastq.sorted.fastq.gz", "fastq", 1040177366.0, 17589308.0, "GSM5416992 r2", "0:59.14", "A:301061458;C:228573966;G:200110423;T:310422293;N:9226", 59, null, null, null, 301061458, 228573966, 200110423, 310422293, 9226, "SRX11347509", "SRS9393428", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.80252, null, 0.09472, null, 0.82708, null, 0.5189, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65332, "SRR15036059", "SRX11347509", "SRS9393428", "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", null, "pubmed:34415995", null, "WT zebrafish kidney marrow sample animal 2", "GSM5416992", null, "source name:WT zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "WT zebrafish kidney marrow sample animal 2", "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", "WT 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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "GSM5416992", "GSM5416992: WT zebrafish kidney marrow sample animal 2; Danio rerio; RNA Seq", "GSM5416992", null, "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:GSM5416992", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "WT_rep2_run1_CGGAGAGA_L003.fastq.sorted.fastq.gz", "fastq", 1096710594.0, 18541153.0, "GSM5416992 r3", "0:59.15", "A:317535237;C:241516822;G:211153746;T:326502090;N:2699", 59, null, null, null, 317535237, 241516822, 211153746, 326502090, 2699, "SRX11347509", "SRS9393428", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.80081, null, 0.09244, null, 0.82483, null, 0.54017, null, 61, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65333, "SRR15036060", "SRX11347509", "SRS9393428", "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", null, "pubmed:34415995", null, "WT zebrafish kidney marrow sample animal 2", "GSM5416992", null, "source name:WT zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "WT zebrafish kidney marrow sample animal 2", "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", "WT 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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "GSM5416992", "GSM5416992: WT zebrafish kidney marrow sample animal 2; Danio rerio; RNA Seq", "GSM5416992", null, "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:GSM5416992", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "WT_rep2_run1_CGGAGAGA_L004.fastq.sorted.fastq.gz", "fastq", 1068310915.0, 18065457.0, "GSM5416992 r4", "0:59.14", "A:309536619;C:234533609;G:205451194;T:318783671;N:5822", 59, null, null, null, 309536619, 234533609, 205451194, 318783671, 5822, "SRX11347509", "SRS9393428", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.80118, null, 0.09406, null, 0.82729, null, 0.53232, null, 17, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65334, "SRR15036054", "SRX11347508", "SRS9393427", "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", null, "pubmed:34415995", null, "WT zebrafish kidney marrow sample animal 1", "GSM5416991", null, "source name:WT zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "WT zebrafish kidney marrow sample animal 1", "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", "WT 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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "GSM5416991", "GSM5416991: WT zebrafish kidney marrow sample animal 1; Danio rerio; RNA Seq", "GSM5416991", null, "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:GSM5416991", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "WT_rep1_run1_AGGCTTAG_L001.fastq.sorted.fastq.gz", "fastq", 535767772.0, 10056200.0, "GSM5416991 r1", "0:53.28", "A:161358086;C:115991861;G:100428415;T:157987333;N:2077", 53, null, null, null, 161358086, 115991861, 100428415, 157987333, 2077, "SRX11347508", "SRS9393427", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.74319, null, 0.07334, null, 0.83272, null, 0.54608, null, 18, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65335, "SRR15036055", "SRX11347508", "SRS9393427", "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", null, "pubmed:34415995", null, "WT zebrafish kidney marrow sample animal 1", "GSM5416991", null, "source name:WT zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "WT zebrafish kidney marrow sample animal 1", "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", "WT 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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "GSM5416991", "GSM5416991: WT zebrafish kidney marrow sample animal 1; Danio rerio; RNA Seq", "GSM5416991", null, "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:GSM5416991", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "WT_rep1_run1_AGGCTTAG_L003.fastq.sorted.fastq.gz", "fastq", 547226774.0, 10264379.0, "GSM5416991 r2", "0:53.31", "A:164424405;C:118548162;G:103014421;T:161237932;N:1854", 53, null, null, null, 164424405, 118548162, 103014421, 161237932, 1854, "SRX11347508", "SRS9393427", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.74711, null, 0.07271, null, 0.83276, null, 0.55026, null, 23, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [65336, "SRR15036056", "SRX11347508", "SRS9393427", "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", null, "pubmed:34415995", null, "WT zebrafish kidney marrow sample animal 1", "GSM5416991", null, "source name:WT zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "WT zebrafish kidney marrow sample animal 1", "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", "WT 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\u2206/\u2206 and rag2\u2206/\u2206  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted", "tissue:Kidney marrow|cell type:Immune cells|genotype:Wild type", "GSM5416991", "GSM5416991: WT zebrafish kidney marrow sample animal 1; Danio rerio; RNA Seq", "GSM5416991", null, "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:GSM5416991", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP326822", null, null, "WT_rep1_run1_AGGCTTAG_L004.fastq.sorted.fastq.gz", "fastq", 502169589.0, 9439162.0, "GSM5416991 r3", "0:53.20", "A:151361206;C:107584405;G:94289485;T:148934301;N:192", 53, null, null, null, 151361206, 107584405, 94289485, 148934301, 192, "SRX11347508", "SRS9393427", "SRA1254398", "GEO", "Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital", 1, 0.7521, null, 0.07485, null, 0.83112, null, 0.54925, null, 60, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2021-07-03", "Juvenile", "Juvenile", "Multi-tissue", "Multi-system"], [74460, "SRR23802569", "SRX19634451", "SRS17003621", "SRP426621", "PRJNA943252", "Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail]", "GSE227118", "Other", "We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized  filtered  and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.", "parent bioproject:PRJNA510836", null, null, "Whole tail  72 hpf", "GSM7091920", null, "source name:transgenic zebrafish embryos wild type|tissue:Whole tail|developmental stage:72 hpf", "Whole tail  72 hpf", "the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode", "transgenic zebrafish embryos wild type", "No treatments", "Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", "Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were bisected on the axial plane towards the caudal end of the yolk extension  tail tissues were then homogenized  filtered  and viable cells sorted using live dead staining FACS into PBS  collecting at least 25 000 cells.", "tissue:Whole tail|developmental stage:72 hpf", "GSM7091920", "GSM7091920: Whole tail  72 hpf; Danio rerio; RNA Seq", "GSM7091920 r1", "GSM7091920", "1", "Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP426621", null, null, "EH_Tails_Single_Cell_GAGACGGA_L001.fastq.sorted.fastq.gz", "fastq", 715456535.0, 12017381.0, "GSM7091920 r1", "0:59.54", "A:205982879;C:141307848;G:135221384;T:232940601;N:3823", 59, null, null, null, 205982879, 141307848, 135221384, 232940601, 3823, "SRX19634451", "SRS17003621", null, null, "Oncology/Hematology, Boston Children's Hospital", 1, 0.88315, null, 0.14516, null, 0.78257, null, 0.49661, null, 61, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2023-03-10", "Larval", "Larval", "Tail", "Multi-system"], [74461, "SRR23802570", "SRX19634451", "SRS17003621", "SRP426621", "PRJNA943252", "Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail]", "GSE227118", "Other", "We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized  filtered  and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.", "parent bioproject:PRJNA510836", null, null, "Whole tail  72 hpf", "GSM7091920", null, "source name:transgenic zebrafish embryos wild type|tissue:Whole tail|developmental stage:72 hpf", "Whole tail  72 hpf", "the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode", "transgenic zebrafish embryos wild type", "No treatments", "Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", "Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were bisected on the axial plane towards the caudal end of the yolk extension  tail tissues were then homogenized  filtered  and viable cells sorted using live dead staining FACS into PBS  collecting at least 25 000 cells.", "tissue:Whole tail|developmental stage:72 hpf", "GSM7091920", "GSM7091920: Whole tail  72 hpf; Danio rerio; RNA Seq", "GSM7091920 r1", "GSM7091920", "1", "Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP426621", null, null, "EH_Tails_Single_Cell_GAGACGGA_L002.fastq.sorted.fastq.gz", "fastq", 589786185.0, 9927008.0, "GSM7091920 r2", "0:59.41", "A:170171480;C:115960508;G:111370241;T:192283114;N:842", 59, null, null, null, 170171480, 115960508, 111370241, 192283114, 842, "SRX19634451", "SRS17003621", null, null, "Oncology/Hematology, Boston Children's Hospital", 1, 0.88418, null, 0.1452, null, 0.78173, null, 0.48617, null, 61, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2023-03-10", "Larval", "Larval", "Tail", "Multi-system"], [74462, "SRR23802571", "SRX19634451", "SRS17003621", "SRP426621", "PRJNA943252", "Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail]", "GSE227118", "Other", "We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized  filtered  and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.", "parent bioproject:PRJNA510836", null, null, "Whole tail  72 hpf", "GSM7091920", null, "source name:transgenic zebrafish embryos wild type|tissue:Whole tail|developmental stage:72 hpf", "Whole tail  72 hpf", "the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode", "transgenic zebrafish embryos wild type", "No treatments", "Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", "Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were bisected on the axial plane towards the caudal end of the yolk extension  tail tissues were then homogenized  filtered  and viable cells sorted using live dead staining FACS into PBS  collecting at least 25 000 cells.", "tissue:Whole tail|developmental stage:72 hpf", "GSM7091920", "GSM7091920: Whole tail  72 hpf; Danio rerio; RNA Seq", "GSM7091920 r1", "GSM7091920", "1", "Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP426621", null, null, "EH_Tails_Single_Cell_GAGACGGA_L003.fastq.sorted.fastq.gz", "fastq", 683131915.0, 11477240.0, "GSM7091920 r3", "0:59.52", "A:196805573;C:134822600;G:129142852;T:222358115;N:2775", 59, null, null, null, 196805573, 134822600, 129142852, 222358115, 2775, "SRX19634451", "SRS17003621", null, null, "Oncology/Hematology, Boston Children's Hospital", 1, 0.88169, null, 0.14457, null, 0.78054, null, 0.49459, null, 61, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2023-03-10", "Larval", "Larval", "Tail", "Multi-system"], [74463, "SRR23802572", "SRX19634451", "SRS17003621", "SRP426621", "PRJNA943252", "Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail]", "GSE227118", "Other", "We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized  filtered  and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.", "parent bioproject:PRJNA510836", null, null, "Whole tail  72 hpf", "GSM7091920", null, "source name:transgenic zebrafish embryos wild type|tissue:Whole tail|developmental stage:72 hpf", "Whole tail  72 hpf", "the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode", "transgenic zebrafish embryos wild type", "No treatments", "Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", "Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were bisected on the axial plane towards the caudal end of the yolk extension  tail tissues were then homogenized  filtered  and viable cells sorted using live dead staining FACS into PBS  collecting at least 25 000 cells.", "tissue:Whole tail|developmental stage:72 hpf", "GSM7091920", "GSM7091920: Whole tail  72 hpf; Danio rerio; RNA Seq", "GSM7091920 r1", "GSM7091920", "1", "Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP426621", null, null, "EH_Tails_Single_Cell_GAGACGGA_L004.fastq.sorted.fastq.gz", "fastq", 584432554.0, 9840065.0, "GSM7091920 r4", "0:59.39", "A:168684456;C:114891950;G:110562368;T:190292465;N:1315", 59, null, null, null, 168684456, 114891950, 110562368, 190292465, 1315, "SRX19634451", "SRS17003621", null, null, "Oncology/Hematology, Boston Children's Hospital", 1, 0.88266, null, 0.14397, null, 0.78001, null, 0.49223, null, 61, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2023-03-10", "Larval", "Larval", "Tail", "Multi-system"], [75092, "SRR24239717", "SRX20035842", "SRS17374857", "SRP433739", "PRJNA958104", "The secreted neuronal signal Spock1 regulates the blood brain barrier", "GSE230236", "Transcriptome Analysis", "The blood brain barrier BBB is a unique set of properties of the brain vasculature which severely restricts its permeability to proteins and small molecules. Classic chick quail chimera studies showed that these properties are not intrinsic to the brain vasculature but rather are induced by surrounding neural tissue. Here we identify Spock1 as a candidate neuronal signal for regulating BBB permeability in zebrafish and mice. Mosaic genetic analysis shows that neuronally expressed Spock1 is cell non autonomously required for a functional BBB. Leakage in spock1 mutants is associated with altered extracellular matrix ECM  increased endothelial transcytosis  and altered pericyte endothelial interactions. Furthermore  a single dose of recombinant SPOCK1  into spock1 mutants quenches gelatinase activity  restores vascular expression of BBB genes including mcamb   and partially restores barrier function. These analyses support a model in which neuronally secreted Spock1 induces BBB properties by altering the ECM  thereby regulating pericyte endothelial interactions and downstream vascular gene expression. Overall design: Bulk RNAseq Libraries 66 71 of leaky mutant and wild type siblings to identify the genetic lesion responsible for the leaky phenotype. These analyses revealed linkage to chr14  and more specifically to the spock1 gene. scRNAseq Library scDRBrain of dissected spock1 mutant and wild type brains was then used to identify all cell type specific changes in gene expression in the mutant background.", null, "pubmed:37437574", null, "scRNA seq for WT and hm41 larval heads  3 and 5dpf", "GSM7208220", null, "tissue:mixed|cell type:mixed|genotype:mixed|time:3 dpf  5 dpf|geo loc name:missing|collection date:missing", "scRNA seq for WT and hm41 larval heads  3 and 5dpf", "Sequencing reads were mapped to the Zebrafish GRCz11 R101 genome assembly using a custom python pipeline as previously described see Zilionis et al.  Nature Protocols 2017 and https://github.com/indrops/. Multi seq hashtags were identified using custom code available at: https://github.com/AllonKleinLab/klunctions/tree/master/Ignas/Hashing. We first removed background cell barcodes by only considering transcriptomes with greater than 350 UMIs for downstream analysis. In order to remove dead cells  transcriptomes were further filtered by mitochondrial read percentage >20%. Cell demultiplexing was performed by manual inspection. Specifically  thresholds were drawn to delineate single cells from background and multiplet populations. The resulting counts matrix was normalized to the mean UMIs per cell in the dataset. Assembly: GRCz11 Supplementary files format and content: The gene counts matrix is an output from rsem differential gene expression analysis and is a raw counts estimate   not normalized for each gene. The first column is gene name and then post that each column represents an individual sample WT for the first 3 and then MUT for the last 3. Supplementary files format and content: The h5ad file contains the counts matrix for the demultiplexed single cell data. This file also holds relevant genotype and timepoint annotations as well as Multi seq barcode counts for each cell.", "mixed", null, "Dissected brain tissues were dissociated using a modified protocol adapted from Bresciani et. al. 2018 PMID: 30364607. Briefly  chemical dissociations were performed at 30.5\u00b0C using a mixture of 0.25% Trypsin EDTA  Collagenase/Dispase 8 mg/mL and DNaseI 20 \u00b5g/mL for 15 20 minutes with gentle pipetting every 2.5 minutes. The dissociations were quenched using DMEM + 10% fetal bovine serum and filtered through a 40 \u00b5M cell strainer. The dissociation mixtures were spun down twice at 700g for 5 min and washed with PBS. The mixtures were then resuspended in PBS and barcoded using Multi seq as described in McGinnis et. al. 2019 PMID: 31209384 with slight modifications. For each sample  80 pmoles of Lipid modified oligos LMOs were used to hash every 500k cells. The hashing reaction was quenched using PBS + 1% BSA. The barcoded samples were pooled into a single tube and washed twice with PBS + 1% BSA 700g for 5 min.. The pooled cell mixture was resuspended in PBS + 0.1%BSA + 18% Optiprep at a final concentration of 300k cells/mL prior to single cell capture with inDrops. Single cell transcriptomes were captured by the Single cell Core SCC at the Harvard Medical School as previously described Zilionis et al.  Nature Protocols 2017 using the inDrops V3 chemistry. The Single cell Core at the Harvard Medical School prepared the gene expression inDrops v3 chemistry and Multi seq libraries.", null, "cell type:mixed|genotype:mixed|time:3 dpf  5 dpf", "GSM7208220", "GSM7208220: scRNA seq for WT and hm41 larval heads  3 and 5dpf; Danio rerio; RNA Seq", "GSM7208220 r1", "GSM7208220", "1", "Dissected brain tissues were dissociated using a modified protocol adapted from Bresciani et. al. 2018 PMID: 30364607. Briefly  chemical dissociations were performed at 30.5\u00b0C using a mixture of 0.25% Trypsin EDTA  Collagenase/Dispase 8 mg/mL and DNaseI 20 \u00b5g/mL for 15 20 minutes with gentle pipetting every 2.5 minutes. The dissociations were quenched using DMEM + 10% fetal bovine serum and filtered through a 40 \u00b5M cell strainer. The dissociation mixtures were spun down twice at 700g for 5 min and washed with PBS. The mixtures were then resuspended in PBS and barcoded using Multi seq as described in McGinnis et. al. 2019 PMID: 31209384 with slight modifications. For each sample  80 pmoles of Lipid modified oligos LMOs were used to hash every 500k cells. The hashing reaction was quenched using PBS + 1% BSA. The barcoded samples were pooled into a single tube and washed twice with PBS + 1% BSA 700g for 5 min.. The pooled cell mixture was resuspended in PBS + 0.1%BSA + 18% Optiprep at a final concentration of 300k cells/mL prior to single cell capture with inDrops. Single cell transcriptomes were captured by the Single cell Core SCC at the Harvard Medical School as previously described Zilionis et al.  Nature Protocols 2017 using the inDrops V3 chemistry. The Single cell Core at the Harvard Medical School prepared the gene expression inDrops v3 chemistry and Multi seq libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP433739", null, "loader:fastq load.py|options:  readTypes=BTBT   read1PairFiles=Undetermined S0 L001 R1 001.fastq.gz   read2PairFiles=Undetermined S0 L001 R2 001.fastq.gz   read3PairFiles=Undetermined S0 L001 R3 001.fastq.gz   read4PairFiles=Undetermined S0 L001 R4 001.fastq.gz", null, null, 548653863228.0, 4729774683.0, "GSM7208220 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX20035842", "SRS17374857", "SRA1728506", "Megason Lab, Systems Biology, Harvard Medical School", "Megason Lab, Systems Biology, Harvard Medical School", 2, 0.83589, 0.0, 0.23127, 0.0, 0.7723, 1.0, 0.46689, null, 86, 8, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", 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