run_metadata: 71758

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
71758	SRR22013539	SRX17995701	SRS15506855	SRP404046	PRJNA893216	Insulin like growth factor receptor / mTOR signaling elevates global translation to accelerate zebrafish fin regenerative outgrowth	GSE216359	Transcriptome Analysis	We generate a single cell transcriptome dataset to characterize zebrafish fin regenerative outgrowth and explore coordinated cell behaviors. Overall design: Regenerated fin tissue was collected from 3 and 7 dy post amputation zebrafish caudal fins and analyzed using scRNA seq		pubmed:37290497		3 dpa scRNA seq	GSM6670934		source name:Caudal fin\|tissue:Caudal fin\|time:3 dpa\|genotype:Tgsp7:EGFP;Tgtph1b:mCherry\|Stage:Adult\|geo loc name:missing\|collection date:missing	3 dpa scRNA seq	Pseudoalignment and processing of raw reads was done in Kallisto/Bustools https://github.com/pachterlab/kb python to generate a cell data set for Monocle3 https://cole trapnell lab.github.io/monocle3/ Assembly: GRCz11.99 Supplementary files format and content: rds file of cell data set	Caudal fin		Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice diced then washed with L 15 media supplemented with 1X GlutaMax 1X Antibiotic Antimycotic and 1X Penicillin Streptomycin all Thermo Fisher. The tissue was then enzymatically digested using 0.25% Trypsin EDTA Thermo Fisher and Liberase DL 2 mg/ml Sigma at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 μm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re suspended in PBS + 0.04% bovine serum albumin. Library was performed according to the manufacturer’s instructions single cell 3’ v3 protocol 10x Genomics. Briefly cells from fin tissue were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up amplified by PCR and the appropiate sized fragments were selected for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.		tissue:Caudal fin\|time:3 dpa\|genotype:Tgsp7:EGFP;Tgtph1b:mCherry\|Stage:Adult	GSM6670934	GSM6670934: 3 dpa scRNA seq; Danio rerio; RNA Seq	GSM6670934 r1	GSM6670934	1	Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice diced then washed with L 15 media supplemented with 1X GlutaMax 1X Antibiotic Antimycotic and 1X Penicillin Streptomycin all Thermo Fisher. The tissue was then enzymatically digested using 0.25% Trypsin EDTA Thermo Fisher and Liberase DL 2 mg/ml Sigma at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 μm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re suspended in PBS + 0.04% bovine serum albumin. Library was performed according to the manufacturer'		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP404046		loader:fastq load.py	3669_3dpa_S4_L002_I1_001.fastq.gz 3669_3dpa_S4_L002_R1_001.fastq.gz 3669_3dpa_S4_L002_R2_001.fastq.gz	fastq fastq fastq	18947450035.0	138302555.0	GSM6670934 r2	0:8 1:28 2:101	A:4126083375;C:2867407006;G:2991995583;T:3979778947;N:3293144	8	28	101		4126083375	2867407006	2991995583	3979778947	3293144	SRX17995701	SRS15506855	SRA1525679	Stankunas, Institute of Molecular Biology, University of Oregon	Stankunas, Institute of Molecular Biology, University of Oregon	1	0.91921		0.19517		0.78524		0.57129		101		B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x		United States	2022-10-22	Adult	Adult	Fin	Surface Structure