{"database": "metadata", "table": "run_metadata", "rows": [[52972, "SRR9621258", "SRX6384172", "SRS5043690", "SRP212628", "PRJNA551686", "Gene expression profile of cells with unfit Wnt morphogen gradient during cell competition", "GSE133526", "Transcriptome Analysis", "Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However  developing tissues also undergo dynamic morphogenesis  which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/\u00df catenin signalling gradient  which acts as a morphogen to establish embryonic anterior posterior patterning  revealed that unfit cells with abnormal Wnt/\u00df catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/\u00df catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues  this system may support tissue robustness and disease prevention. Overall design: \u00df catCA constitutive active form of \u00df catenin expressing cells from \u00df catCA mosaically introduced or \u00df catCA ubiquitously expressing zebrafish early embryos  or cells from uninjected zebrafish embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.", null, "pubmed:31624259", null, "Ubiquitous beta catCA GFP pls lot2", "GSM3911297", null, "tissue:Ubiquitous beta catCA GFP pls|strain:AB|cell type:early embryonic cell|developmental stage:9 hpf", "Ubiquitous beta catCA GFP pls lot2", "Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Genome build: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.", "Ubiquitous beta catCA GFP pls", null, "Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "strain:AB|cell type:early embryonic cell|developmental stage:9 hpf", "GSM3911297", "GSM3911297: Ubiquitous beta catCA GFP pls lot2; Danio rerio; RNA Seq", "GSM3911297", null, "1", "Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", "GEO Accession:GSM3911297", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP212628", null, null, "Ubiquitous_beta-catCA_GFP_pls_lot2.fastq.gz", "fastq", 4191336.0, 116426.0, "GSM3911297 r1", "0:36", "A:1023598;C:694666;G:854764;T:1618296;N:12", 36, null, null, null, 1023598, 694666, 854764, 1618296, 12, "SRX6384172", "SRS5043690", "SRA915905", "GEO", "Division of Transcriptomics, Medical Institute of Bioregulation", 1, 0.83432, null, 0.2051, null, 0.88998, null, 0.58415, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Japan", "2019-06-28", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "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": ["52972"], "units": {}, "query_ms": 11.821607004094403}