rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
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,,pubmed:34415995,,rag2∆/∆  il2rga /  zebrafish kidney marrow animal 3,GSM5416999,,source name:rag2∆/∆  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,rag2∆/∆  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∆/∆  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∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,GSM5416999,GSM5416999: rag2∆/∆  il2rga /  zebrafish kidney marrow animal 3; Danio rerio; RNA Seq,GSM5416999,,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,,SRP326822,,,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,,,,453086964,337301672,300857192,449622475,8503,SRX11347516,SRS9393434,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.80729,,0.07332,,0.82055,,0.60511,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,rag2∆/∆  il2rga /  zebrafish kidney marrow animal 3,GSM5416999,,source name:rag2∆/∆  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,rag2∆/∆  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∆/∆  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∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,GSM5416999,GSM5416999: rag2∆/∆  il2rga /  zebrafish kidney marrow animal 3; Danio rerio; RNA Seq,GSM5416999,,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,,SRP326822,,,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,,,,430310565,320135615,286001024,428308829,5354,SRX11347516,SRS9393434,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.80697,,0.07529,,0.81921,,0.60121,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,rag2∆/∆  il2rga /  zebrafish kidney marrow animal 3,GSM5416999,,source name:rag2∆/∆  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,rag2∆/∆  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∆/∆  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∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,GSM5416999,GSM5416999: rag2∆/∆  il2rga /  zebrafish kidney marrow animal 3; Danio rerio; RNA Seq,GSM5416999,,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,,SRP326822,,,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,,,,457962961,341679675,304164183,455257776,7095,SRX11347516,SRS9393434,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.80662,,0.07406,,0.82154,,0.56588,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,rag2∆/∆  il2rga /  zebrafish kidney marrow animal 3,GSM5416999,,source name:rag2∆/∆  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,rag2∆/∆  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∆/∆  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∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,GSM5416999,GSM5416999: rag2∆/∆  il2rga /  zebrafish kidney marrow animal 3; Danio rerio; RNA Seq,GSM5416999,,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,,SRP326822,,,rag2il2rga_rep3_run1_TACTCCTT_L004.fastq.sorted.fastq.gz,fastq,1513369748.0,25736846.0,GSM5416999 r4,0:58.80,A:444596274;C:330932558;G:295084021;T:442751574;N:5321,58,,,,444596274,330932558,295084021,442751574,5321,SRX11347516,SRS9393434,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.80787,,0.07297,,0.8201,,0.58363,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
65308,SRR15036079,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,,pubmed:34415995,,rag2∆/∆  il2rga /  zebrafish kidney marrow animal 2,GSM5416998,,source name:rag2∆/∆  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,rag2∆/∆  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∆/∆  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∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,GSM5416998,GSM5416998: rag2∆/∆  il2rga /  zebrafish kidney marrow animal 2; Danio rerio; RNA Seq,GSM5416998,,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,,SRP326822,,,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,,,,348615404,279444276,237318155,333180819,8110,SRX11347515,SRS9393433,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.78095,,0.05246,,0.83422,,0.60686,,60,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,rag2∆/∆  il2rga /  zebrafish kidney marrow animal 2,GSM5416998,,source name:rag2∆/∆  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,rag2∆/∆  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∆/∆  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∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,GSM5416998,GSM5416998: rag2∆/∆  il2rga /  zebrafish kidney marrow animal 2; Danio rerio; RNA Seq,GSM5416998,,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,,SRP326822,,,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,,,,334924475,266975981,228180514,320550327,10709,SRX11347515,SRS9393433,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.78751,,0.05418,,0.83471,,0.61606,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,rag2∆/∆  il2rga /  zebrafish kidney marrow animal 2,GSM5416998,,source name:rag2∆/∆  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,rag2∆/∆  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∆/∆  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∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,GSM5416998,GSM5416998: rag2∆/∆  il2rga /  zebrafish kidney marrow animal 2; Danio rerio; RNA Seq,GSM5416998,,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,,SRP326822,,,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,,,,356526291,284995125,242763299,340516650,3168,SRX11347515,SRS9393433,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.78411,,0.05285,,0.83447,,0.56902,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,rag2∆/∆  il2rga /  zebrafish kidney marrow animal 2,GSM5416998,,source name:rag2∆/∆  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,rag2∆/∆  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∆/∆  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∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,GSM5416998,GSM5416998: rag2∆/∆  il2rga /  zebrafish kidney marrow animal 2; Danio rerio; RNA Seq,GSM5416998,,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,,SRP326822,,,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,,,,345040424,274431327,234489457,329861445,6779,SRX11347515,SRS9393433,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.78584,,0.05337,,0.83457,,0.61081,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,rag2∆/∆  il2rga /  zebrafish kidney marrow animal 1,GSM5416997,,source name:rag2∆/∆  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,rag2∆/∆  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∆/∆  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∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,GSM5416997,GSM5416997: rag2∆/∆  il2rga /  zebrafish kidney marrow animal 1; Danio rerio; RNA Seq,GSM5416997,,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,,SRP326822,,,rag2il2rga_rep1_run1_CTCCTTAC_L001.fastq.sorted.fastq.gz,fastq,1216292553.0,22857043.0,GSM5416997 r1,0:53.21,A:382329028;C:252281093;G:217421522;T:364256278;N:4632,53,,,,382329028,252281093,217421522,364256278,4632,SRX11347514,SRS9393432,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.75098,,0.0683,,0.84159,,0.58318,,60,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
65313,SRR15036077,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,,pubmed:34415995,,rag2∆/∆  il2rga /  zebrafish kidney marrow animal 1,GSM5416997,,source name:rag2∆/∆  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,rag2∆/∆  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∆/∆  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∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,GSM5416997,GSM5416997: rag2∆/∆  il2rga /  zebrafish kidney marrow animal 1; Danio rerio; RNA Seq,GSM5416997,,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,,SRP326822,,,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,,,,384419718,254006293,219689014,366669699,4085,SRX11347514,SRS9393432,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.75456,,0.06946,,0.84082,,0.58125,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,rag2∆/∆  il2rga /  zebrafish kidney marrow animal 1,GSM5416997,,source name:rag2∆/∆  il2rga /  zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,rag2∆/∆  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∆/∆  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∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta}  il2rga / ,GSM5416997,GSM5416997: rag2∆/∆  il2rga /  zebrafish kidney marrow animal 1; Danio rerio; RNA Seq,GSM5416997,,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,,SRP326822,,,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,,,,364837636,239223801,207638568,349212231,450,SRX11347514,SRS9393432,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.75964,,0.07051,,0.84122,,0.59786,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
65315,SRR15036072,SRX11347513,SRS9393431,SRP326822,PRJNA743561,Single cell imaging of T cell immunotherapy responses in vivo,GSE179401,Transcriptome Analysis,T cell immunotherapies have revolutionized treatment for a subset of cancers. Yet  a major hurdle has been the lack of facile and predicative preclinical animal models that permit dynamic visualization of T cell immune responses at single cell resolution in vivo. Here  optically clear immunocompromised zebrafish were engrafted with fluorescent labelled human cancers along with chimeric antigen receptor T CAR T cells  bispecific T cell engagers BiTEs  and antibody peptide epitope conjugates APECs  allowing real time single cell visualization of T cell based immunotherapies in vivo. This work uncovered important differences in the kinetics of T cell infiltration  tumor cell engagement and killing between these immunotherapies and established early endpoint analysis to predict therapy responses. We also established EGFR targeted immunotherapies as a powerful approach to kill rhabdomyosarcoma muscle cancers  providing strong preclinical rationale for assessing a wider array of T cell immunotherapies in this disease. Overall design: Blood Lineage analysis of zebrafish kidney marrow samples from WT  rag2?/? and rag2?/?  il2rga /  immunocompromised zebrafish,,pubmed:34415995,,rag2∆/∆ zebrafish kidney marrow animal 3,GSM5416996,,source name:rag2∆/∆ zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},rag2∆/∆ zebrafish kidney marrow animal 3,bcl2fastq2 v2.17.1 was used to convert BCL into FASTQ indrops pipeline https://github.com/indrops/indrops was used to demultiplex  align  sort and quantify the gene expression of barcoded cells. indrops sort output fastq.gz was uploaded Seurat was used for downstream analysis the preprocessing and analysis script is at https://github.com/qinqian/zebrafish indrop/. Genome build: GRCz10 Supplementary files format and content: indrop..counts.tsv.gz,rag2∆/∆ zebrafish kidney marrow,Extracted kidney marrow are dissociated into single cell suspension and subjected to indrop single cell sequencing,Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,WT  rag2∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},GSM5416996,GSM5416996: rag2∆/∆ zebrafish kidney marrow animal 3; Danio rerio; RNA Seq,GSM5416996,,1,Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5416996,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP326822,,,rag2_rep3_run1_ATTAGACG_L001.fastq.sorted.fastq.gz,fastq,2222304640.0,37787809.0,GSM5416996 r1,0:58.81,A:645345287;C:476804005;G:443148112;T:656994972;N:12264,58,,,,645345287,476804005,443148112,656994972,12264,SRX11347513,SRS9393431,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.84762,,0.09206,,0.81253,,0.56514,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,rag2∆/∆ zebrafish kidney marrow animal 3,GSM5416996,,source name:rag2∆/∆ zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},rag2∆/∆ zebrafish kidney marrow animal 3,bcl2fastq2 v2.17.1 was used to convert BCL into FASTQ indrops pipeline https://github.com/indrops/indrops was used to demultiplex  align  sort and quantify the gene expression of barcoded cells. indrops sort output fastq.gz was uploaded Seurat was used for downstream analysis the preprocessing and analysis script is at https://github.com/qinqian/zebrafish indrop/. Genome build: GRCz10 Supplementary files format and content: indrop..counts.tsv.gz,rag2∆/∆ zebrafish kidney marrow,Extracted kidney marrow are dissociated into single cell suspension and subjected to indrop single cell sequencing,Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,WT  rag2∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},GSM5416996,GSM5416996: rag2∆/∆ zebrafish kidney marrow animal 3; Danio rerio; RNA Seq,GSM5416996,,1,Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5416996,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP326822,,,rag2_rep3_run1_ATTAGACG_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,,,,611831337,451383668,420138423,624296408,7952,SRX11347513,SRS9393431,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.84465,,0.09069,,0.81207,,0.56951,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,rag2∆/∆ zebrafish kidney marrow animal 3,GSM5416996,,source name:rag2∆/∆ zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},rag2∆/∆ zebrafish kidney marrow animal 3,bcl2fastq2 v2.17.1 was used to convert BCL into FASTQ indrops pipeline https://github.com/indrops/indrops was used to demultiplex  align  sort and quantify the gene expression of barcoded cells. indrops sort output fastq.gz was uploaded Seurat was used for downstream analysis the preprocessing and analysis script is at https://github.com/qinqian/zebrafish indrop/. Genome build: GRCz10 Supplementary files format and content: indrop..counts.tsv.gz,rag2∆/∆ zebrafish kidney marrow,Extracted kidney marrow are dissociated into single cell suspension and subjected to indrop single cell sequencing,Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,WT  rag2∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},GSM5416996,GSM5416996: rag2∆/∆ zebrafish kidney marrow animal 3; Danio rerio; RNA Seq,GSM5416996,,1,Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5416996,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP326822,,,rag2_rep3_run1_ATTAGACG_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,,,,651287231,482208798,447299624,663990887,10592,SRX11347513,SRS9393431,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.84552,,0.09016,,0.81349,,0.56434,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,rag2∆/∆ zebrafish kidney marrow animal 3,GSM5416996,,source name:rag2∆/∆ zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},rag2∆/∆ zebrafish kidney marrow animal 3,bcl2fastq2 v2.17.1 was used to convert BCL into FASTQ indrops pipeline https://github.com/indrops/indrops was used to demultiplex  align  sort and quantify the gene expression of barcoded cells. indrops sort output fastq.gz was uploaded Seurat was used for downstream analysis the preprocessing and analysis script is at https://github.com/qinqian/zebrafish indrop/. Genome build: GRCz10 Supplementary files format and content: indrop..counts.tsv.gz,rag2∆/∆ zebrafish kidney marrow,Extracted kidney marrow are dissociated into single cell suspension and subjected to indrop single cell sequencing,Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,WT  rag2∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},GSM5416996,GSM5416996: rag2∆/∆ zebrafish kidney marrow animal 3; Danio rerio; RNA Seq,GSM5416996,,1,Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5416996,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP326822,,,rag2_rep3_run1_ATTAGACG_L004.fastq.sorted.fastq.gz,fastq,2176269239.0,37003554.0,GSM5416996 r4,0:58.81,A:631449563;C:466453544;G:433190878;T:645167515;N:7739,58,,,,631449563,466453544,433190878,645167515,7739,SRX11347513,SRS9393431,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.8492,,0.09208,,0.81148,,0.5629,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
65319,SRR15036068,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,,pubmed:34415995,,rag2∆/∆ zebrafish kidney marrow animal 2,GSM5416995,,source name:rag2∆/∆ zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},rag2∆/∆ 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∆/∆ zebrafish kidney marrow,Extracted kidney marrow are dissociated into single cell suspension and subjected to indrop single cell sequencing,Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,WT  rag2∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},GSM5416995,GSM5416995: rag2∆/∆ zebrafish kidney marrow animal 2; Danio rerio; RNA Seq,GSM5416995,,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,,SRP326822,,,rag2_rep2_run1_AGAGGATA_L001.fastq.sorted.fastq.gz,fastq,1787890700.0,30173901.0,GSM5416995 r1,0:59.25,A:509355118;C:429984789;G:333941302;T:514597320;N:12171,59,,,,509355118,429984789,333941302,514597320,12171,SRX11347512,SRS9393430,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.80781,,0.09019,,0.83124,,0.56519,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
65320,SRR15036069,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,,pubmed:34415995,,rag2∆/∆ zebrafish kidney marrow animal 2,GSM5416995,,source name:rag2∆/∆ zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},rag2∆/∆ 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∆/∆ zebrafish kidney marrow,Extracted kidney marrow are dissociated into single cell suspension and subjected to indrop single cell sequencing,Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,WT  rag2∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},GSM5416995,GSM5416995: rag2∆/∆ zebrafish kidney marrow animal 2; Danio rerio; RNA Seq,GSM5416995,,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,,SRP326822,,,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,,,,490612069,411469635,321613090,496571770,15554,SRX11347512,SRS9393430,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.81467,,0.08996,,0.82879,,0.5598,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,rag2∆/∆ zebrafish kidney marrow animal 2,GSM5416995,,source name:rag2∆/∆ zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},rag2∆/∆ 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∆/∆ zebrafish kidney marrow,Extracted kidney marrow are dissociated into single cell suspension and subjected to indrop single cell sequencing,Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,WT  rag2∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},GSM5416995,GSM5416995: rag2∆/∆ zebrafish kidney marrow animal 2; Danio rerio; RNA Seq,GSM5416995,,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,,SRP326822,,,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,,,,518979591,436620699,340176627,523898644,4636,SRX11347512,SRS9393430,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.81176,,0.08863,,0.82929,,0.57421,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,rag2∆/∆ zebrafish kidney marrow animal 2,GSM5416995,,source name:rag2∆/∆ zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},rag2∆/∆ 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∆/∆ zebrafish kidney marrow,Extracted kidney marrow are dissociated into single cell suspension and subjected to indrop single cell sequencing,Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,WT  rag2∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},GSM5416995,GSM5416995: rag2∆/∆ zebrafish kidney marrow animal 2; Danio rerio; RNA Seq,GSM5416995,,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,,SRP326822,,,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,,,,503631253,421409855,329457720,509057252,9957,SRX11347512,SRS9393430,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.81558,,0.08928,,0.82804,,0.57087,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,rag2∆/∆ zebrafish kidney marrow animal 1,GSM5416994,,source name:rag2∆/∆ zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},rag2∆/∆ 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∆/∆ zebrafish kidney marrow,Extracted kidney marrow are dissociated into single cell suspension and subjected to indrop single cell sequencing,Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,WT  rag2∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},GSM5416994,GSM5416994: rag2∆/∆ zebrafish kidney marrow animal 1; Danio rerio; RNA Seq,GSM5416994,,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,,SRP326822,,,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,,,,218468551,153721094,124232493,202701592,2736,SRX11347511,SRS9393429,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.68917,,0.06168,,0.85117,,0.58413,,25,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,rag2∆/∆ zebrafish kidney marrow animal 1,GSM5416994,,source name:rag2∆/∆ zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},rag2∆/∆ 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∆/∆ zebrafish kidney marrow,Extracted kidney marrow are dissociated into single cell suspension and subjected to indrop single cell sequencing,Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,WT  rag2∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},GSM5416994,GSM5416994: rag2∆/∆ zebrafish kidney marrow animal 1; Danio rerio; RNA Seq,GSM5416994,,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,,SRP326822,,,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,,,,217845323,152574316,124291442,202315510,2381,SRX11347511,SRS9393429,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.69486,,0.06113,,0.85251,,0.59868,,60,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,rag2∆/∆ zebrafish kidney marrow animal 1,GSM5416994,,source name:rag2∆/∆ zebrafish kidney marrow|tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},rag2∆/∆ 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∆/∆ zebrafish kidney marrow,Extracted kidney marrow are dissociated into single cell suspension and subjected to indrop single cell sequencing,Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,WT  rag2∆/∆ and rag2∆/∆  il2rga /  immunocompromised zebrafish are sacrificed at approximately 2 mpf and kidney marrow extracted,tissue:Kidney marrow|cell type:Immune cells|genotype:rag2{delta}/{delta},GSM5416994,GSM5416994: rag2∆/∆ zebrafish kidney marrow animal 1; Danio rerio; RNA Seq,GSM5416994,,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,,SRP326822,,,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,,,,205055005,141133606,116472911,190854009,237,SRX11347511,SRS9393429,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.70594,,0.06468,,0.84999,,0.5849,,34,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,WT zebrafish kidney marrow sample animal 3,GSM5416993,,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∆/∆ and rag2∆/∆  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,,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,,SRP326822,,,WT_rep3_run1_CTAGTCGA_L001.fastq.sorted.fastq.gz,fastq,2565659927.0,43645467.0,GSM5416993 r1,0:58.78,A:737566316;C:530070129;G:506698325;T:791311406;N:13751,58,,,,737566316,530070129,506698325,791311406,13751,SRX11347510,SRS9393426,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.84682,,0.10799,,0.81288,,0.52286,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
65327,SRR15036062,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,,pubmed:34415995,,WT zebrafish kidney marrow sample animal 3,GSM5416993,,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∆/∆ and rag2∆/∆  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,,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,,SRP326822,,,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,,,,698209332,500659631,479258250,751121127,8820,SRX11347510,SRS9393426,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.84518,,0.10802,,0.8127,,0.51482,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,WT zebrafish kidney marrow sample animal 3,GSM5416993,,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∆/∆ and rag2∆/∆  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,,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,,SRP326822,,,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,,,,742309784,534972384,510339526,797838293,11603,SRX11347510,SRS9393426,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.8468,,0.10719,,0.81235,,0.52285,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,WT zebrafish kidney marrow sample animal 3,GSM5416993,,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∆/∆ and rag2∆/∆  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,,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,,SRP326822,,,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,,,,714440946,513072299,490202831,769509072,8583,SRX11347510,SRS9393426,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.8486,,0.10677,,0.81314,,0.52091,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,WT zebrafish kidney marrow sample animal 2,GSM5416992,,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∆/∆ and rag2∆/∆  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,,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,,SRP326822,,,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,,,,314483956,239809718,209071648,323576758,7122,SRX11347509,SRS9393428,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.79795,,0.09375,,0.82522,,0.53498,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,WT zebrafish kidney marrow sample animal 2,GSM5416992,,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∆/∆ and rag2∆/∆  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,,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,,SRP326822,,,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,,,,301061458,228573966,200110423,310422293,9226,SRX11347509,SRS9393428,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.80252,,0.09472,,0.82708,,0.5189,,60,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,WT zebrafish kidney marrow sample animal 2,GSM5416992,,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∆/∆ and rag2∆/∆  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,,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,,SRP326822,,,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,,,,317535237,241516822,211153746,326502090,2699,SRX11347509,SRS9393428,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.80081,,0.09244,,0.82483,,0.54017,,61,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,WT zebrafish kidney marrow sample animal 2,GSM5416992,,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∆/∆ and rag2∆/∆  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,,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,,SRP326822,,,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,,,,309536619,234533609,205451194,318783671,5822,SRX11347509,SRS9393428,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.80118,,0.09406,,0.82729,,0.53232,,17,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,WT zebrafish kidney marrow sample animal 1,GSM5416991,,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∆/∆ and rag2∆/∆  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,,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,,SRP326822,,,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,,,,161358086,115991861,100428415,157987333,2077,SRX11347508,SRS9393427,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.74319,,0.07334,,0.83272,,0.54608,,18,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,WT zebrafish kidney marrow sample animal 1,GSM5416991,,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∆/∆ and rag2∆/∆  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,,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,,SRP326822,,,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,,,,164424405,118548162,103014421,161237932,1854,SRX11347508,SRS9393427,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.74711,,0.07271,,0.83276,,0.55026,,23,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system
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,,pubmed:34415995,,WT zebrafish kidney marrow sample animal 1,GSM5416991,,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∆/∆ and rag2∆/∆  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,,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,,SRP326822,,,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,,,,151361206,107584405,94289485,148934301,192,SRX11347508,SRS9393427,SRA1254398,GEO,"Langenau Lab, Molecular Pathology Unit, Massachusetts General Hospital",1,0.7521,,0.07485,,0.83112,,0.54925,,60,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,sc,single_cell_droplet,indrops,,United States,2021-07-03,Juvenile,Juvenile,Multi-tissue,Multi-system