metadata: run_metadata: 12 rows where experiment.platform = "ILLUMINA", technology = "celseq" and tissue

12 rows where experiment.platform = "ILLUMINA", technology = "celseq" and tissue_curation = "Cancer or Tumor"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	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.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
71397	71397	SRR21571181	SRX17573445	SRS15113179	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593	TIE:EGFP MCR:MCS Tumor 2 GFP+ #3	GSM6580971	source name:MCR:MCS Melanoma\|tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:MCS Tumor 2 GFP+ #3	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:MCS Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+	GSM6580971	GSM6580971: TIE:EGFP MCR:MCS Tumor 2 GFP+ #3; Danio rerio; RNA Seq	GSM6580971 r1	GSM6580971	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130	HAR-HN-s014.R1.fastq.gz HAR-HN-s014.R2.fastq.gz	fastq fastq	2393526200.0	27831700.0	GSM6580971 r1	0:26 1:60	A:587629810;C:436040251;G:440163052;T:929430783;N:262304	26	60	587629810	436040251	440163052	929430783	262304	SRX17573445	SRS15113179	Oncology/Hematology, Boston Children's Hospital	2	0.1102	0.89036	0.10359	0.25006	0.99285	0.81172	0.56209	0.58312	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71398	71398	SRR21571182	SRX17573444	SRS15113178	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593	TIE:EGFP MCR:MCS Tumor 2 GFP /mCherry+	GSM6580970	source name:MCR:MCS Melanoma\|tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP /mCherry+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:MCS Tumor 2 GFP /mCherry+	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:MCS Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP /mCherry+	GSM6580970	GSM6580970: TIE:EGFP MCR:MCS Tumor 2 GFP /mCherry+; Danio rerio; RNA Seq	GSM6580970 r1	GSM6580970	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130	HAR-HN-s013.R1.fastq.gz HAR-HN-s013.R2.fastq.gz	fastq fastq	2799404318.0	32551213.0	GSM6580970 r1	0:26 1:60	A:674562015;C:518279489;G:507732521;T:1093251404;N:5578889	26	60	674562015	518279489	507732521	1093251404	5578889	SRX17573444	SRS15113178	Oncology/Hematology, Boston Children's Hospital	2	0.11385	0.89818	0.10608	0.24805	0.99162	0.80519	0.57833	0.58452	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71399	71399	SRR21571183	SRX17573443	SRS15113177	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593	TIE:EGFP MCR:MCS Tumor 2 GFP+ #2	GSM6580969	source name:MCR:MCS Melanoma\|tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:MCS Tumor 2 GFP+ #2	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:MCS Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+	GSM6580969	GSM6580969: TIE:EGFP MCR:MCS Tumor 2 GFP+ #2; Danio rerio; RNA Seq	GSM6580969 r1	GSM6580969	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130	HAR-HN-s012.R1.fastq.gz HAR-HN-s012.R2.fastq.gz	fastq fastq	2643515042.0	30738547.0	GSM6580969 r1	0:26 1:60	A:644064543;C:487933120;G:466421088;T:1039827853;N:5268438	26	60	644064543	487933120	466421088	1039827853	5268438	SRX17573443	SRS15113177	Oncology/Hematology, Boston Children's Hospital	2	0.11114	0.8924	0.10417	0.25808	0.99151	0.80499	0.60121	0.567	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71400	71400	SRR21571184	SRX17573442	SRS15113176	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593	TIE:EGFP MCR:MCS Tumor 2 GFP+ #1	GSM6580968	source name:MCR:MCS Melanoma\|tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:MCS Tumor 2 GFP+ #1	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:MCS Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+	GSM6580968	GSM6580968: TIE:EGFP MCR:MCS Tumor 2 GFP+ #1; Danio rerio; RNA Seq	GSM6580968 r1	GSM6580968	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130	HAR-HN-s011.R1.fastq.gz HAR-HN-s011.R2.fastq.gz	fastq fastq	2701784858.0	31416103.0	GSM6580968 r1	0:26 1:60	A:654129800;C:498352764;G:495215316;T:1048678271;N:5408707	26	60	654129800	498352764	495215316	1048678271	5408707	SRX17573442	SRS15113176	Oncology/Hematology, Boston Children's Hospital	2	0.10435	0.89555	0.0971	0.26327	0.99354	0.80647	0.56789	0.50648	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71401	71401	SRR21571185	SRX17573441	SRS15113175	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593	TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #3	GSM6580967	source name:MCR:SATB2 Melanoma\|tissue:MCR:SATB2 Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #3	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:SATB2 Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:SATB2 Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+	GSM6580967	GSM6580967: TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #3; Danio rerio; RNA Seq	GSM6580967 r1	GSM6580967	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130	HAR-HN-s007.R1.fastq.gz HAR-HN-s007.R2.fastq.gz	fastq fastq	3169503770.0	36854695.0	GSM6580967 r1	0:26 1:60	A:758395203;C:580012810;G:565741250;T:1265023729;N:330778	26	60	758395203	580012810	565741250	1265023729	330778	SRX17573441	SRS15113175	Oncology/Hematology, Boston Children's Hospital	2	0.11903	0.89395	0.11159	0.29218	0.99243	0.79705	0.54327	0.56983	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71402	71402	SRR21571186	SRX17573440	SRS15113174	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593	TIE:EGFP MCR:SATB2 Tumor 1 GFP /mCherry+	GSM6580966	source name:MCR:SATB2 Melanoma\|tissue:MCR:SATB2 Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP /mCherry+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:SATB2 Tumor 1 GFP /mCherry+	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:SATB2 Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:SATB2 Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP /mCherry+	GSM6580966	GSM6580966: TIE:EGFP MCR:SATB2 Tumor 1 GFP /mCherry+; Danio rerio; RNA Seq	GSM6580966 r1	GSM6580966	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130	HAR-HN-s006.R1.fastq.gz HAR-HN-s006.R2.fastq.gz	fastq fastq	3401223030.0	39549105.0	GSM6580966 r1	0:26 1:60	A:811721089;C:634467013;G:610447766;T:1344233621;N:353541	26	60	811721089	634467013	610447766	1344233621	353541	SRX17573440	SRS15113174	Oncology/Hematology, Boston Children's Hospital	2	0.11728	0.9042	0.11084	0.22711	0.9931	0.79494	0.65306	0.56756	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71403	71403	SRR21571187	SRX17573439	SRS15113173	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593	TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #2	GSM6580965	source name:MCR:SATB2 Melanoma\|tissue:MCR:SATB2 Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #2	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:SATB2 Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:SATB2 Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+	GSM6580965	GSM6580965: TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #2; Danio rerio; RNA Seq	GSM6580965 r1	GSM6580965	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130	HAR-HN-s005.R1.fastq.gz HAR-HN-s005.R2.fastq.gz	fastq fastq	3042431718.0	35377113.0	GSM6580965 r1	0:26 1:60	A:744782141;C:565144430;G:541953297;T:1190237432;N:314418	26	60	744782141	565144430	541953297	1190237432	314418	SRX17573439	SRS15113173	Oncology/Hematology, Boston Children's Hospital	2	0.11149	0.88671	0.10471	0.23988	0.99162	0.79543	0.64395	0.58192	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71404	71404	SRR21571188	SRX17573438	SRS15113172	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593	TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #1	GSM6580964	source name:MCR:SATB2 Melanoma\|tissue:MCR:SATB2 Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #1	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:SATB2 Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:SATB2 Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+	GSM6580964	GSM6580964: TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #1; Danio rerio; RNA Seq	GSM6580964 r1	GSM6580964	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130	HAR-HN-s004.R1.fastq.gz HAR-HN-s004.R2.fastq.gz	fastq fastq	3454727328.0	40171248.0	GSM6580964 r1	0:26 1:60	A:823342460;C:630914117;G:615200919;T:1384911330;N:358502	26	60	823342460	630914117	615200919	1384911330	358502	SRX17573438	SRS15113172	Oncology/Hematology, Boston Children's Hospital	2	0.12493	0.8892	0.11706	0.21947	0.99314	0.79216	0.73215	0.53614	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71405	71405	SRR21571189	SRX17573437	SRS15113171	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593	TIE:EGFP MCR:MCS Tumor 1 GFP+ #3	GSM6580963	source name:MCR:MCS Melanoma\|tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:MCS Tumor 1 GFP+ #3	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:MCS Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+	GSM6580963	GSM6580963: TIE:EGFP MCR:MCS Tumor 1 GFP+ #3; Danio rerio; RNA Seq	GSM6580963 r1	GSM6580963	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130	HAR-SW-s016.R1.fastq.gz HAR-SW-s016.R2.fastq.gz	fastq fastq	2986527160.0	34727060.0	GSM6580963 r1	0:26 1:60	A:741435297;C:548375629;G:534147329;T:1162130158;N:438747	26	60	741435297	548375629	534147329	1162130158	438747	SRX17573437	SRS15113171	Oncology/Hematology, Boston Children's Hospital	2	0.12032	0.87963	0.11182	0.30887	0.99145	0.79926	0.53199	0.59453	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71406	71406	SRR21571190	SRX17573436	SRS15113170	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593	TIE:EGFP MCR:MCS Tumor 1 mCherry+;GFP	GSM6580962	source name:MCR:MCS Melanoma\|tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:mCherry+;GFP \|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:MCS Tumor 1 mCherry+;GFP	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:MCS Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:mCherry+;GFP	GSM6580962	GSM6580962: TIE:EGFP MCR:MCS Tumor 1 mCherry+;GFP ; Danio rerio; RNA Seq	GSM6580962 r1	GSM6580962	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130	HAR-SW-s015.R1.fastq.gz HAR-SW-s015.R2.fastq.gz	fastq fastq	2668318990.0	31026965.0	GSM6580962 r1	0:26 1:60	A:650521761;C:486885070;G:465311971;T:1065210518;N:389670	26	60	650521761	486885070	465311971	1065210518	389670	SRX17573436	SRS15113170	Oncology/Hematology, Boston Children's Hospital	2	0.1142	0.88526	0.10718	0.34648	0.99198	0.80428	0.56024	0.56437	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71407	71407	SRR21571191	SRX17573435	SRS15113168	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593	TIE:EGFP MCR:MCS Tumor 1 GFP+ #2	GSM6580961	source name:MCR:MCS Melanoma\|tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:MCS Tumor 1 GFP+ #2	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:MCS Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+	GSM6580961	GSM6580961: TIE:EGFP MCR:MCS Tumor 1 GFP+ #2; Danio rerio; RNA Seq	GSM6580961 r1	GSM6580961	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130	HAR-SW-s014.R1.fastq.gz HAR-SW-s014.R2.fastq.gz	fastq fastq	2393946138.0	27836583.0	GSM6580961 r1	0:26 1:60	A:596410784;C:437801560;G:418907527;T:940499589;N:326678	26	60	596410784	437801560	418907527	940499589	326678	SRX17573435	SRS15113168	Oncology/Hematology, Boston Children's Hospital	2	0.12342	0.85959	0.11689	0.34528	0.98965	0.80472	0.49199	0.56661	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71408	71408	SRR21571192	SRX17573434	SRS15113169	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593	TIE:EGFP MCR:MCS Tumor 1 GFP+ #1	GSM6580960	source name:MCR:MCS Melanoma\|tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:MCS Tumor 1 GFP+ #1	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:MCS Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+	GSM6580960	GSM6580960: TIE:EGFP MCR:MCS Tumor 1 GFP+ #1; Danio rerio; RNA Seq	GSM6580960 r1	GSM6580960	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130	HAR-SW-s013.R1.fastq.gz HAR-SW-s013.R2.fastq.gz	fastq fastq	3043161084.0	35385594.0	GSM6580960 r1	0:26 1:60	A:750431276;C:555809857;G:537628053;T:1198847837;N:444061	26	60	750431276	555809857	537628053	1198847837	444061	SRX17573434	SRS15113169	Oncology/Hematology, Boston Children's Hospital	2	0.11034	0.86528	0.10371	0.32665	0.99198	0.79695	0.51927	0.58318	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor

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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");;