{"database": "metadata", "table": "run_metadata", "rows": [[71393, "SRR21563985", "SRX17566320", "SRS15108368", "SRP397072", "PRJNA880540", "A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA seq  ZMEL]", "GSE213328", "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: RNA seq +/  TGFB1 Bulk RNA seq on ZMEL1 treated with 10ng/mL TGFB1 ligand or vehicle control ZMEL1 cells were serum starved for 2 hours  then treated with 10ng/mL human recombinant TGFB1 or 4mM HCl containing 1 mg/mL BSA vehicle control for an additional two hours. Experiment performed in technical triplicate.", "parent bioproject:PRJNA880593", null, null, "10ng/mL TGFB1 treated ZMEL1 Replicate 1", "GSM6579023", null, "tissue:ZMEL1 Cells|cell line:ZMEL1 Cells|treatment:TGFB1|geo loc name:missing|collection date:missing", "10ng/mL TGFB1 treated ZMEL1 Replicate 1", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to Ensembl GRCz11 whole genome using tophat 2.1 Transcript abundance were calculated with Htseq count Assembly: GRCz11 Supplementary files format and content: raw count file", "ZMEL1 Cells", "Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours.", "RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented  reverse transcribed  and library prepped NEB #E7530  NEB #E7335.", "ZMEL1 were grown in filter sterilized DMEM  10% FBS  1% PenStrep  1% Glutamine at 28\u00b0C", "cell line:ZMEL1 Cells|treatment:TGFB1", "GSM6579023", "GSM6579023: 10ng/mL TGFB1 treated ZMEL1 Replicate 1; Danio rerio; RNA Seq", "GSM6579023 r1", "GSM6579023", "1", "RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented  reverse transcribed  and library prepped NEB #E7530  NEB #E7335.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP397072", null, null, "HN72_R1_001.fastq.gz HN72_R2_001.fastq.gz", "fastq fastq", 9469796100.0, 31565987.0, "GSM6579023 r1", "0:150 1:150", "A:1779087329;C:2959081502;G:3015100670;T:1715714055;N:812544", 150, 150, null, null, 1779087329, 2959081502, 3015100670, 1715714055, 812544, "SRX17566320", "SRS15108368", null, null, "Oncology/Hematology, Boston Children's Hospital", 2, 0.93963, 0.94978, 0.17963, 0.18558, 0.84691, 0.86032, 0.72223, 0.75653, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "sc_generic", "bulk", "bulk", null, "United States", "2022-09-14", "Undetermined", "Undetermined", "Cell Line", "Cell Line"]], "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": ["71393"], "units": {}, "query_ms": 8.891716002835892}