{"database": "metadata", "table": "run_metadata", "rows": [[42007, "SRR5381355", "SRX2676474", "SRS2074971", "SRP102546", "PRJNA380660", "Oncogenic BRAF disrupts thyroid morphogenesis and function via Twist expression", "GSE97096", "Transcriptome Analysis", "Thyroid cancer is common  yet the sequence of alterations that promote tumor formation are incompletely understood. Here we describe a novel model of thyroid carcinoma in zebrafish that reveals temporal changes due to BRAFV600E. Through the use of real time in vivo imaging we observe disruption in thyroid follicle structure that occurs early in thyroid development. Combinatorial treatment using BRAF and MEK inhibitors reversed the developmental effects induced by BRAFV600E. Adult zebrafish expressing BRAFV600E in thyrocytes developed invasive carcinoma. We identified a gene expression signature from zebrafish thyroid cancer that is predictive of disease free survival in patients with papillary thyroid cancer. Gene expression studies nominated TWIST2 as a key effector downstream of BRAF. Using CRISPR/Cas9 to genetically inactivate a TWIST2 orthologue  we suppressed the effects of BRAFV600E and restored thyroid morphology and hormone synthesis. These data suggest that expression of TWIST2 plays a role in an early step of BRAFV600E mediated transformation. Overall design: 3 embryo tg TOM tg:TdTomato  3 embryo tg BRAFV600E TOM   3 adult tg TOM and 5 adult tg BRAFV600E TOM  biological replicates were sequenced. Strains with tg:TdTomato express the TdTomato fluorophore under control of the zebrafish thyroglobulin promoter tg.", null, "pubmed:28350298", null, "adultbraf 5", "GSM2551534", null, "source name:transgenic adult fish|tissue:TdTOM dissected thyroid|developmental stage:adult zebrafish|genotype:transgenic tg TOM;tg BRAF zebrafish", "adultbraf 5", "Alignment: STAR v2.3 Read Counting: htseq count v0.6.0  parameters  t exon  Ensembl transcriptome v70 Genome build: zv9 Supplementary files format and content: raw reads mapped to Ensembl transcriptome v70", "transgenic adult fish", null, "RNA was extracted using TRIzol Life Technologies followed by RNeasy Mini spin column RNA libraries were prepared for sequencing using standard Illumina protocol", null, "tissue:TdTOM dissected thyroid|developmental stage:adult zebrafish|genotype:transgenic tg TOM;tg BRAF zebrafish", "GSM2551534", "GSM2551534: adultbraf 5; Danio rerio; RNA Seq", "GSM2551534", null, "1", "RNA was extracted using TRIzol Life Technologies followed by RNeasy Mini spin column RNA libraries were prepared for sequencing using standard Illumina protocol", "GEO Accession:GSM2551534", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102546", null, null, "Sample_BRAF5.R1.fastq.gz Sample_BRAF5.R2.fastq.gz", "fastq fastq", 1940919750.0, 19028625.0, "GSM2551534 r1", "0:51 1:51", "A:507148079;C:461510577;G:459738307;T:507437006;N:5085781", 51, 51, null, null, 507148079, 461510577, 459738307, 507437006, 5085781, "SRX2676474", "SRS2074971", "SRA549625", "GEO", "Surgery, Weill Cornell Medical College", 2, 0.79926, 0.81264, 0.09051, 0.09347, 0.70339, 0.70212, 0.49811, 0.5006, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-27", "Adult", "Adult", "Thyroid", "Endocrine System"]], "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": ["42007"], "units": {}, "query_ms": 8.095525990938768}