{"database": "metadata", "table": "run_metadata", "rows": [[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 \u201cinterface\u201d 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 such zebrafish pooled into one reaction.", null, "pubmed:34725363", null, "Nuc seq", "GSM5380072", null, "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", null, "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\u00b0C 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/\u00b5L RNAse inhibitor  the sample was again spun at 4\u00b0C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4\u00b0C 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\u00b0C. Droplet based snRNA seq was performed using the Chromium Single Cell 3\u2019 Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3\u2019 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\u2019s instructions.\u00a0", null, "sample type:Single nucleus suspension", "GSM5380072", "GSM5380072: Nuc seq; Danio rerio; RNA Seq", "GSM5380072", null, "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\u00b0C 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/\u00b5L RNAse inhibitor  the sample was again spun at 4\u00b0C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4\u00b0C 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\u00b0C. 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", null, "SRP287858", null, null, "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, null, null, 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", null, "United States", "2021-06-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["61556"], "units": {}, "query_ms": 8.41746901278384}