run_metadata: 56821

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
56821	SRR15414666	SRX11716796	SRS9747214	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 ß signaling and blocking glucose metabolism largely mimicked inhibition of TGF ß 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.		pubmed:34518542		UI ctrl	GSM5513440		tissue:Regenerating embryonic zebrafish tail\|strain:TAB 5\|embryo age:3 dpf	UI ctrl	Binary Base Call BCL files generated from an Illumina 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 Supplementary files format and content: clouple files are provided which can be visiualized with the Loupe Cell Browser 10x Genomics	Regenerating embryonic zebrafish tail		Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries was generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics		strain:TAB 5\|embryo age:3 dpf	GSM5513440	GSM5513440: UI ctrl; Danio rerio; RNA Seq	GSM5513440		1	Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries was generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics	GEO Accession:GSM5513440	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550		SRP249927		assembly:Danio Rerio 11\|intentional duplicate	UI_ctrl.bam	10X Genomics bam file	8002896265.0	87943915.0	GSM5513440 r1	0:91	A:2325005630;C:1613869115;G:2033844364;T:2021144325;N:9032831	91				2325005630	1613869115	2033844364	2021144325	9032831	SRX11716796	SRS9747214	SRA1044429	GEO	National Human Genome Research Institute, National Institutes of Health	1	0.93599		0.15189		0.83603		0.50802		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2021-08-11	Larval	Larval	Tail	Multi-system