run_metadata: 34876

This data as json

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
34876	SRR32289998	SRX27626940	SRS24034209	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.				FAC sorted RGCs at naive condition biological replicate 1	GSM8784907		tissue:Retinal ganglion cells\|cell type:Retinal ganglion cells\|genotype:Tgisl2b:eGFPzc7Tg\|treatment:Non injured\|batch:RNA extraction batch 1\|geo loc name:missing\|collection date:missing	FAC sorted RGCs at naive condition biological replicate 1	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		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		cell type:Retinal ganglion cells\|genotype:Tgisl2b:eGFPzc7Tg\|treatment:Non injured\|batch:RNA extraction batch 1	GSM8784907	GSM8784907: FAC sorted RGCs at naive condition biological replicate 1; Danio rerio; RNA Seq	GSM8784907 r1	GSM8784907	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP562853			GC121290.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz	fastq	384155460.0	7532460.0	GSM8784907 r2	0:51	A:107214095;C:82732789;G:84490928;T:109680699;N:36949	51				107214095	82732789	84490928	109680699	36949	SRX27626940	SRS24034209	SRA2075201	KU Leuven	KU Leuven												B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq		Belgium	2025-02-10	Undetermined	Adult	Eye	Sensory System