metadata: run_metadata: 34 rows where technology = "indrops", tissue_curation = "Multi-tissue" and tissue_curation

34 rows where technology = "indrops", tissue_curation = "Multi-tissue" and tissue_curation_coarse = "Multi-system"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	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.study_ref	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.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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
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
75092	75092	SRR24239717	SRX20035842	SRS17374857	SRP433739	PRJNA958104	The secreted neuronal signal Spock1 regulates the blood brain barrier	GSE230236	Transcriptome Analysis	The blood brain barrier BBB is a unique set of properties of the brain vasculature which severely restricts its permeability to proteins and small molecules. Classic chick quail chimera studies showed that these properties are not intrinsic to the brain vasculature but rather are induced by surrounding neural tissue. Here we identify Spock1 as a candidate neuronal signal for regulating BBB permeability in zebrafish and mice. Mosaic genetic analysis shows that neuronally expressed Spock1 is cell non autonomously required for a functional BBB. Leakage in spock1 mutants is associated with altered extracellular matrix ECM increased endothelial transcytosis and altered pericyte endothelial interactions. Furthermore a single dose of recombinant SPOCK1 into spock1 mutants quenches gelatinase activity restores vascular expression of BBB genes including mcamb and partially restores barrier function. These analyses support a model in which neuronally secreted Spock1 induces BBB properties by altering the ECM thereby regulating pericyte endothelial interactions and downstream vascular gene expression. Overall design: Bulk RNAseq Libraries 66 71 of leaky mutant and wild type siblings to identify the genetic lesion responsible for the leaky phenotype. These analyses revealed linkage to chr14 and more specifically to the spock1 gene. scRNAseq Library scDRBrain of dissected spock1 mutant and wild type brains was then used to identify all cell type specific changes in gene expression in the mutant background.	pubmed:37437574	scRNA seq for WT and hm41 larval heads 3 and 5dpf	GSM7208220	tissue:mixed\|cell type:mixed\|genotype:mixed\|time:3 dpf 5 dpf\|geo loc name:missing\|collection date:missing	scRNA seq for WT and hm41 larval heads 3 and 5dpf	Sequencing reads were mapped to the Zebrafish GRCz11 R101 genome assembly using a custom python pipeline as previously described see Zilionis et al. Nature Protocols 2017 and https://github.com/indrops/. Multi seq hashtags were identified using custom code available at: https://github.com/AllonKleinLab/klunctions/tree/master/Ignas/Hashing. We first removed background cell barcodes by only considering transcriptomes with greater than 350 UMIs for downstream analysis. In order to remove dead cells transcriptomes were further filtered by mitochondrial read percentage >20%. Cell demultiplexing was performed by manual inspection. Specifically thresholds were drawn to delineate single cells from background and multiplet populations. The resulting counts matrix was normalized to the mean UMIs per cell in the dataset. Assembly: GRCz11 Supplementary files format and content: The gene counts matrix is an output from rsem differential gene expression analysis and is a raw counts estimate not normalized for each gene. The first column is gene name and then post that each column represents an individual sample WT for the first 3 and then MUT for the last 3. Supplementary files format and content: The h5ad file contains the counts matrix for the demultiplexed single cell data. This file also holds relevant genotype and timepoint annotations as well as Multi seq barcode counts for each cell.	mixed		Dissected brain tissues were dissociated using a modified protocol adapted from Bresciani et. al. 2018 PMID: 30364607. Briefly chemical dissociations were performed at 30.5°C using a mixture of 0.25% Trypsin EDTA Collagenase/Dispase 8 mg/mL and DNaseI 20 µg/mL for 15 20 minutes with gentle pipetting every 2.5 minutes. The dissociations were quenched using DMEM + 10% fetal bovine serum and filtered through a 40 µM cell strainer. The dissociation mixtures were spun down twice at 700g for 5 min and washed with PBS. The mixtures were then resuspended in PBS and barcoded using Multi seq as described in McGinnis et. al. 2019 PMID: 31209384 with slight modifications. For each sample 80 pmoles of Lipid modified oligos LMOs were used to hash every 500k cells. The hashing reaction was quenched using PBS + 1% BSA. The barcoded samples were pooled into a single tube and washed twice with PBS + 1% BSA 700g for 5 min.. The pooled cell mixture was resuspended in PBS + 0.1%BSA + 18% Optiprep at a final concentration of 300k cells/mL prior to single cell capture with inDrops. Single cell transcriptomes were captured by the Single cell Core SCC at the Harvard Medical School as previously described Zilionis et al. Nature Protocols 2017 using the inDrops V3 chemistry. The Single cell Core at the Harvard Medical School prepared the gene expression inDrops v3 chemistry and Multi seq libraries.		cell type:mixed\|genotype:mixed\|time:3 dpf 5 dpf	GSM7208220	GSM7208220: scRNA seq for WT and hm41 larval heads 3 and 5dpf; Danio rerio; RNA Seq	GSM7208220 r1	GSM7208220	1	Dissected brain tissues were dissociated using a modified protocol adapted from Bresciani et. al. 2018 PMID: 30364607. Briefly chemical dissociations were performed at 30.5°C using a mixture of 0.25% Trypsin EDTA Collagenase/Dispase 8 mg/mL and DNaseI 20 µg/mL for 15 20 minutes with gentle pipetting every 2.5 minutes. The dissociations were quenched using DMEM + 10% fetal bovine serum and filtered through a 40 µM cell strainer. The dissociation mixtures were spun down twice at 700g for 5 min and washed with PBS. The mixtures were then resuspended in PBS and barcoded using Multi seq as described in McGinnis et. al. 2019 PMID: 31209384 with slight modifications. For each sample 80 pmoles of Lipid modified oligos LMOs were used to hash every 500k cells. The hashing reaction was quenched using PBS + 1% BSA. The barcoded samples were pooled into a single tube and washed twice with PBS + 1% BSA 700g for 5 min.. The pooled cell mixture was resuspended in PBS + 0.1%BSA + 18% Optiprep at a final concentration of 300k cells/mL prior to single cell capture with inDrops. Single cell transcriptomes were captured by the Single cell Core SCC at the Harvard Medical School as previously described Zilionis et al. Nature Protocols 2017 using the inDrops V3 chemistry. The Single cell Core at the Harvard Medical School prepared the gene expression inDrops v3 chemistry and Multi seq libraries.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP433739	loader:fastq load.py\|options: readTypes=BTBT read1PairFiles=Undetermined S0 L001 R1 001.fastq.gz read2PairFiles=Undetermined S0 L001 R2 001.fastq.gz read3PairFiles=Undetermined S0 L001 R3 001.fastq.gz read4PairFiles=Undetermined S0 L001 R4 001.fastq.gz			548653863228.0	4729774683.0	GSM7208220 r1									SRX20035842	SRS17374857	SRA1728506	Megason Lab, Systems Biology, Harvard Medical School	Megason Lab, Systems Biology, Harvard Medical School	2	0.83589	0.0	0.23127	0.0	0.7723	1.0	0.46689	86	8	B	T	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2023-04-21	Larval	Larval	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");;