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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
71397 SRR21571181 SRX17573445 SRS15113179 SRP397130 PRJNA880596 A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq] GSE213359 Transcriptome Analysis Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed parent bioproject:PRJNA880593     TIE:EGFP MCR:MCS Tumor 2 GFP+ #3 GSM6580971   source name:MCR:MCS Melanoma|tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+|geo loc name:missing|collection date:missing TIE:EGFP MCR:MCS Tumor 2 GFP+ #3 The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv MCR:MCS Melanoma Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors. Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq N/A tissue:MCR:MCS Melanoma|genotype:expressing TIE:EGFP|sorted cells:GFP+ GSM6580971 GSM6580971: TIE:EGFP MCR:MCS Tumor 2 GFP+ #3; Danio rerio; RNA Seq GSM6580971 r1 GSM6580971 1 Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP397130     HAR-HN-s014.R1.fastq.gz HAR-HN-s014.R2.fastq.gz fastq fastq 2393526200.0 27831700.0 GSM6580971 r1 0:26 1:60 A:587629810;C:436040251;G:440163052;T:929430783;N:262304 26 60     587629810 436040251 440163052 929430783 262304 SRX17573445 SRS15113179     Oncology/Hematology, Boston Children's Hospital 2 0.1102 0.89036 0.10359 0.25006 0.99285 0.81172 0.56209 0.58312 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   United States 2022-09-14 Undetermined Undetermined Cancer or Tumor Cancer or Tumor