{"database": "metadata", "table": "run_metadata", "rows": [[52389, "SRR9198643", "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", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "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\u00b0C  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", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  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", null, "SRP200391", null, null, "E1_R1.fastq.gz", "fastq", 41009788.0, 953716.0, "GSM3851760 r107", "0:43", "A:11633133;C:8565119;G:8761780;T:12049756;N:0", 43, null, null, null, 11633133, 8565119, 8761780, 12049756, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.83802, null, 0.32341, null, 0.88038, null, 0.49748, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["52389"], "units": {}, "query_ms": 11.239374001888791}