run_metadata
35 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "indrops" and tissue_curation_coarse = "Multi-system"
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| Link | 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 |
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| 32781 | 32781 | SRR29411985 | SRX24925451 | SRS21630866 | SRP513930 | PRJNA1124008 | Cell state transitions are decoupled from cell division during early embryo development [II] | GSE269848 | Other | Paper abstract: As tissues develop cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. However in the absence of cell division differentiation slows down in some cell types and cells exhibit global stress responses. While differentiation is robust to blocking cell division the proportions of cells across cell states are not but show evidence of partial compensation. This work clarifies our understanding of the role of cell division in development and showcases the utility of combining embryo wide perturbations with single cell RNA sequencing to uncover the role of common biological processes across multiple tissues. Overall design: Design of experiment for this particular dataset: Forty tails from zebrafish embryos at 24 38 hpf and 48 hpf were collected. Cells were dissociated from these tails and multi seq tags were added to the cells for each time point. Cells from all time points were pooled and single cell sequencing was performed using Indrops. Four gene expression GEX libraries were prepared for transcriptomic information and four multiseq tag libraries TAG were prepared for reading out the multiseq tags. We provide the raw data .fastq files processed data both raw counts.tsv.gz and filtered by total UMI counts filtered.h5ad files and the entire filtered data post removing doublets as all data.h5ad. We also provide counts for multi seq tags example TAG 1.counts.csv. Information about pooling libraries and library indices is provided in Pooling Samples.xlsx. Only 24 hpf data was used for Kukreja et. al. 2024 and hence the cell state informa… | pubmed:37546736 | 24 38 hpf and 48 hpf tails | GSM8328864 | source name:embryo tail|tissue:embryo tail|geo loc name:missing|collection date:missing | 24 38 hpf and 48 hpf tails | Reads were mapped onto the Zebrafish genome as described in Kukreja et al. 2024 manuscript. Multi seq barcodes for each sample were identified using a custom pipeline available here: https://github.com/AllonKleinLab/klunctions/. Barcode abundance was used to manually remove multiplet populations as well as assign cells to their appropriate sample. Data from only 24 hpf tails were used for the manuscript. We provide 8 FASTQ files 2 lanes x 4 reads per lane. The read files from an inDrops run have the following content: * R1 001.fastq.gz : contains the three prime UTR cDNA read * R2 001.fastq.gz : contains the first half of the cell barcode * R3 001.fastq.gz : contains the library index for demultiplexing libraries * R4 001.fastq.gz : contains the second half of the barcode and the UMI. All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis github.com/indrops. Single cell transcriptomes were barcoded using inDrops Klein et al Cell 2015. Standard transcriptome RNA seq libraries were processed as reported in Zilionis et al. Nature Protocol 2016 using inDrops v3 protocol. The transcriptome libraries were sequenced on reads Illumina NextSeq 500. Libraries used standard Illumina sequencing primers and 61 cycles for Read1 14 cycles for Read2 8 cycles each for IndexRead1 and IndexRead2. Raw fastq files was processed using inDrops.py pipeline github.com/indrops/indrops. Sequenced reads were mapped to a zebrafish reference transcriptome built from the zebrafish GRCz10 genome assembly Assembly Accession: GCF 000002035.5 using bowtie version 1.1.143. To obtain the final counts matrix used for data analysis total count filters were applied as described in Kukreja et. al. 2024 method section "Single cell RNA seq Data preprocessing" Assembly: GRCz10 genome assembly Assembly Accession: GCF 000002035.5 Supplementary files format and content: Raw counts for transcriptome tsv.gz: cell barcode gene names and raw counts for all cells Supplementary f… | embryo tail | Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20µg/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit. | tissue:embryo tail | GSM8328864 | GSM8328864: 24 38 hpf and 48 hpf tails; Danio rerio; OTHER | GSM8328864 r1 | GSM8328864 | 1 | Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20µg/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit. | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP513930 | Undetermined_S0_L002_R1_001.fastq.gz Undetermined_S0_L002_R2_001.fastq.gz Undetermined_S0_L002_R3_001.fastq.gz Undetermined_S0_L002_R4_001.fastq.gz | fastq fastq fastq fastq | 58603546956.0 | 505202991.0 | GSM8328864 r1 | 0:86 1:8 2:8 3:14 | A:13191204330;C:9162028793;G:9431065581;T:11662090182;N:1068340 | 86 | 8 | 8 | 14 | 13191204330 | 9162028793 | 9431065581 | 11662090182 | 1068340 | SRX24925451 | SRS21630866 | SRA1899240 | Harvard University | Harvard University | B | usable mapping rate | illumina | novaseq_era | unknown | other | trueseq | sc | single_cell_droplet | indrops | United States | 2024-06-14 | Multi-stage | Embryo | Tail | Multi-system | ||||||||||||||||||||||
| 32782 | 32782 | SRR29411986 | SRX24925451 | SRS21630866 | SRP513930 | PRJNA1124008 | Cell state transitions are decoupled from cell division during early embryo development [II] | GSE269848 | Other | Paper abstract: As tissues develop cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. However in the absence of cell division differentiation slows down in some cell types and cells exhibit global stress responses. While differentiation is robust to blocking cell division the proportions of cells across cell states are not but show evidence of partial compensation. This work clarifies our understanding of the role of cell division in development and showcases the utility of combining embryo wide perturbations with single cell RNA sequencing to uncover the role of common biological processes across multiple tissues. Overall design: Design of experiment for this particular dataset: Forty tails from zebrafish embryos at 24 38 hpf and 48 hpf were collected. Cells were dissociated from these tails and multi seq tags were added to the cells for each time point. Cells from all time points were pooled and single cell sequencing was performed using Indrops. Four gene expression GEX libraries were prepared for transcriptomic information and four multiseq tag libraries TAG were prepared for reading out the multiseq tags. We provide the raw data .fastq files processed data both raw counts.tsv.gz and filtered by total UMI counts filtered.h5ad files and the entire filtered data post removing doublets as all data.h5ad. We also provide counts for multi seq tags example TAG 1.counts.csv. Information about pooling libraries and library indices is provided in Pooling Samples.xlsx. Only 24 hpf data was used for Kukreja et. al. 2024 and hence the cell state informa… | pubmed:37546736 | 24 38 hpf and 48 hpf tails | GSM8328864 | source name:embryo tail|tissue:embryo tail|geo loc name:missing|collection date:missing | 24 38 hpf and 48 hpf tails | Reads were mapped onto the Zebrafish genome as described in Kukreja et al. 2024 manuscript. Multi seq barcodes for each sample were identified using a custom pipeline available here: https://github.com/AllonKleinLab/klunctions/. Barcode abundance was used to manually remove multiplet populations as well as assign cells to their appropriate sample. Data from only 24 hpf tails were used for the manuscript. We provide 8 FASTQ files 2 lanes x 4 reads per lane. The read files from an inDrops run have the following content: * R1 001.fastq.gz : contains the three prime UTR cDNA read * R2 001.fastq.gz : contains the first half of the cell barcode * R3 001.fastq.gz : contains the library index for demultiplexing libraries * R4 001.fastq.gz : contains the second half of the barcode and the UMI. All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis github.com/indrops. Single cell transcriptomes were barcoded using inDrops Klein et al Cell 2015. Standard transcriptome RNA seq libraries were processed as reported in Zilionis et al. Nature Protocol 2016 using inDrops v3 protocol. The transcriptome libraries were sequenced on reads Illumina NextSeq 500. Libraries used standard Illumina sequencing primers and 61 cycles for Read1 14 cycles for Read2 8 cycles each for IndexRead1 and IndexRead2. Raw fastq files was processed using inDrops.py pipeline github.com/indrops/indrops. Sequenced reads were mapped to a zebrafish reference transcriptome built from the zebrafish GRCz10 genome assembly Assembly Accession: GCF 000002035.5 using bowtie version 1.1.143. To obtain the final counts matrix used for data analysis total count filters were applied as described in Kukreja et. al. 2024 method section "Single cell RNA seq Data preprocessing" Assembly: GRCz10 genome assembly Assembly Accession: GCF 000002035.5 Supplementary files format and content: Raw counts for transcriptome tsv.gz: cell barcode gene names and raw counts for all cells Supplementary f… | embryo tail | Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20µg/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit. | tissue:embryo tail | GSM8328864 | GSM8328864: 24 38 hpf and 48 hpf tails; Danio rerio; OTHER | GSM8328864 r1 | GSM8328864 | 1 | Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20µg/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit. | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP513930 | Undetermined_S0_L001_R1_001.fastq.gz Undetermined_S0_L001_R2_001.fastq.gz Undetermined_S0_L001_R3_001.fastq.gz Undetermined_S0_L001_R4_001.fastq.gz | fastq fastq fastq fastq | 44072422880.0 | 379934680.0 | GSM8328864 r2 | 0:86 1:8 2:8 3:14 | A:9919784228;C:6894965731;G:7094749745;T:8764100624;N:782152 | 86 | 8 | 8 | 14 | 9919784228 | 6894965731 | 7094749745 | 8764100624 | 782152 | SRX24925451 | SRS21630866 | SRA1899240 | Harvard University | Harvard University | B | usable mapping rate | illumina | novaseq_era | unknown | other | trueseq | sc | single_cell_droplet | indrops | United States | 2024-06-14 | Multi-stage | Embryo | Tail | Multi-system | ||||||||||||||||||||||
| 65304 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;