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23 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "10x" and tissue_curation_coarse = "Cancer or Tumor"

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  • Cancer or Tumor · 23 ✖

tissue_curation 1

technology 1

  • 10x · 23 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 23 ✖

experiment.library_selection 1

experiment.library_layout 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
61554 61554 SRR14804251 SRX11137027 SRS9200152 SRP287858 PRJNA670235 Spatially resolved transcriptomics reveals the architecture of the tumor microenvironment interface GSE159709 Transcriptome Analysis Cancer cells interact with a wide variety of other cell types but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single cell RNA seq scRNA seq has helped define these TME cell types it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here we integrate spatial transcriptomics with scRNA seq to define the architecture and nature of nascent tumor and surrounding microenvironment cells as they come into contact through the process of invasion. Using a well defined transgenic zebrafish model of BRAFV600E driven melanoma we identify a transcriptionally unique “interface” cluster localized at the boundary between tumor cells and surrounding tissues. Using an unbiased data driven approach we identify spatially patterned gene modules specific to the interface and show that the interface is a distinct transcriptional entity that histologically resembles the microenvironment but transcriptionally resembles the tumor. By complementing ST with scRNA seq we demonstrate that the interface is composed of specialized tumor and microenvironment cells. Both cell types in the interface upregulate a common set of cilia genes and we find enrichment of cilia proteins only where the tumor meets the TME. Cilia gene expression is regulated by ETS family transcription factors which normally act to suppress their expression outside of this region. This unique ETS driven interface transcriptional state is conserved across ten different human patient samples suggesting this is a conserved feature of human melanoma. Taken together our results demonstrate the power of spatial and single cell transcriptomics techniques in uncovering novel biological mechanisms that drive tumor invasion into new tissues. Overall design: Spatial transcriptomics Visium platform of zebrafish bearing BRAF V600E driven melanomas. Single cell RNA seq 10X Genomics v3 of two such zebrafish. Single nucleus RNA seq 10X Genomics v3 of three suc…   pubmed:34725363   Nuc seq GSM5380072   tissue:Zebrafish melanomas BRAF V600E|sample type:Single nucleus suspension Nuc seq Illumina RTA v2 software was used for basecalling and quality determination. The 10x Genomics three prime v3 raw FASTQ data was processed using 10X Genomics proprietary CellRanger v5.0.1 pipeline. Genome build: GRCz10.88 Supplementary files format and content: For 10x Genomics three prime GEX v3 data: output of CellRanger pipeline including gene expression matrix features and barcodes. Zebrafish melanomas BRAF V600E   Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. The tissue was then ground in a Dounce homogenizer on ice in Nuclei EZ Prep Lysis Buffer Sigma Aldrich #NUC101. The nuclear suspension was then spun down at 4°C 500g 5 min. post resuspending the pellet in 1 mL wash buffer 250 mM sucrose 50 mM citric acid 1% BSA 20 mM DTT 0.2U/µL RNAse inhibitor the sample was again spun at 4°C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4°C to isolate individual nuclei using a BD FACSAria III cell sorter BD Biosciences. Approximately equal numbers of GFP+ tumor and GFP microenvironment nuclei were collected. Equal numbers of sorted GFP+ tumor and GFP microenvironment nuclei were centrifuged at 600g for 5 minutes at 4°C. Droplet based snRNA seq was performed using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 12 000 nuclei were encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions.    sample type:Single nucleus suspension GSM5380072 GSM5380072: Nuc seq; Danio rerio; RNA Seq GSM5380072   1 Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. The tissue was then ground in a Dounce homogenizer on ice in Nuclei EZ Prep Lysis Buffer Sigma Aldrich #NUC101. The nuclear suspension was then spun down at 4°C 500g 5 min. post resuspending the pellet in 1 mL wash buffer 250 mM sucrose 50 mM citric acid 1% BSA 20 mM DTT 0.2U/µL RNAse inhibitor the sample was again spun at 4°C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4°C to isolate individual nuclei using a BD FACSAria III cell sorter BD Biosciences. Approximately equal numbers of GFP+ tumor and GFP microenvironment nuclei were collected. Equal numbers of sorted GFP+ tumor and GFP microenvironment nuclei were centrifuged at 600g for 5 minutes at 4°C. Droplet based snRNA seq was performed using the Chromium Single Cell three prime Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 12 000 nuclei were encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. GEO Accession:GSM5380072 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP287858     2498_Zebrafish_IGO_11175_B_17_S16_L001_R1_001.fastq-001.gz 2498_Zebrafish_IGO_11175_B_17_S16_L001_R2_001.fastq-003.gz fastq fastq 16881438541.0 139516021.0 GSM5380072 r1 0:29 1:92 A:4751346944;C:3672149977;G:3866179079;T:4591370192;N:392349 29 92     4751346944 3672149977 3866179079 4591370192 392349 SRX11137027 SRS9200152 SRA1145723 GEO Memorial Sloan Kettering Cancer Center 2 0.0064 0.82934 0.00273 0.1289 0.99462 0.75615 0.43651 0.54303 29 92 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-06-14 Adult Adult Cancer or Tumor Cancer or Tumor
61555 61555 SRR14804252 SRX11137027 SRS9200152 SRP287858 PRJNA670235 Spatially resolved transcriptomics reveals the architecture of the tumor microenvironment interface GSE159709 Transcriptome Analysis Cancer cells interact with a wide variety of other cell types but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single cell RNA seq scRNA seq has helped define these TME cell types it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here we integrate spatial transcriptomics with scRNA seq to define the architecture and nature of nascent tumor and surrounding microenvironment cells as they come into contact through the process of invasion. Using a well defined transgenic zebrafish model of BRAFV600E driven melanoma we identify a transcriptionally unique “interface” cluster localized at the boundary between tumor cells and surrounding tissues. Using an unbiased data driven approach we identify spatially patterned gene modules specific to the interface and show that the interface is a distinct transcriptional entity that histologically resembles the microenvironment but transcriptionally resembles the tumor. By complementing ST with scRNA seq we demonstrate that the interface is composed of specialized tumor and microenvironment cells. Both cell types in the interface upregulate a common set of cilia genes and we find enrichment of cilia proteins only where the tumor meets the TME. Cilia gene expression is regulated by ETS family transcription factors which normally act to suppress their expression outside of this region. This unique ETS driven interface transcriptional state is conserved across ten different human patient samples suggesting this is a conserved feature of human melanoma. Taken together our results demonstrate the power of spatial and single cell transcriptomics techniques in uncovering novel biological mechanisms that drive tumor invasion into new tissues. Overall design: Spatial transcriptomics Visium platform of zebrafish bearing BRAF V600E driven melanomas. Single cell RNA seq 10X Genomics v3 of two such zebrafish. Single nucleus RNA seq 10X Genomics v3 of three suc…   pubmed:34725363   Nuc seq GSM5380072   tissue:Zebrafish melanomas BRAF V600E|sample type:Single nucleus suspension Nuc seq Illumina RTA v2 software was used for basecalling and quality determination. The 10x Genomics three prime v3 raw FASTQ data was processed using 10X Genomics proprietary CellRanger v5.0.1 pipeline. Genome build: GRCz10.88 Supplementary files format and content: For 10x Genomics three prime GEX v3 data: output of CellRanger pipeline including gene expression matrix features and barcodes. Zebrafish melanomas BRAF V600E   Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. The tissue was then ground in a Dounce homogenizer on ice in Nuclei EZ Prep Lysis Buffer Sigma Aldrich #NUC101. The nuclear suspension was then spun down at 4°C 500g 5 min. post resuspending the pellet in 1 mL wash buffer 250 mM sucrose 50 mM citric acid 1% BSA 20 mM DTT 0.2U/µL RNAse inhibitor the sample was again spun at 4°C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4°C to isolate individual nuclei using a BD FACSAria III cell sorter BD Biosciences. Approximately equal numbers of GFP+ tumor and GFP microenvironment nuclei were collected. Equal numbers of sorted GFP+ tumor and GFP microenvironment nuclei were centrifuged at 600g for 5 minutes at 4°C. Droplet based snRNA seq was performed using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 12 000 nuclei were encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions.    sample type:Single nucleus suspension GSM5380072 GSM5380072: Nuc seq; Danio rerio; RNA Seq GSM5380072   1 Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. The tissue was then ground in a Dounce homogenizer on ice in Nuclei EZ Prep Lysis Buffer Sigma Aldrich #NUC101. The nuclear suspension was then spun down at 4°C 500g 5 min. post resuspending the pellet in 1 mL wash buffer 250 mM sucrose 50 mM citric acid 1% BSA 20 mM DTT 0.2U/µL RNAse inhibitor the sample was again spun at 4°C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4°C to isolate individual nuclei using a BD FACSAria III cell sorter BD Biosciences. Approximately equal numbers of GFP+ tumor and GFP microenvironment nuclei were collected. Equal numbers of sorted GFP+ tumor and GFP microenvironment nuclei were centrifuged at 600g for 5 minutes at 4°C. Droplet based snRNA seq was performed using the Chromium Single Cell three prime Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 12 000 nuclei were encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. GEO Accession:GSM5380072 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP287858     2498_Zebrafish_IGO_11175_B_17_S16_L002_R1_001.fastq-002.gz 2498_Zebrafish_IGO_11175_B_17_S16_L002_R2_001.fastq-004.gz fastq fastq 16950408541.0 140086021.0 GSM5380072 r2 0:29 1:92 A:4767053400;C:3688816562;G:3885746735;T:4608355293;N:436551 29 92     4767053400 3688816562 3885746735 4608355293 436551 SRX11137027 SRS9200152 SRA1145723 GEO Memorial Sloan Kettering Cancer Center 2 0.00657 0.8291 0.00269 0.12832 0.9946 0.75657 0.45883 0.54175 29 92 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-06-14 Adult Adult Cancer or Tumor Cancer or Tumor
61556 61556 SRR14804253 SRX11137027 SRS9200152 SRP287858 PRJNA670235 Spatially resolved transcriptomics reveals the architecture of the tumor microenvironment interface GSE159709 Transcriptome Analysis Cancer cells interact with a wide variety of other cell types but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single cell RNA seq scRNA seq has helped define these TME cell types it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here we integrate spatial transcriptomics with scRNA seq to define the architecture and nature of nascent tumor and surrounding microenvironment cells as they come into contact through the process of invasion. Using a well defined transgenic zebrafish model of BRAFV600E driven melanoma we identify a transcriptionally unique “interface” cluster localized at the boundary between tumor cells and surrounding tissues. Using an unbiased data driven approach we identify spatially patterned gene modules specific to the interface and show that the interface is a distinct transcriptional entity that histologically resembles the microenvironment but transcriptionally resembles the tumor. By complementing ST with scRNA seq we demonstrate that the interface is composed of specialized tumor and microenvironment cells. Both cell types in the interface upregulate a common set of cilia genes and we find enrichment of cilia proteins only where the tumor meets the TME. Cilia gene expression is regulated by ETS family transcription factors which normally act to suppress their expression outside of this region. This unique ETS driven interface transcriptional state is conserved across ten different human patient samples suggesting this is a conserved feature of human melanoma. Taken together our results demonstrate the power of spatial and single cell transcriptomics techniques in uncovering novel biological mechanisms that drive tumor invasion into new tissues. Overall design: Spatial transcriptomics Visium platform of zebrafish bearing BRAF V600E driven melanomas. Single cell RNA seq 10X Genomics v3 of two such zebrafish. Single nucleus RNA seq 10X Genomics v3 of three suc…   pubmed:34725363   Nuc seq GSM5380072   tissue:Zebrafish melanomas BRAF V600E|sample type:Single nucleus suspension Nuc seq Illumina RTA v2 software was used for basecalling and quality determination. The 10x Genomics three prime v3 raw FASTQ data was processed using 10X Genomics proprietary CellRanger v5.0.1 pipeline. Genome build: GRCz10.88 Supplementary files format and content: For 10x Genomics three prime GEX v3 data: output of CellRanger pipeline including gene expression matrix features and barcodes. Zebrafish melanomas BRAF V600E   Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. The tissue was then ground in a Dounce homogenizer on ice in Nuclei EZ Prep Lysis Buffer Sigma Aldrich #NUC101. The nuclear suspension was then spun down at 4°C 500g 5 min. post resuspending the pellet in 1 mL wash buffer 250 mM sucrose 50 mM citric acid 1% BSA 20 mM DTT 0.2U/µL RNAse inhibitor the sample was again spun at 4°C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4°C to isolate individual nuclei using a BD FACSAria III cell sorter BD Biosciences. Approximately equal numbers of GFP+ tumor and GFP microenvironment nuclei were collected. Equal numbers of sorted GFP+ tumor and GFP microenvironment nuclei were centrifuged at 600g for 5 minutes at 4°C. Droplet based snRNA seq was performed using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 12 000 nuclei were encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions.    sample type:Single nucleus suspension GSM5380072 GSM5380072: Nuc seq; Danio rerio; RNA Seq GSM5380072   1 Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. The tissue was then ground in a Dounce homogenizer on ice in Nuclei EZ Prep Lysis Buffer Sigma Aldrich #NUC101. The nuclear suspension was then spun down at 4°C 500g 5 min. post resuspending the pellet in 1 mL wash buffer 250 mM sucrose 50 mM citric acid 1% BSA 20 mM DTT 0.2U/µL RNAse inhibitor the sample was again spun at 4°C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4°C to isolate individual nuclei using a BD FACSAria III cell sorter BD Biosciences. Approximately equal numbers of GFP+ tumor and GFP microenvironment nuclei were collected. Equal numbers of sorted GFP+ tumor and GFP microenvironment nuclei were centrifuged at 600g for 5 minutes at 4°C. Droplet based snRNA seq was performed using the Chromium Single Cell three prime Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 12 000 nuclei were encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. GEO Accession:GSM5380072 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP287858     2498_Zebrafish_HTO_IGO_11175_B_18_S18_L001_R1_001.fastq.gz 2498_Zebrafish_HTO_IGO_11175_B_18_S18_L001_R2_001.fastq-004.gz fastq fastq 6220719747.0 51410907.0 GSM5380072 r3 0:29 1:92 A:3158621534;C:796885709;G:1264774949;T:1000285734;N:151821 29 92     3158621534 796885709 1264774949 1000285734 151821 SRX11137027 SRS9200152 SRA1145723 GEO Memorial Sloan Kettering Cancer Center 2 0.00012 0.14112 9e-05 0.135 0.99993 0.99953 0.33333 0.55555 29 92 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-06-14 Adult Adult Cancer or Tumor Cancer or Tumor
61557 61557 SRR14804254 SRX11137027 SRS9200152 SRP287858 PRJNA670235 Spatially resolved transcriptomics reveals the architecture of the tumor microenvironment interface GSE159709 Transcriptome Analysis Cancer cells interact with a wide variety of other cell types but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single cell RNA seq scRNA seq has helped define these TME cell types it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here we integrate spatial transcriptomics with scRNA seq to define the architecture and nature of nascent tumor and surrounding microenvironment cells as they come into contact through the process of invasion. Using a well defined transgenic zebrafish model of BRAFV600E driven melanoma we identify a transcriptionally unique “interface” cluster localized at the boundary between tumor cells and surrounding tissues. Using an unbiased data driven approach we identify spatially patterned gene modules specific to the interface and show that the interface is a distinct transcriptional entity that histologically resembles the microenvironment but transcriptionally resembles the tumor. By complementing ST with scRNA seq we demonstrate that the interface is composed of specialized tumor and microenvironment cells. Both cell types in the interface upregulate a common set of cilia genes and we find enrichment of cilia proteins only where the tumor meets the TME. Cilia gene expression is regulated by ETS family transcription factors which normally act to suppress their expression outside of this region. This unique ETS driven interface transcriptional state is conserved across ten different human patient samples suggesting this is a conserved feature of human melanoma. Taken together our results demonstrate the power of spatial and single cell transcriptomics techniques in uncovering novel biological mechanisms that drive tumor invasion into new tissues. Overall design: Spatial transcriptomics Visium platform of zebrafish bearing BRAF V600E driven melanomas. Single cell RNA seq 10X Genomics v3 of two such zebrafish. Single nucleus RNA seq 10X Genomics v3 of three suc…   pubmed:34725363   Nuc seq GSM5380072   tissue:Zebrafish melanomas BRAF V600E|sample type:Single nucleus suspension Nuc seq Illumina RTA v2 software was used for basecalling and quality determination. The 10x Genomics three prime v3 raw FASTQ data was processed using 10X Genomics proprietary CellRanger v5.0.1 pipeline. Genome build: GRCz10.88 Supplementary files format and content: For 10x Genomics three prime GEX v3 data: output of CellRanger pipeline including gene expression matrix features and barcodes. Zebrafish melanomas BRAF V600E   Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. The tissue was then ground in a Dounce homogenizer on ice in Nuclei EZ Prep Lysis Buffer Sigma Aldrich #NUC101. The nuclear suspension was then spun down at 4°C 500g 5 min. post resuspending the pellet in 1 mL wash buffer 250 mM sucrose 50 mM citric acid 1% BSA 20 mM DTT 0.2U/µL RNAse inhibitor the sample was again spun at 4°C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4°C to isolate individual nuclei using a BD FACSAria III cell sorter BD Biosciences. Approximately equal numbers of GFP+ tumor and GFP microenvironment nuclei were collected. Equal numbers of sorted GFP+ tumor and GFP microenvironment nuclei were centrifuged at 600g for 5 minutes at 4°C. Droplet based snRNA seq was performed using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 12 000 nuclei were encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions.    sample type:Single nucleus suspension GSM5380072 GSM5380072: Nuc seq; Danio rerio; RNA Seq GSM5380072   1 Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. The tissue was then ground in a Dounce homogenizer on ice in Nuclei EZ Prep Lysis Buffer Sigma Aldrich #NUC101. The nuclear suspension was then spun down at 4°C 500g 5 min. post resuspending the pellet in 1 mL wash buffer 250 mM sucrose 50 mM citric acid 1% BSA 20 mM DTT 0.2U/µL RNAse inhibitor the sample was again spun at 4°C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4°C to isolate individual nuclei using a BD FACSAria III cell sorter BD Biosciences. Approximately equal numbers of GFP+ tumor and GFP microenvironment nuclei were collected. Equal numbers of sorted GFP+ tumor and GFP microenvironment nuclei were centrifuged at 600g for 5 minutes at 4°C. Droplet based snRNA seq was performed using the Chromium Single Cell three prime Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 12 000 nuclei were encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. GEO Accession:GSM5380072 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP287858     2498_Zebrafish_HTO_IGO_11175_B_18_S18_L002_R1_001.fastq.gz 2498_Zebrafish_HTO_IGO_11175_B_18_S18_L002_R2_001.fastq-003.gz fastq fastq 6140782307.0 50750267.0 GSM5380072 r4 0:29 1:92 A:3118957514;C:786290907;G:1248322710;T:987056069;N:155107 29 92     3118957514 786290907 1248322710 987056069 155107 SRX11137027 SRS9200152 SRA1145723 GEO Memorial Sloan Kettering Cancer Center 2 0.00011 0.13904 9e-05 0.13261 0.99995 0.99959 1.0 0.42857 29 92 T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-06-14 Adult Adult Cancer or Tumor Cancer or Tumor
61558 61558 SRR12851622 SRX9318589 SRS7543399 SRP287858 PRJNA670235 Spatially resolved transcriptomics reveals the architecture of the tumor microenvironment interface GSE159709 Transcriptome Analysis Cancer cells interact with a wide variety of other cell types but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single cell RNA seq scRNA seq has helped define these TME cell types it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here we integrate spatial transcriptomics with scRNA seq to define the architecture and nature of nascent tumor and surrounding microenvironment cells as they come into contact through the process of invasion. Using a well defined transgenic zebrafish model of BRAFV600E driven melanoma we identify a transcriptionally unique “interface” cluster localized at the boundary between tumor cells and surrounding tissues. Using an unbiased data driven approach we identify spatially patterned gene modules specific to the interface and show that the interface is a distinct transcriptional entity that histologically resembles the microenvironment but transcriptionally resembles the tumor. By complementing ST with scRNA seq we demonstrate that the interface is composed of specialized tumor and microenvironment cells. Both cell types in the interface upregulate a common set of cilia genes and we find enrichment of cilia proteins only where the tumor meets the TME. Cilia gene expression is regulated by ETS family transcription factors which normally act to suppress their expression outside of this region. This unique ETS driven interface transcriptional state is conserved across ten different human patient samples suggesting this is a conserved feature of human melanoma. Taken together our results demonstrate the power of spatial and single cell transcriptomics techniques in uncovering novel biological mechanisms that drive tumor invasion into new tissues. Overall design: Spatial transcriptomics Visium platform of zebrafish bearing BRAF V600E driven melanomas. Single cell RNA seq 10X Genomics v3 of two such zebrafish. Single nucleus RNA seq 10X Genomics v3 of three suc…   pubmed:34725363   SingleCell F GSM4838135   tissue:Zebrafish melanomas BRAF V600E|sample type:Single cell suspension SingleCell F Illumina RTA v2 software was used for basecalling and quality determination. The Visium raw FASTQ data was processed using 10X Genomics proprietary SpaceRanger v1.0.0 pipeline. The single cell RNA seq raw FASTQ data was processed using the 10X Genomics proprietary CellRanger v3.1.0 pipeline Genome build: GRCz10.88 Supplementary files format and content: For 10x Genomics spatial transcriptomic data: output of SpaceRanger pipeline including gene expression and spatial contents. For 10x Genomics single cell RNA Seq: output of CellRanger pipeline including gene expression features and barcodes. Zebrafish melanomas BRAF V600E   For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor bearing fish were euthanized on ice and washed in 1X PBS. post dissection of the head and tail the remaining tissue was equilibrated in cold OCT for 2 minutes before transfer to a tissue mold filled with fresh OCT for snap freezing in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C. For cryosectioning both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide Visium Spatial Gene Expression Slides 10X Genomics. ST slides containing sections were stored at 80°C for a maximum of one week before use. For single cell RNA seq using the 10X genomics 3’ GEX v3 platform: Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase Sigma Aldrich #5401020001 in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide bore P1000 followed by incubation for an additional 15 minutes at RT. post adding 500 uL FBS to stop the dissociation reaction samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS and cells were sorted at room temperature to remove debris and doublets using a BD FACSAria III cell sorter BD Biosciences. Equal numbers of GFP+ tumor and GFP macroenvironment cells were collected.  For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide 10X Genomics and all reagents were from the Visium Spatial Gene Expression Kit 10X Genomics. Briefly sections were fixed in chilled methanol for 30 min at 20°C stained with hematoxylin and eosin and mounted in…   sample type:Single cell suspension GSM4838135 GSM4838135: SingleCell F; Danio rerio; RNA Seq GSM4838135   1 For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor bearing fish were euthanized on ice and washed in 1X PBS. post dissection of the head and tail the remaining tissue was equilibrated in cold OCT for 2 minutes before transfer to a tissue mold filled with fresh OCT for snap freezing in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C. For cryosectioning both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide Visium Spatial Gene Expression Slides 10X Genomics. ST slides containing sections were stored at 80°C for a maximum of one week before use. For single cell RNA seq using the 10X genomics three prime GEX v3 platform: Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase Sigma Aldrich #5401020001 in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide bore P1000 followed by incubation for an additional 15 minutes at RT. post adding 500 uL FBS to stop the dissociation reaction samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS and cells were sorted at room temperature to remove debris and doublets using a BD FACSAria III cell sorter BD Biosciences. Equal numbers of GFP+ tumor and GFP macroenvironment cells were collected. For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide 10X Genomics and all reagents were from the Visium Spatial Gene Expression Kit 10X Genomics. Briefly sections were fixed in chilled methanol for 30 min at 20°C stained with hematoxylin and eosin and m… GEO Accession:GSM4838135 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP287858     10X_SingleCell_Sample_F_S1_L000_R1_001.fastq.gz 10X_SingleCell_Sample_F_S1_L000_R2_001.fastq.gz fastq fastq 44547263840.0 278420399.0 GSM4838135 r1 0:28 1:132 A:12810925700;C:9421837786;G:9930050611;T:12378989254;N:5460489 28 132     12810925700 9421837786 9930050611 12378989254 5460489 SRX9318589 SRS7543399 SRA1145723 GEO Memorial Sloan Kettering Cancer Center 2 0.00339 0.91854 0.00135 0.1624 0.99494 0.79744 0.35078 0.56648 28 132 T B sc-like readlen illumina nextseq unknown random_priming unknown sc single_cell_droplet 10x   United States 2020-10-20 Adult Adult Cancer or Tumor Cancer or Tumor
61559 61559 SRR12851621 SRX9318588 SRS7543398 SRP287858 PRJNA670235 Spatially resolved transcriptomics reveals the architecture of the tumor microenvironment interface GSE159709 Transcriptome Analysis Cancer cells interact with a wide variety of other cell types but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single cell RNA seq scRNA seq has helped define these TME cell types it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here we integrate spatial transcriptomics with scRNA seq to define the architecture and nature of nascent tumor and surrounding microenvironment cells as they come into contact through the process of invasion. Using a well defined transgenic zebrafish model of BRAFV600E driven melanoma we identify a transcriptionally unique “interface” cluster localized at the boundary between tumor cells and surrounding tissues. Using an unbiased data driven approach we identify spatially patterned gene modules specific to the interface and show that the interface is a distinct transcriptional entity that histologically resembles the microenvironment but transcriptionally resembles the tumor. By complementing ST with scRNA seq we demonstrate that the interface is composed of specialized tumor and microenvironment cells. Both cell types in the interface upregulate a common set of cilia genes and we find enrichment of cilia proteins only where the tumor meets the TME. Cilia gene expression is regulated by ETS family transcription factors which normally act to suppress their expression outside of this region. This unique ETS driven interface transcriptional state is conserved across ten different human patient samples suggesting this is a conserved feature of human melanoma. Taken together our results demonstrate the power of spatial and single cell transcriptomics techniques in uncovering novel biological mechanisms that drive tumor invasion into new tissues. Overall design: Spatial transcriptomics Visium platform of zebrafish bearing BRAF V600E driven melanomas. Single cell RNA seq 10X Genomics v3 of two such zebrafish. Single nucleus RNA seq 10X Genomics v3 of three suc…   pubmed:34725363   SingleCell E GSM4838134   tissue:Zebrafish melanomas BRAF V600E|sample type:Single cell suspension SingleCell E Illumina RTA v2 software was used for basecalling and quality determination. The Visium raw FASTQ data was processed using 10X Genomics proprietary SpaceRanger v1.0.0 pipeline. The single cell RNA seq raw FASTQ data was processed using the 10X Genomics proprietary CellRanger v3.1.0 pipeline Genome build: GRCz10.88 Supplementary files format and content: For 10x Genomics spatial transcriptomic data: output of SpaceRanger pipeline including gene expression and spatial contents. For 10x Genomics single cell RNA Seq: output of CellRanger pipeline including gene expression features and barcodes. Zebrafish melanomas BRAF V600E   For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor bearing fish were euthanized on ice and washed in 1X PBS. post dissection of the head and tail the remaining tissue was equilibrated in cold OCT for 2 minutes before transfer to a tissue mold filled with fresh OCT for snap freezing in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C. For cryosectioning both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide Visium Spatial Gene Expression Slides 10X Genomics. ST slides containing sections were stored at 80°C for a maximum of one week before use. For single cell RNA seq using the 10X genomics 3’ GEX v3 platform: Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase Sigma Aldrich #5401020001 in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide bore P1000 followed by incubation for an additional 15 minutes at RT. post adding 500 uL FBS to stop the dissociation reaction samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS and cells were sorted at room temperature to remove debris and doublets using a BD FACSAria III cell sorter BD Biosciences. Equal numbers of GFP+ tumor and GFP macroenvironment cells were collected.  For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide 10X Genomics and all reagents were from the Visium Spatial Gene Expression Kit 10X Genomics. Briefly sections were fixed in chilled methanol for 30 min at 20°C stained with hematoxylin and eosin and mounted in…   sample type:Single cell suspension GSM4838134 GSM4838134: SingleCell E; Danio rerio; RNA Seq GSM4838134   1 For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor bearing fish were euthanized on ice and washed in 1X PBS. post dissection of the head and tail the remaining tissue was equilibrated in cold OCT for 2 minutes before transfer to a tissue mold filled with fresh OCT for snap freezing in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C. For cryosectioning both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide Visium Spatial Gene Expression Slides 10X Genomics. ST slides containing sections were stored at 80°C for a maximum of one week before use. For single cell RNA seq using the 10X genomics three prime GEX v3 platform: Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase Sigma Aldrich #5401020001 in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide bore P1000 followed by incubation for an additional 15 minutes at RT. post adding 500 uL FBS to stop the dissociation reaction samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS and cells were sorted at room temperature to remove debris and doublets using a BD FACSAria III cell sorter BD Biosciences. Equal numbers of GFP+ tumor and GFP macroenvironment cells were collected. For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide 10X Genomics and all reagents were from the Visium Spatial Gene Expression Kit 10X Genomics. Briefly sections were fixed in chilled methanol for 30 min at 20°C stained with hematoxylin and eosin and m… GEO Accession:GSM4838134 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP287858     10X_SingleCell_Sample_E_S1_L000_R1_001.fastq.gz 10X_SingleCell_Sample_E_S1_L000_R2_001.fastq.gz fastq fastq 44430354080.0 277689713.0 GSM4838134 r1 0:28 1:132 A:12355044923;C:9923404810;G:10323616312;T:11822807950;N:5480085 28 132     12355044923 9923404810 10323616312 11822807950 5480085 SRX9318588 SRS7543398 SRA1145723 GEO Memorial Sloan Kettering Cancer Center 2 0.00204 0.9315 0.00092 0.09404 0.9964 0.83027 0.40865 0.54937 28 132 T B sc-like readlen illumina nextseq unknown random_priming unknown sc single_cell_droplet 10x   United States 2020-10-20 Adult Adult Cancer or Tumor Cancer or Tumor
61560 61560 SRR12851620 SRX9318587 SRS7543397 SRP287858 PRJNA670235 Spatially resolved transcriptomics reveals the architecture of the tumor microenvironment interface GSE159709 Transcriptome Analysis Cancer cells interact with a wide variety of other cell types but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single cell RNA seq scRNA seq has helped define these TME cell types it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here we integrate spatial transcriptomics with scRNA seq to define the architecture and nature of nascent tumor and surrounding microenvironment cells as they come into contact through the process of invasion. Using a well defined transgenic zebrafish model of BRAFV600E driven melanoma we identify a transcriptionally unique “interface” cluster localized at the boundary between tumor cells and surrounding tissues. Using an unbiased data driven approach we identify spatially patterned gene modules specific to the interface and show that the interface is a distinct transcriptional entity that histologically resembles the microenvironment but transcriptionally resembles the tumor. By complementing ST with scRNA seq we demonstrate that the interface is composed of specialized tumor and microenvironment cells. Both cell types in the interface upregulate a common set of cilia genes and we find enrichment of cilia proteins only where the tumor meets the TME. Cilia gene expression is regulated by ETS family transcription factors which normally act to suppress their expression outside of this region. This unique ETS driven interface transcriptional state is conserved across ten different human patient samples suggesting this is a conserved feature of human melanoma. Taken together our results demonstrate the power of spatial and single cell transcriptomics techniques in uncovering novel biological mechanisms that drive tumor invasion into new tissues. Overall design: Spatial transcriptomics Visium platform of zebrafish bearing BRAF V600E driven melanomas. Single cell RNA seq 10X Genomics v3 of two such zebrafish. Single nucleus RNA seq 10X Genomics v3 of three suc…   pubmed:34725363   Visium C GSM4838133   tissue:Zebrafish melanomas BRAF V600E|sample type:Tissue cryosections Visium C Illumina RTA v2 software was used for basecalling and quality determination. The Visium raw FASTQ data was processed using 10X Genomics proprietary SpaceRanger v1.0.0 pipeline. The single cell RNA seq raw FASTQ data was processed using the 10X Genomics proprietary CellRanger v3.1.0 pipeline Genome build: GRCz10.88 Supplementary files format and content: For 10x Genomics spatial transcriptomic data: output of SpaceRanger pipeline including gene expression and spatial contents. For 10x Genomics single cell RNA Seq: output of CellRanger pipeline including gene expression features and barcodes. Supplementary files format and content: * image.tif: Tissue section used for Spatial Transcriptomics experiment. Zebrafish melanomas BRAF V600E   For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor bearing fish were euthanized on ice and washed in 1X PBS. post dissection of the head and tail the remaining tissue was equilibrated in cold OCT for 2 minutes before transfer to a tissue mold filled with fresh OCT for snap freezing in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C. For cryosectioning both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide Visium Spatial Gene Expression Slides 10X Genomics. ST slides containing sections were stored at 80°C for a maximum of one week before use. For single cell RNA seq using the 10X genomics 3’ GEX v3 platform: Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase Sigma Aldrich #5401020001 in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide bore P1000 followed by incubation for an additional 15 minutes at RT. post adding 500 uL FBS to stop the dissociation reaction samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS and cells were sorted at room temperature to remove debris and doublets using a BD FACSAria III cell sorter BD Biosciences. Equal numbers of GFP+ tumor and GFP macroenvironment cells were collected.  For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide 10X Genomics and all reagents were from the Visium Spatial Gene Expression Kit 10X Genomics. Briefly sections were fixed in chilled methanol for 30 min at 20°C stained with hematoxylin and eosin and mounted in…   sample type:Tissue cryosections GSM4838133 GSM4838133: Visium C; Danio rerio; RNA Seq GSM4838133   1 For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor bearing fish were euthanized on ice and washed in 1X PBS. post dissection of the head and tail the remaining tissue was equilibrated in cold OCT for 2 minutes before transfer to a tissue mold filled with fresh OCT for snap freezing in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C. For cryosectioning both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide Visium Spatial Gene Expression Slides 10X Genomics. ST slides containing sections were stored at 80°C for a maximum of one week before use. For single cell RNA seq using the 10X genomics three prime GEX v3 platform: Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase Sigma Aldrich #5401020001 in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide bore P1000 followed by incubation for an additional 15 minutes at RT. post adding 500 uL FBS to stop the dissociation reaction samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS and cells were sorted at room temperature to remove debris and doublets using a BD FACSAria III cell sorter BD Biosciences. Equal numbers of GFP+ tumor and GFP macroenvironment cells were collected. For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide 10X Genomics and all reagents were from the Visium Spatial Gene Expression Kit 10X Genomics. Briefly sections were fixed in chilled methanol for 30 min at 20°C stained with hematoxylin and eosin and m… GEO Accession:GSM4838133 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP287858     Visium_Sample_C_S3_L000_R1_001.fastq.gz Visium_Sample_C_S3_L000_R2_001.fastq.gz fastq fastq 13306156376.0 89906462.0 GSM4838133 r1 0:28 1:120 A:4587866955;C:2519579655;G:2801896206;T:3387510435;N:9303125 28 120     4587866955 2519579655 2801896206 3387510435 9303125 SRX9318587 SRS7543397 SRA1145723 GEO Memorial Sloan Kettering Cancer Center 2 0.0035 0.64737 0.00263 0.05262 0.99734 0.91959 0.55029 0.53722 28 120 T B sc-like readlen illumina nextseq unknown random_priming unknown sc single_cell_droplet 10x   United States 2020-10-20 Adult Adult Cancer or Tumor Cancer or Tumor
61561 61561 SRR12851619 SRX9318586 SRS7543396 SRP287858 PRJNA670235 Spatially resolved transcriptomics reveals the architecture of the tumor microenvironment interface GSE159709 Transcriptome Analysis Cancer cells interact with a wide variety of other cell types but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single cell RNA seq scRNA seq has helped define these TME cell types it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here we integrate spatial transcriptomics with scRNA seq to define the architecture and nature of nascent tumor and surrounding microenvironment cells as they come into contact through the process of invasion. Using a well defined transgenic zebrafish model of BRAFV600E driven melanoma we identify a transcriptionally unique “interface” cluster localized at the boundary between tumor cells and surrounding tissues. Using an unbiased data driven approach we identify spatially patterned gene modules specific to the interface and show that the interface is a distinct transcriptional entity that histologically resembles the microenvironment but transcriptionally resembles the tumor. By complementing ST with scRNA seq we demonstrate that the interface is composed of specialized tumor and microenvironment cells. Both cell types in the interface upregulate a common set of cilia genes and we find enrichment of cilia proteins only where the tumor meets the TME. Cilia gene expression is regulated by ETS family transcription factors which normally act to suppress their expression outside of this region. This unique ETS driven interface transcriptional state is conserved across ten different human patient samples suggesting this is a conserved feature of human melanoma. Taken together our results demonstrate the power of spatial and single cell transcriptomics techniques in uncovering novel biological mechanisms that drive tumor invasion into new tissues. Overall design: Spatial transcriptomics Visium platform of zebrafish bearing BRAF V600E driven melanomas. Single cell RNA seq 10X Genomics v3 of two such zebrafish. Single nucleus RNA seq 10X Genomics v3 of three suc…   pubmed:34725363   Visium B GSM4838132   tissue:Zebrafish melanomas BRAF V600E|sample type:Tissue cryosections Visium B Illumina RTA v2 software was used for basecalling and quality determination. The Visium raw FASTQ data was processed using 10X Genomics proprietary SpaceRanger v1.0.0 pipeline. The single cell RNA seq raw FASTQ data was processed using the 10X Genomics proprietary CellRanger v3.1.0 pipeline Genome build: GRCz10.88 Supplementary files format and content: For 10x Genomics spatial transcriptomic data: output of SpaceRanger pipeline including gene expression and spatial contents. For 10x Genomics single cell RNA Seq: output of CellRanger pipeline including gene expression features and barcodes. Supplementary files format and content: * image.tif: Tissue section used for Spatial Transcriptomics experiment. Zebrafish melanomas BRAF V600E   For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor bearing fish were euthanized on ice and washed in 1X PBS. post dissection of the head and tail the remaining tissue was equilibrated in cold OCT for 2 minutes before transfer to a tissue mold filled with fresh OCT for snap freezing in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C. For cryosectioning both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide Visium Spatial Gene Expression Slides 10X Genomics. ST slides containing sections were stored at 80°C for a maximum of one week before use. For single cell RNA seq using the 10X genomics 3’ GEX v3 platform: Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase Sigma Aldrich #5401020001 in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide bore P1000 followed by incubation for an additional 15 minutes at RT. post adding 500 uL FBS to stop the dissociation reaction samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS and cells were sorted at room temperature to remove debris and doublets using a BD FACSAria III cell sorter BD Biosciences. Equal numbers of GFP+ tumor and GFP macroenvironment cells were collected.  For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide 10X Genomics and all reagents were from the Visium Spatial Gene Expression Kit 10X Genomics. Briefly sections were fixed in chilled methanol for 30 min at 20°C stained with hematoxylin and eosin and mounted in…   sample type:Tissue cryosections GSM4838132 GSM4838132: Visium B; Danio rerio; RNA Seq GSM4838132   1 For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor bearing fish were euthanized on ice and washed in 1X PBS. post dissection of the head and tail the remaining tissue was equilibrated in cold OCT for 2 minutes before transfer to a tissue mold filled with fresh OCT for snap freezing in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C. For cryosectioning both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide Visium Spatial Gene Expression Slides 10X Genomics. ST slides containing sections were stored at 80°C for a maximum of one week before use. For single cell RNA seq using the 10X genomics three prime GEX v3 platform: Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase Sigma Aldrich #5401020001 in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide bore P1000 followed by incubation for an additional 15 minutes at RT. post adding 500 uL FBS to stop the dissociation reaction samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS and cells were sorted at room temperature to remove debris and doublets using a BD FACSAria III cell sorter BD Biosciences. Equal numbers of GFP+ tumor and GFP macroenvironment cells were collected. For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide 10X Genomics and all reagents were from the Visium Spatial Gene Expression Kit 10X Genomics. Briefly sections were fixed in chilled methanol for 30 min at 20°C stained with hematoxylin and eosin and m… GEO Accession:GSM4838132 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP287858     Visium_Sample_B_S2_L000_R2_001.fastq.gz Visium_Sample_B_S2_L000_R1_001.fastq.gz fastq fastq 9316849676.0 62951687.0 GSM4838132 r1 0:28 1:120 A:2870712770;C:1917570201;G:2077620827;T:2444412876;N:6533002 28 120     2870712770 1917570201 2077620827 2444412876 6533002 SRX9318586 SRS7543396 SRA1145723 GEO Memorial Sloan Kettering Cancer Center 2 0.00194 0.80482 0.00091 0.06131 0.99711 0.90325 0.5736 0.52314 28 120 T B sc-like readlen illumina nextseq unknown random_priming unknown sc single_cell_droplet 10x   United States 2020-10-20 Adult Adult Cancer or Tumor Cancer or Tumor
61562 61562 SRR12851618 SRX9318585 SRS7543395 SRP287858 PRJNA670235 Spatially resolved transcriptomics reveals the architecture of the tumor microenvironment interface GSE159709 Transcriptome Analysis Cancer cells interact with a wide variety of other cell types but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single cell RNA seq scRNA seq has helped define these TME cell types it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here we integrate spatial transcriptomics with scRNA seq to define the architecture and nature of nascent tumor and surrounding microenvironment cells as they come into contact through the process of invasion. Using a well defined transgenic zebrafish model of BRAFV600E driven melanoma we identify a transcriptionally unique “interface” cluster localized at the boundary between tumor cells and surrounding tissues. Using an unbiased data driven approach we identify spatially patterned gene modules specific to the interface and show that the interface is a distinct transcriptional entity that histologically resembles the microenvironment but transcriptionally resembles the tumor. By complementing ST with scRNA seq we demonstrate that the interface is composed of specialized tumor and microenvironment cells. Both cell types in the interface upregulate a common set of cilia genes and we find enrichment of cilia proteins only where the tumor meets the TME. Cilia gene expression is regulated by ETS family transcription factors which normally act to suppress their expression outside of this region. This unique ETS driven interface transcriptional state is conserved across ten different human patient samples suggesting this is a conserved feature of human melanoma. Taken together our results demonstrate the power of spatial and single cell transcriptomics techniques in uncovering novel biological mechanisms that drive tumor invasion into new tissues. Overall design: Spatial transcriptomics Visium platform of zebrafish bearing BRAF V600E driven melanomas. Single cell RNA seq 10X Genomics v3 of two such zebrafish. Single nucleus RNA seq 10X Genomics v3 of three suc…   pubmed:34725363   Visium A GSM4838131   tissue:Zebrafish melanomas BRAF V600E|sample type:Tissue cryosections Visium A Illumina RTA v2 software was used for basecalling and quality determination. The Visium raw FASTQ data was processed using 10X Genomics proprietary SpaceRanger v1.0.0 pipeline. The single cell RNA seq raw FASTQ data was processed using the 10X Genomics proprietary CellRanger v3.1.0 pipeline Genome build: GRCz10.88 Supplementary files format and content: For 10x Genomics spatial transcriptomic data: output of SpaceRanger pipeline including gene expression and spatial contents. For 10x Genomics single cell RNA Seq: output of CellRanger pipeline including gene expression features and barcodes. Supplementary files format and content: * image.tif: Tissue section used for Spatial Transcriptomics experiment. Zebrafish melanomas BRAF V600E   For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor bearing fish were euthanized on ice and washed in 1X PBS. post dissection of the head and tail the remaining tissue was equilibrated in cold OCT for 2 minutes before transfer to a tissue mold filled with fresh OCT for snap freezing in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C. For cryosectioning both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide Visium Spatial Gene Expression Slides 10X Genomics. ST slides containing sections were stored at 80°C for a maximum of one week before use. For single cell RNA seq using the 10X genomics 3’ GEX v3 platform: Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase Sigma Aldrich #5401020001 in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide bore P1000 followed by incubation for an additional 15 minutes at RT. post adding 500 uL FBS to stop the dissociation reaction samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS and cells were sorted at room temperature to remove debris and doublets using a BD FACSAria III cell sorter BD Biosciences. Equal numbers of GFP+ tumor and GFP macroenvironment cells were collected.  For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide 10X Genomics and all reagents were from the Visium Spatial Gene Expression Kit 10X Genomics. Briefly sections were fixed in chilled methanol for 30 min at 20°C stained with hematoxylin and eosin and mounted in…   sample type:Tissue cryosections GSM4838131 GSM4838131: Visium A; Danio rerio; RNA Seq GSM4838131   1 For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor bearing fish were euthanized on ice and washed in 1X PBS. post dissection of the head and tail the remaining tissue was equilibrated in cold OCT for 2 minutes before transfer to a tissue mold filled with fresh OCT for snap freezing in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C. For cryosectioning both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide Visium Spatial Gene Expression Slides 10X Genomics. ST slides containing sections were stored at 80°C for a maximum of one week before use. For single cell RNA seq using the 10X genomics three prime GEX v3 platform: Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase Sigma Aldrich #5401020001 in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide bore P1000 followed by incubation for an additional 15 minutes at RT. post adding 500 uL FBS to stop the dissociation reaction samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS and cells were sorted at room temperature to remove debris and doublets using a BD FACSAria III cell sorter BD Biosciences. Equal numbers of GFP+ tumor and GFP macroenvironment cells were collected. For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide 10X Genomics and all reagents were from the Visium Spatial Gene Expression Kit 10X Genomics. Briefly sections were fixed in chilled methanol for 30 min at 20°C stained with hematoxylin and eosin and m… GEO Accession:GSM4838131 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP287858     Visium_Sample_A_S1_L001_R1_001.fastq.gz Visium_Sample_A_S1_L001_R2_001.fastq.gz fastq fastq 8186801004.0 55316223.0 GSM4838131 r1 0:28 1:120 A:3045741900;C:1541903021;G:1757255221;T:1836190790;N:5710072 28 120     3045741900 1541903021 1757255221 1836190790 5710072 SRX9318585 SRS7543395 SRA1145723 GEO Memorial Sloan Kettering Cancer Center 2 0.00549 0.65605 0.00319 0.10569 0.99734 0.93545 0.52914 0.56848 28 120 T B sc-like readlen illumina nextseq unknown random_priming unknown sc single_cell_droplet 10x   United States 2020-10-20 Adult Adult Cancer or Tumor Cancer or Tumor
63239 63239 SRR13693865 SRX10083163 SRS8241179 SRP305927 PRJNA701473 Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors GSE166646 Transcriptome Analysis Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4. Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter. Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry. Normal cells was prepared from a control zebrafish which overexpresses only mCherry. Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique. parent bioproject:PRJNA701471 pubmed:35504924   Tumor cells Late stage IRF4;p53+/ fish 5 scRNA Seq GSM5076953   source name:Zebrafish cells transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression and p53 mutation|time:Late stage Tumor cells Late stage IRF4;p53+/ fish 5 scRNA Seq Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information. Single cell data were generated using mkref from cellranger package. Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count id zv11 {sampleID} fastqs={directory scSeq} sample={sampleID} transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells. The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze Zebrafish cells transgenic No treatment post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. A zebrafish which was transduced only with mCherry was used as a control. tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression and p53 mutation|time:Late stage GSM5076953 GSM5076953: Tumor cells Late stage IRF4;p53+/ fish 5 scRNA Seq; Danio rerio; RNA Seq GSM5076953   1 post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq GEO Accession:GSM5076953 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP305927   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=S3 I1.fastq.gz read2PairFiles=S3 R1.fastq.gz read3PairFiles=S3 R2.fastq.gz     30902398692.0 234109081.0 GSM5076953 r1 0:8 1:26 2:98 A:8591012397;C:7005723022;G:7425233397;T:7870465271;N:9964605 8 26 98   8591012397 7005723022 7425233397 7870465271 9964605 SRX10083163 SRS8241179 SRA1195246 GEO Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore 1 0.92664   0.18689   0.83376   0.51575   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Singapore 2021-02-11 Undetermined Undetermined Cancer or Tumor Cancer or Tumor
63240 63240 SRR13693864 SRX10083162 SRS8241178 SRP305927 PRJNA701473 Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors GSE166646 Transcriptome Analysis Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4. Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter. Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry. Normal cells was prepared from a control zebrafish which overexpresses only mCherry. Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique. parent bioproject:PRJNA701471 pubmed:35504924   Tumor cells Late stage IRF4;p53+/ fish 4 scRNA Seq GSM5076952   source name:Zebrafish cells transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression and p53 mutation|time:Late stage Tumor cells Late stage IRF4;p53+/ fish 4 scRNA Seq Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information. Single cell data were generated using mkref from cellranger package. Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count id zv11 {sampleID} fastqs={directory scSeq} sample={sampleID} transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells. The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze Zebrafish cells transgenic No treatment post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. A zebrafish which was transduced only with mCherry was used as a control. tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression and p53 mutation|time:Late stage GSM5076952 GSM5076952: Tumor cells Late stage IRF4;p53+/ fish 4 scRNA Seq; Danio rerio; RNA Seq GSM5076952   1 post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq GEO Accession:GSM5076952 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP305927   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=S2 I1.fastq.gz read2PairFiles=S2 R1.fastq.gz read3PairFiles=S2 R2.fastq.gz S2_I1.fastq S2_R1.fastq S2_R2.fastq fastq fastq fastq 31435037700.0 238144225.0 GSM5076952 r1 0:8 1:26 2:98 A:8766861031;C:6971129836;G:7458655794;T:8228099570;N:10291469 8 26 98   8766861031 6971129836 7458655794 8228099570 10291469 SRX10083162 SRS8241178 SRA1195246 GEO Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore 1 0.92786   0.2437   0.82406   0.51326   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Singapore 2021-02-11 Undetermined Undetermined Cancer or Tumor Cancer or Tumor
63241 63241 SRR13693863 SRX10083161 SRS8241177 SRP305927 PRJNA701473 Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors GSE166646 Transcriptome Analysis Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4. Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter. Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry. Normal cells was prepared from a control zebrafish which overexpresses only mCherry. Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique. parent bioproject:PRJNA701471 pubmed:35504924   Tumor cells Late stage IRF4;p53+/ fish 3 scRNA Seq GSM5076951   source name:Zebrafish cells transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression and p53 mutation|time:Late stage Tumor cells Late stage IRF4;p53+/ fish 3 scRNA Seq Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information. Single cell data were generated using mkref from cellranger package. Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count id zv11 {sampleID} fastqs={directory scSeq} sample={sampleID} transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells. The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze Zebrafish cells transgenic No treatment post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. A zebrafish which was transduced only with mCherry was used as a control. tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression and p53 mutation|time:Late stage GSM5076951 GSM5076951: Tumor cells Late stage IRF4;p53+/ fish 3 scRNA Seq; Danio rerio; RNA Seq GSM5076951   1 post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq GEO Accession:GSM5076951 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP305927   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=D3 I1.fastq.gz read2PairFiles=D3 R1.fastq.gz read3PairFiles=D3 R2.fastq.gz D3_I1.fastq.gz D3_R1.fastq.gz D3_R2.fastq.gz fastq fastq fastq 28995027468.0 219659299.0 GSM5076951 r1 0:8 1:26 2:98 A:8296536133;C:6414043957;G:6689913049;T:7585241915;N:9292414 8 26 98   8296536133 6414043957 6689913049 7585241915 9292414 SRX10083161 SRS8241177 SRA1195246 GEO Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore 1 0.91752   0.20118   0.82903   0.51629   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Singapore 2021-02-11 Undetermined Undetermined Cancer or Tumor Cancer or Tumor
63242 63242 SRR13693862 SRX10083160 SRS8241176 SRP305927 PRJNA701473 Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors GSE166646 Transcriptome Analysis Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4. Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter. Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry. Normal cells was prepared from a control zebrafish which overexpresses only mCherry. Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique. parent bioproject:PRJNA701471 pubmed:35504924   Tumor cells Late stage IRF4;p53+/ fish 2 scRNA Seq GSM5076950   source name:Zebrafish cells transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression and p53 mutation|time:Late stage Tumor cells Late stage IRF4;p53+/ fish 2 scRNA Seq Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information. Single cell data were generated using mkref from cellranger package. Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count id zv11 {sampleID} fastqs={directory scSeq} sample={sampleID} transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells. The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze Zebrafish cells transgenic No treatment post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. A zebrafish which was transduced only with mCherry was used as a control. tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression and p53 mutation|time:Late stage GSM5076950 GSM5076950: Tumor cells Late stage IRF4;p53+/ fish 2 scRNA Seq; Danio rerio; RNA Seq GSM5076950   1 post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq GEO Accession:GSM5076950 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP305927   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=D2 I1.fastq.gz read2PairFiles=D2 R1.fastq.gz read3PairFiles=D2 R2.fastq.gz D2_I1.fastq.gz D2_R1.fastq.gz D2_R2.fastq.gz fastq fastq fastq 34413827844.0 260710817.0 GSM5076950 r1 0:8 1:26 2:98 A:9806323881;C:7657614846;G:7929340289;T:9009399182;N:11149646 8 26 98   9806323881 7657614846 7929340289 9009399182 11149646 SRX10083160 SRS8241176 SRA1195246 GEO Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore 1 0.91903   0.19966   0.83591   0.53703   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Singapore 2021-02-11 Undetermined Undetermined Cancer or Tumor Cancer or Tumor
63243 63243 SRR13693861 SRX10083159 SRS8241175 SRP305927 PRJNA701473 Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors GSE166646 Transcriptome Analysis Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4. Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter. Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry. Normal cells was prepared from a control zebrafish which overexpresses only mCherry. Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique. parent bioproject:PRJNA701471 pubmed:35504924   Tumor cells Late stage IRF4;p53+/ fish 1 scRNA Seq GSM5076949   source name:Zebrafish cells transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression and p53 mutation|time:Late stage Tumor cells Late stage IRF4;p53+/ fish 1 scRNA Seq Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information. Single cell data were generated using mkref from cellranger package. Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count id zv11 {sampleID} fastqs={directory scSeq} sample={sampleID} transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells. The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze Zebrafish cells transgenic No treatment post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. A zebrafish which was transduced only with mCherry was used as a control. tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression and p53 mutation|time:Late stage GSM5076949 GSM5076949: Tumor cells Late stage IRF4;p53+/ fish 1 scRNA Seq; Danio rerio; RNA Seq GSM5076949   1 post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq GEO Accession:GSM5076949 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP305927   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=D1 I1.fastq.gz read2PairFiles=D1 R1.fastq.gz read3PairFiles=D1 R2.fastq.gz D1_I1.fastq.gz D1_R1.fastq.gz D1_R2.fastq.gz fastq fastq fastq 32611994976.0 247060568.0 GSM5076949 r1 0:8 1:26 2:98 A:9284005966;C:7280091614;G:7543060588;T:8494420994;N:10415814 8 26 98   9284005966 7280091614 7543060588 8494420994 10415814 SRX10083159 SRS8241175 SRA1195246 GEO Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore 1 0.92638   0.18797   0.83713   0.55228   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Singapore 2021-02-11 Undetermined Undetermined Cancer or Tumor Cancer or Tumor
63244 63244 SRR13693860 SRX10083158 SRS8241174 SRP305927 PRJNA701473 Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors GSE166646 Transcriptome Analysis Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4. Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter. Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry. Normal cells was prepared from a control zebrafish which overexpresses only mCherry. Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique. parent bioproject:PRJNA701471 pubmed:35504924   Tumor cells Late stage Ick:IRF4 fish 6 scRNA Seq GSM5076948   source name:Zebrafish cells transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage Tumor cells Late stage Ick:IRF4 fish 6 scRNA Seq Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information. Single cell data were generated using mkref from cellranger package. Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count id zv11 {sampleID} fastqs={directory scSeq} sample={sampleID} transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells. The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze Zebrafish cells transgenic No treatment post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. A zebrafish which was transduced only with mCherry was used as a control. tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage GSM5076948 GSM5076948: Tumor cells Late stage Ick:IRF4 fish 6 scRNA Seq; Danio rerio; RNA Seq GSM5076948   1 post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq GEO Accession:GSM5076948 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP305927   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=3S I1.fastq.gz read2PairFiles=3S R1.fastq.gz read3PairFiles=3S R2.fastq.gz 3S_I1.fastq.gz 3S_R1.fastq.gz 3S_R2.fastq.gz fastq fastq fastq 27615581268.0 209208949.0 GSM5076948 r1 0:8 1:26 2:98 A:7903060121;C:6181635403;G:6459419292;T:7062664494;N:8801958 8 26 98   7903060121 6181635403 6459419292 7062664494 8801958 SRX10083158 SRS8241174 SRA1195246 GEO Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore 1 0.91885   0.167   0.84952   0.49561   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Singapore 2021-02-11 Undetermined Undetermined Cancer or Tumor Cancer or Tumor
63245 63245 SRR13693859 SRX10083157 SRS8241173 SRP305927 PRJNA701473 Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors GSE166646 Transcriptome Analysis Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4. Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter. Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry. Normal cells was prepared from a control zebrafish which overexpresses only mCherry. Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique. parent bioproject:PRJNA701471 pubmed:35504924   Tumor cells Late stage Ick:IRF4 fish 5 scRNA Seq GSM5076947   source name:Zebrafish cells transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage Tumor cells Late stage Ick:IRF4 fish 5 scRNA Seq Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information. Single cell data were generated using mkref from cellranger package. Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count id zv11 {sampleID} fastqs={directory scSeq} sample={sampleID} transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells. The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze Zebrafish cells transgenic No treatment post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. A zebrafish which was transduced only with mCherry was used as a control. tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage GSM5076947 GSM5076947: Tumor cells Late stage Ick:IRF4 fish 5 scRNA Seq; Danio rerio; RNA Seq GSM5076947   1 post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq GEO Accession:GSM5076947 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP305927   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=2S I1.fastq.gz read2PairFiles=2S R1.fastq.gz read3PairFiles=2S R2.fastq.gz 2S_I1.fastq.gz 2S_R1.fastq.gz 2S_R2.fastq.gz fastq fastq fastq 27096206280.0 205274290.0 GSM5076947 r1 0:8 1:26 2:98 A:7673974628;C:6078379871;G:6323826541;T:7011380350;N:8644890 8 26 98   7673974628 6078379871 6323826541 7011380350 8644890 SRX10083157 SRS8241173 SRA1195246 GEO Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore 1 0.92045   0.17808   0.83942   0.50762   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Singapore 2021-02-11 Undetermined Undetermined Cancer or Tumor Cancer or Tumor
63246 63246 SRR13693858 SRX10083156 SRS8241172 SRP305927 PRJNA701473 Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors GSE166646 Transcriptome Analysis Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4. Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter. Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry. Normal cells was prepared from a control zebrafish which overexpresses only mCherry. Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique. parent bioproject:PRJNA701471 pubmed:35504924   Tumor cells Late stage Ick:IRF4 fish 4 scRNA Seq GSM5076946   source name:Zebrafish cells transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage Tumor cells Late stage Ick:IRF4 fish 4 scRNA Seq Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information. Single cell data were generated using mkref from cellranger package. Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count id zv11 {sampleID} fastqs={directory scSeq} sample={sampleID} transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells. The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze Zebrafish cells transgenic No treatment post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. A zebrafish which was transduced only with mCherry was used as a control. tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage GSM5076946 GSM5076946: Tumor cells Late stage Ick:IRF4 fish 4 scRNA Seq; Danio rerio; RNA Seq GSM5076946   1 post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq GEO Accession:GSM5076946 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP305927   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=1S I1.fastq.gz read2PairFiles=1S R1.fastq.gz read3PairFiles=1S R2.fastq.gz 1S_I1.fastq.gz 1S_R1.fastq.gz 1S_R2.fastq.gz fastq fastq fastq 25321669296.0 191830828.0 GSM5076946 r1 0:8 1:26 2:98 A:7267370389;C:5631756169;G:5928757429;T:6485676974;N:8108335 8 26 98   7267370389 5631756169 5928757429 6485676974 8108335 SRX10083156 SRS8241172 SRA1195246 GEO Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore 1 0.92297   0.2138   0.84218   0.52396   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Singapore 2021-02-11 Undetermined Undetermined Cancer or Tumor Cancer or Tumor
63247 63247 SRR13693857 SRX10083155 SRS8241171 SRP305927 PRJNA701473 Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors GSE166646 Transcriptome Analysis Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4. Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter. Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry. Normal cells was prepared from a control zebrafish which overexpresses only mCherry. Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique. parent bioproject:PRJNA701471 pubmed:35504924   Tumor cells Late stage Ick:IRF4 fish 3 scRNA Seq GSM5076945   source name:Zebrafish cells transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage Tumor cells Late stage Ick:IRF4 fish 3 scRNA Seq Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information. Single cell data were generated using mkref from cellranger package. Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count id zv11 {sampleID} fastqs={directory scSeq} sample={sampleID} transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells. The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze Zebrafish cells transgenic No treatment post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. A zebrafish which was transduced only with mCherry was used as a control. tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage GSM5076945 GSM5076945: Tumor cells Late stage Ick:IRF4 fish 3 scRNA Seq; Danio rerio; RNA Seq GSM5076945   1 post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq GEO Accession:GSM5076945 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP305927   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=10G I1.fastq.gz read2PairFiles=10G R1.fastq.gz read3PairFiles=10G R2.fastq.gz     29362596648.0 222443914.0 GSM5076945 r1 0:8 1:26 2:98 A:8309910202;C:6578384206;G:7008276151;T:7440260771;N:25765318 8 26 98   8309910202 6578384206 7008276151 7440260771 25765318 SRX10083155 SRS8241171 SRA1195246 GEO Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore 1 0.92108   0.20892   0.85484   0.52156   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Singapore 2021-02-11 Undetermined Undetermined Cancer or Tumor Cancer or Tumor
63248 63248 SRR13693856 SRX10083154 SRS8241170 SRP305927 PRJNA701473 Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors GSE166646 Transcriptome Analysis Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4. Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter. Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry. Normal cells was prepared from a control zebrafish which overexpresses only mCherry. Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique. parent bioproject:PRJNA701471 pubmed:35504924   Tumor cells Late stage Ick:IRF4 fish 2 scRNA Seq GSM5076944   source name:Zebrafish cells transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage Tumor cells Late stage Ick:IRF4 fish 2 scRNA Seq Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information. Single cell data were generated using mkref from cellranger package. Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count id zv11 {sampleID} fastqs={directory scSeq} sample={sampleID} transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells. The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze Zebrafish cells transgenic No treatment post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. A zebrafish which was transduced only with mCherry was used as a control. tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage GSM5076944 GSM5076944: Tumor cells Late stage Ick:IRF4 fish 2 scRNA Seq; Danio rerio; RNA Seq GSM5076944   1 post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq GEO Accession:GSM5076944 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP305927   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=10F I1.fastq.gz read2PairFiles=10F R1.fastq.gz read3PairFiles=10F R2.fastq.gz 10F_I1.fastq.gz 10F_R1.fastq.gz 10F_R2.fastq.gz fastq fastq fastq 30225931824.0 228984332.0 GSM5076944 r1 0:8 1:26 2:98 A:8484220529;C:6779948314;G:7231863744;T:7703283562;N:26615675 8 26 98   8484220529 6779948314 7231863744 7703283562 26615675 SRX10083154 SRS8241170 SRA1195246 GEO Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore 1 0.92746   0.1895   0.85817   0.49147   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Singapore 2021-02-11 Undetermined Undetermined Cancer or Tumor Cancer or Tumor
63249 63249 SRR13693855 SRX10083153 SRS8241169 SRP305927 PRJNA701473 Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors GSE166646 Transcriptome Analysis Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4. Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter. Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry. Normal cells was prepared from a control zebrafish which overexpresses only mCherry. Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique. parent bioproject:PRJNA701471 pubmed:35504924   Tumor cells Late stage Ick:IRF4 fish 1 scRNA Seq GSM5076943   source name:Zebrafish cells transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage Tumor cells Late stage Ick:IRF4 fish 1 scRNA Seq Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information. Single cell data were generated using mkref from cellranger package. Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count id zv11 {sampleID} fastqs={directory scSeq} sample={sampleID} transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells. The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze Zebrafish cells transgenic No treatment post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. A zebrafish which was transduced only with mCherry was used as a control. tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Late stage GSM5076943 GSM5076943: Tumor cells Late stage Ick:IRF4 fish 1 scRNA Seq; Danio rerio; RNA Seq GSM5076943   1 post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq GEO Accession:GSM5076943 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP305927   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=10E I1.fastq.gz read2PairFiles=10E R1.fastq.gz read3PairFiles=10E R2.fastq.gz 10E_I1.fastq 10E_R1.fastq 10E_R2.fastq fastq fastq fastq 34321213080.0 260009190.0 GSM5076943 r1 0:8 1:26 2:98 A:9548435346;C:7827936248;G:8159132985;T:8755456452;N:30252049 8 26 98   9548435346 7827936248 8159132985 8755456452 30252049 SRX10083153 SRS8241169 SRA1195246 GEO Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore 1 0.92658   0.1882   0.84861   0.50119   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Singapore 2021-02-11 Undetermined Undetermined Cancer or Tumor Cancer or Tumor
63250 63250 SRR13693854 SRX10083152 SRS8241168 SRP305927 PRJNA701473 Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors GSE166646 Transcriptome Analysis Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4. Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter. Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry. Normal cells was prepared from a control zebrafish which overexpresses only mCherry. Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique. parent bioproject:PRJNA701471 pubmed:35504924   Tumor cells Early stage Ick:IRF4 fish 3 scRNA Seq GSM5076942   source name:Zebrafish cells transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Early stage Tumor cells Early stage Ick:IRF4 fish 3 scRNA Seq Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information. Single cell data were generated using mkref from cellranger package. Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count id zv11 {sampleID} fastqs={directory scSeq} sample={sampleID} transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells. The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze Zebrafish cells transgenic No treatment post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. A zebrafish which was transduced only with mCherry was used as a control. tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Early stage GSM5076942 GSM5076942: Tumor cells Early stage Ick:IRF4 fish 3 scRNA Seq; Danio rerio; RNA Seq GSM5076942   1 post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq GEO Accession:GSM5076942 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP305927   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=3D I1.fastq.gz read2PairFiles=3D R1.fastq.gz read3PairFiles=3D R2.fastq.gz 3D_I1.fastq 3D_R1.fastq 3D_R2.fastq fastq fastq fastq 29652167556.0 224637633.0 GSM5076942 r1 0:8 1:26 2:98 A:8364846981;C:6574443334;G:6910197942;T:7776537448;N:26141851 8 26 98   8364846981 6574443334 6910197942 7776537448 26141851 SRX10083152 SRS8241168 SRA1195246 GEO Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore 1 0.91807   0.19059   0.83205   0.56087   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Singapore 2021-02-11 Undetermined Undetermined Cancer or Tumor Cancer or Tumor
63251 63251 SRR13693853 SRX10083151 SRS8241167 SRP305927 PRJNA701473 Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors GSE166646 Transcriptome Analysis Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4. Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter. Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry. Normal cells was prepared from a control zebrafish which overexpresses only mCherry. Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique. parent bioproject:PRJNA701471 pubmed:35504924   Tumor cells Early stage Ick:IRF4 fish 2 scRNA Seq GSM5076941   source name:Zebrafish cells transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Early stage Tumor cells Early stage Ick:IRF4 fish 2 scRNA Seq Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information. Single cell data were generated using mkref from cellranger package. Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count id zv11 {sampleID} fastqs={directory scSeq} sample={sampleID} transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells. The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze Zebrafish cells transgenic No treatment post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. A zebrafish which was transduced only with mCherry was used as a control. tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Early stage GSM5076941 GSM5076941: Tumor cells Early stage Ick:IRF4 fish 2 scRNA Seq; Danio rerio; RNA Seq GSM5076941   1 post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq GEO Accession:GSM5076941 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP305927   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=3C I1.fastq.gz read2PairFiles=3C R1.fastq.gz read3PairFiles=3C R2.fastq.gz 3C_I1.fastq.gz 3C_R1.fastq.gz 3C_R2.fastq.gz fastq fastq fastq 29997585156.0 227254433.0 GSM5076941 r1 0:8 1:26 2:98 A:8572344693;C:6580024899;G:7240023287;T:7578830064;N:26362213 8 26 98   8572344693 6580024899 7240023287 7578830064 26362213 SRX10083151 SRS8241167 SRA1195246 GEO Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore 1 0.93097   0.27389   0.86318   0.50798   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Singapore 2021-02-11 Undetermined Undetermined Cancer or Tumor Cancer or Tumor
63252 63252 SRR13693852 SRX10083150 SRS8241166 SRP305927 PRJNA701473 Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors GSE166646 Transcriptome Analysis Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4. Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter. Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry. Normal cells was prepared from a control zebrafish which overexpresses only mCherry. Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique. parent bioproject:PRJNA701471 pubmed:35504924   Tumor cells Early stage Ick:IRF4 fish 1 scRNA Seq GSM5076940   source name:Zebrafish cells transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Early stage Tumor cells Early stage Ick:IRF4 fish 1 scRNA Seq Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information. Single cell data were generated using mkref from cellranger package. Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count id zv11 {sampleID} fastqs={directory scSeq} sample={sampleID} transcriptome={mkgtf generated STAR library} Genome build: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells. The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze Zebrafish cells transgenic No treatment post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. A zebrafish which was transduced only with mCherry was used as a control. tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Early stage GSM5076940 GSM5076940: Tumor cells Early stage Ick:IRF4 fish 1 scRNA Seq; Danio rerio; RNA Seq GSM5076940   1 post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis. Single cell RNA Seq GEO Accession:GSM5076940 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP305927   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=3A I1.fastq.gz read2PairFiles=3A R1.fastq.gz read3PairFiles=3A R2.fastq.gz     29170933836.0 220991923.0 GSM5076940 r1 0:8 1:26 2:98 A:8114837766;C:6514920127;G:6820788482;T:7694661638;N:25725823 8 26 98   8114837766 6514920127 6820788482 7694661638 25725823 SRX10083150 SRS8241166 SRA1195246 GEO Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore 1 0.91826   0.16532   0.82755   0.51956   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Singapore 2021-02-11 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");;