run_metadata: 62942

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
62942	SRR13447021	SRX9860257	SRS8040688	SRP301983	PRJNA692494	Localized EMT reprograms glial progenitors to promote spinal cord repair [single cell RNA seq]	GSE164944	Other	Single nuclear RNA sequencing was performed on spinal cord tissues from Tggfap:EGFP zebrafish at 1 xxx post injury using the 10x Genomics platform. Overall design: Single nuclear RNA sequencing of spinal cord tissue.	parent bioproject:PRJNA692492	pubmed:33609461		single cell injured spinal cord	GSM5023610		tissue:5 xxx post injury spinal cord nuclear\|tissues:spinal cord\|rna population:nuclear\|time point:5 xxx post injury	single cell injured spinal cord	Aligned reads were analyzed using the Seurat package v3.1.4 within R v3.6.3. Cells that have unique number of genes between 200 to 4000 and a mitochondrial gene percentage less than five were filtered. The “SCTransform” function was used for normalization scaling and finding variable features. SCTransform returned 3000 highly variable features for downstream analysis. Significant principal components were determined using “ElbowPlot” function. Forty principal components were selected to create a Shared Nearest Neighbour SNN graph using the “FindNeighbours” function. Clustering was performed by the Louvain algorithm using the function “FindClusters” and the resolution parameter was set to one. Uniform Manifold Approximation and Reduction UMAP was used for non linear dimensional reduction of the first 40 principle components and to visualize the data in two dimensional space “RunUMAP” function Differential gene expression for individual cluster was identified using Wilcoxon rank sum tests in the “FindAllMarkers” function. Supplementary files format and content: RDS file	5 xxx post injury spinal cord nuclear	Adult zebrafish were subjected to complete spinal cord transection.	gfap:EGFP transgenic animals were subjected to SCI and 2 mm SC tissue sections spanning the lesion site were collected at 1 wpi. Nuclei were isolated from 45 pooled SC tissues. For single nuclear library preparation on the 10x Genomics platform the Chromium Single Cell 3′ GEM Library and Gel Bead Kit v3 cat# 1000092 and the Chromium Chip B Single Cell Kit cat# 1000074 were used according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagents Kits V3 User Guide. The resulting cDNA libraries were quantified on an Agilent Tapestation and sequenced on Illumina HiSeq 3000.		tissues:spinal cord\|rna population:nuclear\|time point:5 xxx post injury	GSM5023610	GSM5023610: single cell injured spinal cord; Danio rerio; RNA Seq	GSM5023610		1	gfap:EGFP transgenic animals were subjected to SCI and 2 mm SC tissue sections spanning the lesion site were collected at 1 wpi. Nuclei were isolated from 45 pooled SC tissues. For single nuclear library preparation on the 10x Genomics platform the Chromium Single Cell 3′ GEM Library and Gel Bead Kit v3 cat# 1000092 and the Chromium Chip B Single Cell Kit cat# 1000074 were used according to the manufacturer's instructions in the Chromium Single Cell 3′ Reagents Kits V3 User Guide. The resulting cDNA libraries were quantified on an Agilent Tapestation and sequenced on Illumina HiSeq 3000.	GEO Accession:GSM5023610	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000		SRP301983		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=ZB nuc S1 L007 I1 001.fastq.gz read2PairFiles=ZB nuc S1 L007 R1 001.fastq.gz read3PairFiles=ZB nuc S1 L007 R2 001.fastq.gz	ZB_nuc_S1_L007_R2_001.fastq.gz ZB_nuc_S1_L007_R1_001.fastq.gz ZB_nuc_S1_L007_I1_001.fastq.gz	fastq fastq fastq	134333186988.0	436146711.0	GSM5023610 r1	0:8 1:150 2:150	A:34573306207;C:23174725516;G:24790836286;T:51771968988;N:22349991	8	150	150		34573306207	23174725516	24790836286	51771968988	22349991	SRX9860257	SRS8040688	SRA1184553	GEO	Developmental Biology, Washington University	1	0.72186		0.41754		0.80551		0.54979		150		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2021-01-15	Adult	Adult	Spinal Cord	Nervous System