run_metadata: 52475

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
52475	SRR9198729	SRX5970646	SRS4876620	SRP200391	PRJNA546235	Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation	GSE132166	Other	Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones single cell RNA sequencing in vivo calcium imaging and manipulation of neural activity we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity but infrequently differentiates despite contact with permissive axons. Instead these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs which readily differentiates and which shows less elaborate more dynamic processes and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate with implications for myelin development plasticity and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations and in vivo live cell imaging data to map cell fates. Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2		pubmed:32066987		Zfish OPCs	GSM3851760		source name:oligodendrocyte precursor cells\|transgenic line:Tgolig1:memEYFP\|tissue:EYFP cells FACS sorted from dissociated whole animal\|cell type:oligodendrocyte precursor cells\|age:5 dpf	Zfish OPCs	Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10 1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310 individual cells in specific celltypes. The R object .rds consists of a Seurat v.3 object. Cells were clustered with Seurat v.3 and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions tsne and metadata Celltype the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix where columns belong to celltype and rows to cells. R object .rds.	oligodendrocyte precursor cells	no treatment	A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al. Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10 1096 1098 2013	Tgolig1:memYFP zebrafish were raised until 5 dpf	transgenic line:Tgolig1:memEYFP\|tissue:EYFP cells FACS sorted from dissociated whole animal\|cell type:oligodendrocyte precursor cells\|age:5 dpf	GSM3851760	GSM3851760: Zfish OPCs; Danio rerio; RNA Seq	GSM3851760		1	A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al. Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10 1096 1098 2013	GEO Accession:GSM3851760	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP200391			H2_R1.fastq.gz	fastq	47400620.0	1102340.0	GSM3851760 r185	0:43	A:12972898;C:10576318;G:10850948;T:13000456;N:0	43				12972898	10576318	10850948	13000456	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.89148		0.13951		0.93716		0.5256		43		B		usable mapping rate	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq		Sweden	2019-06-04	Larval	Larval	Whole Organism	All anatomical structures