{"database": "metadata", "table": "run_metadata", "rows": [[56823, "SRR11107234", "SRX7744905", "SRS6165316", "SRP249927", "PRJNA607316", "The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration", "GSE145497", "Transcriptome Analysis", "Throughout their lifetime  fish maintain a high capacity for regenerating complex xxx post injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio  which serves as an ideal model of appendage regeneration due to its easy manipulation  relatively simple mixture of cell types  and superior imaging properties. Regeneration of the embryonic zebrafish tail requires development of a blastema  a mass of dedifferentiated cells capable of replacing lost tissue  a crucial step in all known examples of appendage regeneration. Using this model  we show that tail amputation triggers an obligate metabolic shift to promote glucose metabolism during early regeneration similar to the Warburg effect observed in tumor forming cells. Inhibition of glucose metabolism did not affect the overall health of the embryo but completely blocked the fin from regenerating post amputation due to the failure to form a functional blastema. We performed a time series of single cell RNA sequencing on regenerating tails with and without xxx of glucose metabolism. We demonstrated that metabolic reprogramming is required for sustained TGF \u00df signaling and blocking glucose metabolism largely mimicked inhibition of TGF \u00df receptors  both resulting in an aberrant blastema. Finally  we showed using genetic ablation of three possible metabolic pathways for glucose  that metabolic reprogramming is required to provide glucose specifically to the hexosamine biosynthetic pathway while neither glycolysis nor the pentose phosphate pathway were necessary for regeneration. Overall design: Single cell RNAseq data was generated from uninjured or regenerating embryonic zebrafish tails at 24 and 48 hours post amputation with and without xxx deoxyglucose. Please note that the UI ctrl.cloupe is a single sample from uninjured  untreated embryo tails and the ctrl cloupe.cloupe is an aggregate file of all non 2DG treated samples UI ctrl  24hpa ctrl  and 48hpa ctrl.", null, "pubmed:34518542", null, "48hpa ctrl", "GSM4319212", null, "source name:Regenerating embryonic zebrafish tail|strain:TAB 5|tissue:Regenerating embryonic tail|embryo age:5 dpf point:48hpa", "48hpa ctrl", "Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2. was used to demultiplex  for barcode processing  for single cell gene counts  and aggregating files. Further analyses of the samples was performed using Loupe Cell Browser 10x Genomics. Genome build: Danio Rerio 11 danRer11  GRCz11 Supplementary files format and content: cloupe files are provided which can be visualized with the Loupe Cell Browser 10x Genomics. Supplementary files format and content: hd5 files.", "Regenerating embryonic zebrafish tail", null, "Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM  Library and Gel Bead Kit V3 10x Genomics.", null, "strain:TAB 5|tissue:Regenerating embryonic tail|embryo age:5 dpf point:48hpa", "GSM4319212", "GSM4319212: 48hpa ctrl; Danio rerio; RNA Seq", "GSM4319212", null, "1", "Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM  Library and Gel Bead Kit V3 10x Genomics.", "GEO Accession:GSM4319212", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP249927", null, "intentional duplicate", "48hpa_ctrl.bam", "10X Genomics bam file", 6315141924.0, 69397164.0, "GSM4319212 r1", "0:91", "A:1820671652;C:1274680094;G:1600555332;T:1612090454;N:7144392", 91, null, null, null, 1820671652, 1274680094, 1600555332, 1612090454, 7144392, "SRX7744905", "SRS6165316", "SRA1044429", "GEO", "National Human Genome Research Institute, National Institutes of Health", 1, 0.94831, null, 0.155, null, 0.80866, null, 0.5428, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-02-18", "Larval", "Larval", "Tail", "Multi-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": ["56823"], "units": {}, "query_ms": 11.119261998828733}