{"database": "metadata", "table": "run_metadata", "rows": [[34820, "SRR32289942", "SRX27626968", "SRS24034237", "SRP562853", "PRJNA1221797", "Successful axonal regeneration is driven by evolutionarily conserved metabolic reprogramming", "GSE289140", "Transcriptome Analysis", "Unlike mammals  zebrafish can regrow xxx post injury and restore circuit function in the central nervous system CNS. Mitochondria have been identified as key players in this process  but how different metabolic pathways work together to sustain regeneration remains unclear. Using RNA sequencing of adult zebrafish retinal ganglion cells RGCs post optic nerve crush injury  we demonstrate that oxidative phosphorylation is downregulated during axonal regrowth. Simultaneously  the thioredoxin antioxidant system is upregulated  likely to limit oxidative damage. Additionally  we observe an integrated upregulation of glycolysis and the pentose phosphate pathway during the initial regrowth phases  possibly to provide energy while supplying NADPH for biosynthesis and antioxidant responses. We show that this metabolic reprogramming is evolutionarily conserved  as it also occurs in the pro regenerative mammalian Pten and Socs3 co deletion model. Inhibiting glycolysis and thioredoxin in zebrafish impairs axonal regrowth  suggesting that targeting these pathways could enhance CNS regeneration in mammals. Overall design: Bulk RNA sequencing of FAC sorted adult Tgisl2b:eGFPzc7Tg zebrafish retinal ganglion cells under the uninjured naive condition and at 1  3  6  10  and 14 days post optic nerve crush injury.", null, null, null, "FAC sorted RGCs at 10dpi biological replicate 5", "GSM8784935", null, "tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing", "FAC sorted RGCs at 10dpi biological replicate 5", "Technical replicates of RNA seq samples were merged post sequencing  and adapter sequences were removed using TrimGalore v0.6.7. Quality control was conducted using FastQC v0.11.5. Sequencing reads were aligned to the zebrafish reference genome Ensembl GRCz11 using the STAR aligner. Genes with low expression were filtered out using a custom developed R script. Batch effects were corrected with pyCombat. Assembly: Ensembl GRCz11 Supplementary files format and content: Tab delimited text file includes raw counts for each sample Supplementary files format and content: Filtered and batch effects corrected counts for all samples", "Retinal ganglion cells", null, "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer\u2019s instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2", "GSM8784935", "GSM8784935: FAC sorted RGCs at 10dpi biological replicate 5; Danio rerio; RNA Seq", "GSM8784935 r1", "GSM8784935", "1", "RNA was extracted in two separate batches using the Quick RNA Microprep kit according to the manufacturer's instructions. Libraries were prepared using the Smart Seq2 method RGC samples  Nextera XT DNA  Illumina  San Diego  CA  USA", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP562853", null, null, "GC122374.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 411821124.0, 8074924.0, "GSM8784935 r2", "0:51", "A:106698116;C:97949900;G:99548706;T:107586633;N:37769", 51, null, null, null, 106698116, 97949900, 99548706, 107586633, 37769, "SRX27626968", "SRS24034237", "SRA2075201", "KU Leuven", "KU Leuven", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-02-10", "Undetermined", "Adult", "Eye", "Sensory 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": ["34820"], "units": {}, "query_ms": 10.084919995279051}