metadata: run_metadata: 416 rows where experiment.library_selection = "cDNA", technology = "smartseq" and tissue

416 rows where experiment.library_selection = "cDNA", technology = "smartseq" and tissue_curation = "Whole Organism"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	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.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
50527	50527	SRR8129710	SRX4950832	SRS3993023	SRP167139	PRJNA499073	Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes	GSE121917	Transcriptome Analysis	We provide a method for high quality RNA purification out of a small number 5000 100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.	pubmed:30894119	Rneasy unsorted	GSM3449971	tissue:Fli:GFP whole embryo 5 days RNeasy sample 1\|cell type:fli:GFP whole embryo\|age:5 days\|rna isolation kit:RNeasy plus micro kit	Rneasy unsorted	Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data	Fli:GFP whole embryo 5 days RNeasy sample 1		polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology tagmentation and sample barcoding with the Nextera XT kit illumina		cell type:fli:GFP whole embryo\|age:5 days\|rna isolation kit:RNeasy plus micro kit	GSM3449971	GSM3449971: Rneasy unsorted; Danio rerio; RNA Seq	GSM3449971	1	polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology tagmentation and sample barcoding with the Nextera XT kit illumina	GEO Accession:GSM3449971	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP167139	Q_unsorted_R1.fastq.gz Q_unsorted_R2.fastq.gz	fastq fastq	4155128139.0	27505173.0	GSM3449971 r1	0:75.53 1:75.53	A:1075371555;C:1005905830;G:1019395949;T:1054443500;N:11305	75	75	1075371555	1005905830	1019395949	1054443500	11305	SRX4950832	SRS3993023	SRA800291	GEO	Center for Medical Genetics, Ghent University	2	0.92688	0.92569	0.06942	0.0708	0.73241	0.74164	0.44144	0.44652	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Belgium	2018-10-29	Larval	Larval	Whole Organism	All anatomical structures
50528	50528	SRR8129709	SRX4950831	SRS3993022	SRP167139	PRJNA499073	Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes	GSE121917	Transcriptome Analysis	We provide a method for high quality RNA purification out of a small number 5000 100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.	pubmed:30894119	RNAqueous unsorted	GSM3449970	tissue:Fli:GFP whole embryo 5 days RNAqueous sample 1\|cell type:fli:GFP whole embryo\|age:5 days\|rna isolation kit:RNAqueous micro	RNAqueous unsorted	Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data	Fli:GFP whole embryo 5 days RNAqueous sample 1		polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology tagmentation and sample barcoding with the Nextera XT kit illumina		cell type:fli:GFP whole embryo\|age:5 days\|rna isolation kit:RNAqueous micro	GSM3449970	GSM3449970: RNAqueous unsorted; Danio rerio; RNA Seq	GSM3449970	1	polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology tagmentation and sample barcoding with the Nextera XT kit illumina	GEO Accession:GSM3449970	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP167139	A_unsorted_R1.fastq.gz A_unsorted_R2.fastq.gz	fastq fastq	3613198121.0	23920751.0	GSM3449970 r1	0:75.53 1:75.52	A:976322858;C:832409562;G:835538411;T:968916959;N:10331	75	75	976322858	832409562	835538411	968916959	10331	SRX4950831	SRS3993022	SRA800291	GEO	Center for Medical Genetics, Ghent University	2	0.91518	0.91772	0.12399	0.12715	0.71196	0.71764	0.46555	0.45805	72	75	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	Belgium	2018-10-29	Larval	Larval	Whole Organism	All anatomical structures
51258	51258	SRR8632327	SRX5431028	SRS4411023	SRP186864	PRJNA524286	The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation	GSE127174	Transcriptome Analysis	We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils and RNAseq for identification of mRNA targets of miRNA 199 in neutrophils Overall design: for miRNA profiles we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control	pubmed:31451657	total rep 3	GSM3629722	source name:whole embryo\|strain background:AB\|gentoype/variation:wild type\|tissue:whole embryo	total rep 3	Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter: for Samples 1 5: “ alignEndsType EndToEnd outFilterMismatchNmax 1 outFilterMultimapScoreRange 0 outFilterMultimapNmax 10 outSAMunmapped Within outFilterScoreMinOverLread 0 outFilterMatchNminOverLread 0 outFilterMatchNmin 16 alignSJDBoverhangMin 1000” for Samples 6 11: “ outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5: “ s 1 –Q 10” for Samples 6 11 " p Q 10". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples; for Samples 6 11 using read count per million CPM > 0.5 in more than 3 of the samples normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts	whole embryo	transgenic zebrafish lines were used to produce embryos. For miRNA profiling transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.	tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..	zebrafish embryos were grown to 3 dpf in embryonic media	strain background:AB\|gentoype/variation:wild type\|tissue:whole embryo	GSM3629722	GSM3629722: total rep 3; Danio rerio; RNA Seq	GSM3629722	1	tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..	GEO Accession:GSM3629722	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP186864	c3.fastq.gz	fastq	142798100.0	2855962.0	GSM3629722 r1	0:50	A:33558108;C:34453721;G:38902032;T:35874180;N:10059	50		33558108	34453721	38902032	35874180	10059	SRX5431028	SRS4411023	SRA852308	GEO	Department of Biological Sciences, Purdue University	1	0.02673		0.00469		0.98455		0.62342		50		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	trueseq	sc	single_cell_plate	smartseq	United States	2019-02-26	Larval	Larval	Whole Organism	All anatomical structures
51259	51259	SRR8632326	SRX5431027	SRS4411022	SRP186864	PRJNA524286	The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation	GSE127174	Transcriptome Analysis	We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils and RNAseq for identification of mRNA targets of miRNA 199 in neutrophils Overall design: for miRNA profiles we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control	pubmed:31451657	total rep 2	GSM3629721	source name:whole embryo\|strain background:AB\|gentoype/variation:wild type\|tissue:whole embryo	total rep 2	Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter: for Samples 1 5: “ alignEndsType EndToEnd outFilterMismatchNmax 1 outFilterMultimapScoreRange 0 outFilterMultimapNmax 10 outSAMunmapped Within outFilterScoreMinOverLread 0 outFilterMatchNminOverLread 0 outFilterMatchNmin 16 alignSJDBoverhangMin 1000” for Samples 6 11: “ outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5: “ s 1 –Q 10” for Samples 6 11 " p Q 10". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples; for Samples 6 11 using read count per million CPM > 0.5 in more than 3 of the samples normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts	whole embryo	transgenic zebrafish lines were used to produce embryos. For miRNA profiling transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.	tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..	zebrafish embryos were grown to 3 dpf in embryonic media	strain background:AB\|gentoype/variation:wild type\|tissue:whole embryo	GSM3629721	GSM3629721: total rep 2; Danio rerio; RNA Seq	GSM3629721	1	tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..	GEO Accession:GSM3629721	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP186864	c2.fastq.gz	fastq	176136650.0	3522733.0	GSM3629721 r1	0:50	A:42179466;C:41890753;G:47676052;T:44377787;N:12592	50		42179466	41890753	47676052	44377787	12592	SRX5431027	SRS4411022	SRA852308	GEO	Department of Biological Sciences, Purdue University	1	0.01253		0.00298		0.99342		0.67131		50		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	trueseq	sc	single_cell_plate	smartseq	United States	2019-02-26	Larval	Larval	Whole Organism	All anatomical structures
51260	51260	SRR8632325	SRX5431026	SRS4411021	SRP186864	PRJNA524286	The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation	GSE127174	Transcriptome Analysis	We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils and RNAseq for identification of mRNA targets of miRNA 199 in neutrophils Overall design: for miRNA profiles we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control	pubmed:31451657	total rep 1	GSM3629720	source name:whole embryo\|strain background:AB\|gentoype/variation:wild type\|tissue:whole embryo	total rep 1	Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter: for Samples 1 5: “ alignEndsType EndToEnd outFilterMismatchNmax 1 outFilterMultimapScoreRange 0 outFilterMultimapNmax 10 outSAMunmapped Within outFilterScoreMinOverLread 0 outFilterMatchNminOverLread 0 outFilterMatchNmin 16 alignSJDBoverhangMin 1000” for Samples 6 11: “ outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5: “ s 1 –Q 10” for Samples 6 11 " p Q 10". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples; for Samples 6 11 using read count per million CPM > 0.5 in more than 3 of the samples normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts	whole embryo	transgenic zebrafish lines were used to produce embryos. For miRNA profiling transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.	tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..	zebrafish embryos were grown to 3 dpf in embryonic media	strain background:AB\|gentoype/variation:wild type\|tissue:whole embryo	GSM3629720	GSM3629720: total rep 1; Danio rerio; RNA Seq	GSM3629720	1	tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..	GEO Accession:GSM3629720	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP186864	c1.fastq.gz	fastq	180216500.0	3604330.0	GSM3629720 r1	0:50	A:43005950;C:42787875;G:49009406;T:45400170;N:13099	50		43005950	42787875	49009406	45400170	13099	SRX5431026	SRS4411021	SRA852308	GEO	Department of Biological Sciences, Purdue University	1	0.01759		0.00459		0.99101		0.71252		50		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	trueseq	sc	single_cell_plate	smartseq	United States	2019-02-26	Larval	Larval	Whole Organism	All anatomical structures
52380	52380	SRR9198634	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	A10_R1.fastq.gz	fastq	22730187.0	528609.0	GSM3851760 r1	0:43	A:6531713;C:4702880;G:4826497;T:6669097;N:0	43		6531713	4702880	4826497	6669097	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.86984		0.3317		0.86977		0.50211		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
52381	52381	SRR9198635	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	A19_R1.fastq.gz	fastq	25422417.0	591219.0	GSM3851760 r10	0:43	A:7420297;C:5115508;G:5236996;T:7649616;N:0	43		7420297	5115508	5236996	7649616	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.85285		0.39693		0.87675		0.44071		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
52382	52382	SRR9198636	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	E13_R1.fastq.gz	fastq	34049550.0	791850.0	GSM3851760 r100	0:43	A:9807395;C:7041091;G:7187781;T:10013283;N:0	43		9807395	7041091	7187781	10013283	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.86073		0.36367		0.85589		0.48001		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
52383	52383	SRR9198637	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	E14_R1.fastq.gz	fastq	30226893.0	702951.0	GSM3851760 r101	0:43	A:8402351;C:6582983;G:6770609;T:8470950;N:0	43		8402351	6582983	6770609	8470950	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.87786		0.20548		0.92119		0.5325		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
52384	52384	SRR9198638	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	E15_R1.fastq.gz	fastq	31104093.0	723351.0	GSM3851760 r102	0:43	A:8946868;C:6414234;G:6568361;T:9174630;N:0	43		8946868	6414234	6568361	9174630	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.85741		0.37503		0.89073		0.48996		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
52385	52385	SRR9198639	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	E16_R1.fastq.gz	fastq	34438399.0	800893.0	GSM3851760 r103	0:43	A:9959668;C:7061544;G:7228493;T:10188694;N:0	43		9959668	7061544	7228493	10188694	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.85657		0.37381		0.89503		0.47367		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
52386	52386	SRR9198640	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	E17_R1.fastq.gz	fastq	31687560.0	736920.0	GSM3851760 r104	0:43	A:9042349;C:6631079;G:6783803;T:9230329;N:0	43		9042349	6631079	6783803	9230329	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.86922		0.28531		0.87647		0.50906		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
52387	52387	SRR9198641	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	E18_R1.fastq.gz	fastq	28829178.0	670446.0	GSM3851760 r105	0:43	A:8040858;C:6240958;G:6375940;T:8171422;N:0	43		8040858	6240958	6375940	8171422	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.88484		0.25108		0.89796		0.52328		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
52388	52388	SRR9198642	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	E19_R1.fastq.gz	fastq	29456161.0	685027.0	GSM3851760 r106	0:43	A:8185810;C:6362322;G:6490611;T:8417418;N:0	43		8185810	6362322	6490611	8417418	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.87467		0.2568		0.87637		0.44643		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
52389	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	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	E1_R1.fastq.gz	fastq	41009788.0	953716.0	GSM3851760 r107	0:43	A:11633133;C:8565119;G:8761780;T:12049756;N:0	43		11633133	8565119	8761780	12049756	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.83802		0.32341		0.88038		0.49748		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
52390	52390	SRR9198644	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	E20_R1.fastq.gz	fastq	29314777.0	681739.0	GSM3851760 r108	0:43	A:8470707;C:6002913;G:6136651;T:8704506;N:0	43		8470707	6002913	6136651	8704506	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.85476		0.37692		0.87633		0.47456		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
52391	52391	SRR9198645	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	E21_R1.fastq.gz	fastq	39374455.0	915685.0	GSM3851760 r109	0:43	A:11315860;C:8119631;G:8323167;T:11615797;N:0	43		11315860	8119631	8323167	11615797	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.85391		0.36988		0.91039		0.50229		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
52392	52392	SRR9198646	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	A1_R1.fastq.gz	fastq	3574031.0	83117.0	GSM3851760 r11	0:43	A:1037490;C:644669;G:647675;T:1244197;N:0	43		1037490	644669	647675	1244197	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.08124		0.07796		0.99709		0.43644		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
52393	52393	SRR9198647	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	E22_R1.fastq.gz	fastq	45159546.0	1050222.0	GSM3851760 r110	0:43	A:13081668;C:9210038;G:9426293;T:13441547;N:0	43		13081668	9210038	9426293	13441547	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.84853		0.41231		0.90678		0.50893		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
52394	52394	SRR9198648	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	E23_R1.fastq.gz	fastq	46674522.0	1085454.0	GSM3851760 r111	0:43	A:13407038;C:9644708;G:9870254;T:13752522;N:0	43		13407038	9644708	9870254	13752522	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.8528		0.35087		0.91896		0.50728		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
52395	52395	SRR9198649	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	E24_R1.fastq.gz	fastq	40946578.0	952246.0	GSM3851760 r112	0:43	A:11353999;C:8901776;G:9087747;T:11603056;N:0	43		11353999	8901776	9087747	11603056	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.88574		0.2555		0.89203		0.53214		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
52396	52396	SRR9198650	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	E2_R1.fastq.gz	fastq	35795909.0	832463.0	GSM3851760 r113	0:43	A:10008515;C:7658565;G:7846504;T:10282325;N:0	43		10008515	7658565	7846504	10282325	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.8507		0.24931		0.87643		0.51656		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
52397	52397	SRR9198651	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	E3_R1.fastq.gz	fastq	34867496.0	810872.0	GSM3851760 r114	0:43	A:9952111;C:7269477;G:7461395;T:10184513;N:0	43		9952111	7269477	7461395	10184513	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.85806		0.33604		0.85468		0.48609		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
52398	52398	SRR9198652	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	E4_R1.fastq.gz	fastq	4629036.0	107652.0	GSM3851760 r115	0:43	A:1294799;C:1008604;G:1044853;T:1280780;N:0	43		1294799	1008604	1044853	1280780	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.87228		0.19931		0.94229		0.54841		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
52399	52399	SRR9198653	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	E5_R1.fastq.gz	fastq	6320914.0	146998.0	GSM3851760 r116	0:43	A:1861194;C:1147340;G:1160856;T:2151524;N:0	43		1861194	1147340	1160856	2151524	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.0887		0.08394		0.99389		0.4262		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
52400	52400	SRR9198654	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	E6_R1.fastq.gz	fastq	32168257.0	748099.0	GSM3851760 r117	0:43	A:9360276;C:6476288;G:6645427;T:9686266;N:0	43		9360276	6476288	6645427	9686266	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.83653		0.4296		0.91171		0.48995		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
52401	52401	SRR9198655	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	E7_R1.fastq.gz	fastq	36882089.0	857723.0	GSM3851760 r118	0:43	A:10430067;C:7805495;G:7991940;T:10654587;N:0	43		10430067	7805495	7991940	10654587	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.86871		0.29809		0.90011		0.49514		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
52402	52402	SRR9198656	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	E8_R1.fastq.gz	fastq	24809839.0	576973.0	GSM3851760 r119	0:43	A:7144307;C:5119783;G:5223795;T:7321954;N:0	43		7144307	5119783	5223795	7321954	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.86137		0.37732		0.88611		0.49645		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
52403	52403	SRR9198657	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	A20_R1.fastq.gz	fastq	20992729.0	488203.0	GSM3851760 r12	0:43	A:6046890;C:4289153;G:4410467;T:6246219;N:0	43		6046890	4289153	4410467	6246219	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.85185		0.31773		0.91845		0.58528		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
52404	52404	SRR9198658	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	E9_R1.fastq.gz	fastq	40215105.0	935235.0	GSM3851760 r120	0:43	A:11360646;C:8521492;G:8730341;T:11602626;N:0	43		11360646	8521492	8730341	11602626	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.86307		0.33177		0.8982		0.47644		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
52405	52405	SRR9198659	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	F10_R1.fastq.gz	fastq	19107093.0	444351.0	GSM3851760 r121	0:43	A:5563356;C:3848064;G:3951297;T:5744376;N:0	43		5563356	3848064	3951297	5744376	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.84285		0.40366		0.89171		0.48828		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
52406	52406	SRR9198660	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	F11_R1.fastq.gz	fastq	31628951.0	735557.0	GSM3851760 r122	0:43	A:9033354;C:6606929;G:6787882;T:9200786;N:0	43		9033354	6606929	6787882	9200786	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.86464		0.31248		0.90104		0.50525		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
52407	52407	SRR9198661	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	F12_R1.fastq.gz	fastq	24055834.0	559438.0	GSM3851760 r123	0:43	A:6622600;C:5260253;G:5395038;T:6777943;N:0	43		6622600	5260253	5395038	6777943	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.87692		0.2118		0.91238		0.42713		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
52408	52408	SRR9198662	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	F13_R1.fastq.gz	fastq	27688517.0	643919.0	GSM3851760 r124	0:43	A:8080865;C:5560695;G:5700222;T:8346735;N:0	43		8080865	5560695	5700222	8346735	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.83469		0.43252		0.90938		0.48723		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
52409	52409	SRR9198663	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	F14_R1.fastq.gz	fastq	21924754.0	509878.0	GSM3851760 r125	0:43	A:6090527;C:4750408;G:4851102;T:6232717;N:0	43		6090527	4750408	4851102	6232717	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.88707		0.24693		0.89098		0.42985		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
52410	52410	SRR9198664	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	F15_R1.fastq.gz	fastq	24524190.0	570330.0	GSM3851760 r126	0:43	A:7099978;C:5008036;G:5144163;T:7272013;N:0	43		7099978	5008036	5144163	7272013	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.84943		0.37319		0.88542		0.49363		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
52411	52411	SRR9198665	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	F16_R1.fastq.gz	fastq	22940113.0	533491.0	GSM3851760 r127	0:43	A:6806189;C:4493084;G:4602856;T:7037984;N:0	43		6806189	4493084	4602856	7037984	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.83481		0.50302		0.90155		0.55502		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
52412	52412	SRR9198666	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	F17_R1.fastq.gz	fastq	14327600.0	333200.0	GSM3851760 r128	0:43	A:4094254;C:2985444;G:3065124;T:4182778;N:0	43		4094254	2985444	3065124	4182778	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.86023		0.27478		0.9262		0.50627		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
52413	52413	SRR9198667	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	F18_R1.fastq.gz	fastq	13237507.0	307849.0	GSM3851760 r129	0:43	A:3843212;C:2694145;G:2779980;T:3920170;N:0	43		3843212	2694145	2779980	3920170	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.83869		0.33275		0.89802		0.53459		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
52414	52414	SRR9198668	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	A21_R1.fastq.gz	fastq	23607215.0	549005.0	GSM3851760 r13	0:43	A:6949976;C:4679980;G:4802349;T:7174910;N:0	43		6949976	4679980	4802349	7174910	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.84434		0.46159		0.89173		0.46625		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
52415	52415	SRR9198669	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	F19_R1.fastq.gz	fastq	28189725.0	655575.0	GSM3851760 r130	0:43	A:7998454;C:5905042;G:6043708;T:8242521;N:0	43		7998454	5905042	6043708	8242521	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.86503		0.27006		0.89465		0.50557		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
52416	52416	SRR9198670	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	F1_R1.fastq.gz	fastq	19684712.0	457784.0	GSM3851760 r131	0:43	A:5427483;C:4337414;G:4521536;T:5398279;N:0	43		5427483	4337414	4521536	5398279	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.87052		0.16084		0.90276		0.50242		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
52417	52417	SRR9198671	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	F20_R1.fastq.gz	fastq	25811825.0	600275.0	GSM3851760 r132	0:43	A:7620260;C:5037810;G:5184002;T:7969753;N:0	43		7620260	5037810	5184002	7969753	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.81686		0.50881		0.91031		0.52696		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
52418	52418	SRR9198672	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	F21_R1.fastq.gz	fastq	31327564.0	728548.0	GSM3851760 r133	0:43	A:8893372;C:6587100;G:6751304;T:9095788;N:0	43		8893372	6587100	6751304	9095788	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.87094		0.28476		0.87797		0.5071		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
52419	52419	SRR9198673	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	F22_R1.fastq.gz	fastq	25009187.0	581609.0	GSM3851760 r134	0:43	A:6965919;C:5371799;G:5499602;T:7171867;N:0	43		6965919	5371799	5499602	7171867	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.87185		0.25342		0.91214		0.56099		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
52420	52420	SRR9198674	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	F23_R1.fastq.gz	fastq	32902998.0	765186.0	GSM3851760 r135	0:43	A:9533499;C:6716093;G:6870853;T:9782553;N:0	43		9533499	6716093	6870853	9782553	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.85794		0.35536		0.87671		0.50276		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
52421	52421	SRR9198675	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	F24_R1.fastq.gz	fastq	31013578.0	721246.0	GSM3851760 r136	0:43	A:9001008;C:6274940;G:6415769;T:9321861;N:0	43		9001008	6274940	6415769	9321861	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.84095		0.36884		0.92234		0.53474		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
52422	52422	SRR9198676	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	F2_R1.fastq.gz	fastq	23623125.0	549375.0	GSM3851760 r137	0:43	A:6462921;C:5250054;G:5397862;T:6512288;N:0	43		6462921	5250054	5397862	6512288	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.87991		0.23553		0.91173		0.51346		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
52423	52423	SRR9198677	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	F3_R1.fastq.gz	fastq	56849268.0	1322076.0	GSM3851760 r138	0:43	A:15634028;C:12520216;G:12867754;T:15827270;N:0	43		15634028	12520216	12867754	15827270	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.871		0.20701		0.92703		0.49491		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
52424	52424	SRR9198678	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	F4_R1.fastq.gz	fastq	46322653.0	1077271.0	GSM3851760 r139	0:43	A:13343135;C:9581671;G:9823311;T:13574536;N:0	43		13343135	9581671	9823311	13574536	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.85062		0.40373		0.91281		0.50706		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
52425	52425	SRR9198679	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	A22_R1.fastq.gz	fastq	25134059.0	584513.0	GSM3851760 r14	0:43	A:6909921;C:5512326;G:5635533;T:7076279;N:0	43		6909921	5512326	5635533	7076279	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.89127		0.19785		0.90179		0.50794		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
52426	52426	SRR9198680	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	F5_R1.fastq.gz	fastq	51033561.0	1186827.0	GSM3851760 r140	0:43	A:14605293;C:10643260;G:10917516;T:14867492;N:0	43		14605293	10643260	10917516	14867492	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.85584		0.39713		0.90043		0.48754		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
52427	52427	SRR9198681	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	F6_R1.fastq.gz	fastq	11300916.0	262812.0	GSM3851760 r141	0:43	A:3321000;C:2297183;G:2385833;T:3296900;N:0	43		3321000	2297183	2385833	3296900	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.85718		0.4262		0.91914		0.50468		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
52428	52428	SRR9198682	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	F7_R1.fastq.gz	fastq	45278742.0	1052994.0	GSM3851760 r142	0:43	A:13002638;C:9369548;G:9622447;T:13284109;N:0	43		13002638	9369548	9622447	13284109	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.83814		0.37647		0.90554		0.49616		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
52429	52429	SRR9198683	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	F8_R1.fastq.gz	fastq	14835344.0	345008.0	GSM3851760 r143	0:43	A:4110076;C:3245754;G:3325157;T:4154357;N:0	43		4110076	3245754	3325157	4154357	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.86906		0.19318		0.89394		0.51872		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
52430	52430	SRR9198684	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	F9_R1.fastq.gz	fastq	22851017.0	531419.0	GSM3851760 r144	0:43	A:6468358;C:4849150;G:4966680;T:6566829;N:0	43		6468358	4849150	4966680	6566829	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.8823		0.18338		0.88168		0.4915		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
52431	52431	SRR9198685	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	G10_R1.fastq.gz	fastq	10655400.0	247800.0	GSM3851760 r145	0:43	A:2964578;C:2045554;G:1988943;T:3656325;N:0	43		2964578	2045554	1988943	3656325	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.08282		0.07443		0.99553		0.77115		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
52432	52432	SRR9198686	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	G11_R1.fastq.gz	fastq	38720210.0	900470.0	GSM3851760 r146	0:43	A:10652326;C:8557186;G:8758762;T:10751936;N:0	43		10652326	8557186	8758762	10751936	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.87521		0.21283		0.93779		0.50587		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
52433	52433	SRR9198687	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	G12_R1.fastq.gz	fastq	37872809.0	880763.0	GSM3851760 r147	0:43	A:10570260;C:8249277;G:8452653;T:10600619;N:0	43		10570260	8249277	8452653	10600619	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.88166		0.24488		0.87265		0.47744		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
52434	52434	SRR9198688	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	G13_R1.fastq.gz	fastq	46220313.0	1074891.0	GSM3851760 r148	0:43	A:12943521;C:9974404;G:10197868;T:13104520;N:0	43		12943521	9974404	10197868	13104520	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.86369		0.28235		0.90995		0.5024		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
52435	52435	SRR9198689	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	G14_R1.fastq.gz	fastq	22452579.0	522153.0	GSM3851760 r149	0:43	A:6052976;C:5108508;G:5238826;T:6052269;N:0	43		6052976	5108508	5238826	6052269	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.89425		0.12262		0.91234		0.51154		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
52436	52436	SRR9198690	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	A23_R1.fastq.gz	fastq	11064115.0	257305.0	GSM3851760 r15	0:43	A:3312117;C:2015333;G:2092587;T:3644078;N:0	43		3312117	2015333	2092587	3644078	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.67131		0.56353		0.94596		0.46246		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
52437	52437	SRR9198691	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	G15_R1.fastq.gz	fastq	26636608.0	619456.0	GSM3851760 r150	0:43	A:7482453;C:5765357;G:5930514;T:7458284;N:0	43		7482453	5765357	5930514	7458284	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.88297		0.26878		0.85979		0.47992		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
52438	52438	SRR9198692	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	G16_R1.fastq.gz	fastq	38014150.0	884050.0	GSM3851760 r151	0:43	A:10576888;C:8304761;G:8506878;T:10625623;N:0	43		10576888	8304761	8506878	10625623	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.87683		0.25851		0.89767		0.48845		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
52439	52439	SRR9198693	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	G17_R1.fastq.gz	fastq	40972507.0	952849.0	GSM3851760 r152	0:43	A:11958245;C:8186722;G:8404224;T:12423316;N:0	43		11958245	8186722	8404224	12423316	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.79842		0.48846		0.93277		0.51012		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
52440	52440	SRR9198694	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	G18_R1.fastq.gz	fastq	35653149.0	829143.0	GSM3851760 r153	0:43	A:10361320;C:7196014;G:7423127;T:10672688;N:0	43		10361320	7196014	7423127	10672688	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.74257		0.41459		0.92295		0.49361		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
52441	52441	SRR9198695	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	G19_R1.fastq.gz	fastq	58779151.0	1366957.0	GSM3851760 r154	0:43	A:15983923;C:13230000;G:13562419;T:16002809;N:0	43		15983923	13230000	13562419	16002809	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.89528		0.20975		0.91987		0.49223		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
52442	52442	SRR9198696	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	G1_R1.fastq.gz	fastq	18422662.0	428434.0	GSM3851760 r155	0:43	A:5413364;C:3611796;G:3707196;T:5690306;N:0	43		5413364	3611796	3707196	5690306	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.77672		0.34043		0.91443		0.46729		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
52443	52443	SRR9198697	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	G20_R1.fastq.gz	fastq	29950360.0	696520.0	GSM3851760 r156	0:43	A:8421616;C:6488575;G:6651584;T:8388585;N:0	43		8421616	6488575	6651584	8388585	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.89094		0.19484		0.9191		0.44062		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
52444	52444	SRR9198698	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	G21_R1.fastq.gz	fastq	53866229.0	1252703.0	GSM3851760 r157	0:43	A:15166405;C:11553860;G:11826347;T:15319617;N:0	43		15166405	11553860	11826347	15319617	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.86648		0.33619		0.90463		0.49004		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
52445	52445	SRR9198699	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	G22_R1.fastq.gz	fastq	9310704.0	216528.0	GSM3851760 r158	0:43	A:2543678;C:1861320;G:1774622;T:3131084;N:0	43		2543678	1861320	1774622	3131084	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.04555		0.04348		0.99482		0.49447		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
52446	52446	SRR9198700	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	G23_R1.fastq.gz	fastq	13175888.0	306416.0	GSM3851760 r159	0:43	A:3487070;C:2750076;G:2672450;T:4266292;N:0	43		3487070	2750076	2672450	4266292	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.06882		0.06731		0.99606		0.5166		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
52447	52447	SRR9198701	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	A24_R1.fastq.gz	fastq	28699705.0	667435.0	GSM3851760 r16	0:43	A:8266814;C:5871050;G:6032119;T:8529722;N:0	43		8266814	5871050	6032119	8529722	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.84845		0.3295		0.88939		0.50491		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
52448	52448	SRR9198702	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	G24_R1.fastq.gz	fastq	75348470.0	1752290.0	GSM3851760 r160	0:43	A:21094074;C:16187493;G:16488672;T:21578231;N:0	43		21094074	16187493	16488672	21578231	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.80551		0.30831		0.94334		0.51596		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
52449	52449	SRR9198703	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	G2_R1.fastq.gz	fastq	8384441.0	194987.0	GSM3851760 r161	0:43	A:2438879;C:1665843;G:1736699;T:2543020;N:0	43		2438879	1665843	1736699	2543020	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.63926		0.27349		0.89057		0.53862		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
52450	52450	SRR9198704	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	G3_R1.fastq.gz	fastq	12290389.0	285823.0	GSM3851760 r162	0:43	A:3553459;C:2412441;G:2534162;T:3790327;N:0	43		3553459	2412441	2534162	3790327	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.5383		0.27761		0.89487		0.47728		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
52451	52451	SRR9198705	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	G4_R1.fastq.gz	fastq	10535043.0	245001.0	GSM3851760 r163	0:43	A:3074933;C:2095777;G:2167984;T:3196349;N:0	43		3074933	2095777	2167984	3196349	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.72807		0.04561		0.99364		0.98695		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
52452	52452	SRR9198706	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	G5_R1.fastq.gz	fastq	17507708.0	407156.0	GSM3851760 r164	0:43	A:4958788;C:3638219;G:3781433;T:5129268;N:0	43		4958788	3638219	3781433	5129268	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.64994		0.27247		0.92176		0.5096		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
52453	52453	SRR9198707	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	G6_R1.fastq.gz	fastq	16399598.0	381386.0	GSM3851760 r165	0:43	A:4757550;C:3293128;G:3404182;T:4944738;N:0	43		4757550	3293128	3404182	4944738	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.73868		0.31535		0.88542		0.48811		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
52454	52454	SRR9198708	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	G7_R1.fastq.gz	fastq	29106528.0	676896.0	GSM3851760 r166	0:43	A:8388025;C:5882023;G:6059831;T:8776649;N:0	43		8388025	5882023	6059831	8776649	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.73615		0.31958		0.90378		0.4742		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
52455	52455	SRR9198709	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	G8_R1.fastq.gz	fastq	19035369.0	442683.0	GSM3851760 r167	0:43	A:5651630;C:3723693;G:3795932;T:5864114;N:0	43		5651630	3723693	3795932	5864114	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.81669		0.44579		0.88692		0.48782		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
52456	52456	SRR9198710	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	G9_R1.fastq.gz	fastq	47493027.0	1104489.0	GSM3851760 r168	0:43	A:14081922;C:9600619;G:9859124;T:13951362;N:0	43		14081922	9600619	9859124	13951362	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.86784		0.32159		0.92622		0.88108		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
52457	52457	SRR9198711	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	H10_R1.fastq.gz	fastq	38075081.0	885467.0	GSM3851760 r169	0:43	A:10732477;C:8168105;G:8389454;T:10785045;N:0	43		10732477	8168105	8389454	10785045	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.85726		0.26182		0.88475		0.47804		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
52458	52458	SRR9198712	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	A2_R1.fastq.gz	fastq	3149793.0	73251.0	GSM3851760 r17	0:43	A:954961;C:528265;G:537024;T:1129543;N:0	43		954961	528265	537024	1129543	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.10255		0.0973		0.99598		0.47692		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
52459	52459	SRR9198713	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	H11_R1.fastq.gz	fastq	48302373.0	1123311.0	GSM3851760 r170	0:43	A:13028742;C:11011752;G:11313776;T:12948103;N:0	43		13028742	11011752	11313776	12948103	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.90737		0.13748		0.92269		0.50344		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
52460	52460	SRR9198714	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	H12_R1.fastq.gz	fastq	49739433.0	1156731.0	GSM3851760 r171	0:43	A:14002894;C:10651502;G:10903792;T:14181245;N:0	43		14002894	10651502	10903792	14181245	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.86476		0.33504		0.91512		0.46101		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
52461	52461	SRR9198715	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	H13_R1.fastq.gz	fastq	46245726.0	1075482.0	GSM3851760 r172	0:43	A:12478168;C:10513963;G:10818674;T:12434921;N:0	43		12478168	10513963	10818674	12434921	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.9048		0.14194		0.92594		0.48191		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
52462	52462	SRR9198716	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	H14_R1.fastq.gz	fastq	28145005.0	654535.0	GSM3851760 r173	0:43	A:7767816;C:6217562;G:6350522;T:7809105;N:0	43		7767816	6217562	6350522	7809105	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.88711		0.26383		0.90727		0.4402		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
52463	52463	SRR9198717	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	H15_R1.fastq.gz	fastq	43802380.0	1018660.0	GSM3851760 r174	0:43	A:12261979;C:9483808;G:9736915;T:12319678;N:0	43		12261979	9483808	9736915	12319678	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.88369		0.27284		0.89282		0.47488		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
52464	52464	SRR9198718	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	H16_R1.fastq.gz	fastq	38297993.0	890651.0	GSM3851760 r175	0:43	A:10495141;C:8576354;G:8793653;T:10432845;N:0	43		10495141	8576354	8793653	10432845	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.90568		0.14249		0.87142		0.46966		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
52465	52465	SRR9198719	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	H17_R1.fastq.gz	fastq	41239150.0	959050.0	GSM3851760 r176	0:43	A:11260901;C:9246700;G:9491743;T:11239806;N:0	43		11260901	9246700	9491743	11239806	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.89452		0.16392		0.91656		0.50875		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
52466	52466	SRR9198720	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	H18_R1.fastq.gz	fastq	52660681.0	1224667.0	GSM3851760 r177	0:43	A:14788913;C:11301955;G:11536363;T:15033450;N:0	43		14788913	11301955	11536363	15033450	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.8623		0.34612		0.93375		0.47992		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
52467	52467	SRR9198721	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	H19_R1.fastq.gz	fastq	50616805.0	1177135.0	GSM3851760 r178	0:43	A:13985703;C:11162936;G:11409752;T:14058414;N:0	43		13985703	11162936	11409752	14058414	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.88075		0.27284		0.91622		0.48317		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
52468	52468	SRR9198722	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	H1_R1.fastq.gz	fastq	11343658.0	263806.0	GSM3851760 r179	0:43	A:3060506;C:2423324;G:2327436;T:3532392;N:0	43		3060506	2423324	2327436	3532392	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.08839		0.07853		0.99362		0.86148		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
52469	52469	SRR9198723	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	A3_R1.fastq.gz	fastq	4151693.0	96551.0	GSM3851760 r18	0:43	A:1279837;C:672157;G:704872;T:1494827;N:0	43		1279837	672157	704872	1494827	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.09936		0.09565		0.99744		0.378		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
52470	52470	SRR9198724	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	H20_R1.fastq.gz	fastq	42995528.0	999896.0	GSM3851760 r180	0:43	A:12135494;C:9206778;G:9413783;T:12239473;N:0	43		12135494	9206778	9413783	12239473	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.86841		0.3358		0.91299		0.48741		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
52471	52471	SRR9198725	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	H21_R1.fastq.gz	fastq	48336343.0	1124101.0	GSM3851760 r181	0:43	A:13325803;C:10688758;G:10961737;T:13360045;N:0	43		13325803	10688758	10961737	13360045	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.8851		0.22577		0.86785		0.47804		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
52472	52472	SRR9198726	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	H22_R1.fastq.gz	fastq	56223790.0	1307530.0	GSM3851760 r182	0:43	A:15732403;C:12192698;G:12478859;T:15819830;N:0	43		15732403	12192698	12478859	15819830	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.87758		0.30454		0.92046		0.48746		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
52473	52473	SRR9198727	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	H23_R1.fastq.gz	fastq	54852305.0	1275635.0	GSM3851760 r183	0:43	A:15301779;C:11918920;G:12187706;T:15443900;N:0	43		15301779	11918920	12187706	15443900	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.86242		0.33292		0.89718		0.46806		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
52474	52474	SRR9198728	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	H24_R1.fastq.gz	fastq	68726298.0	1598286.0	GSM3851760 r184	0:43	A:18778971;C:15348875;G:15627938;T:18970514;N:0	43		18778971	15348875	15627938	18970514	0	SRX5970646	SRS4876620	SRA893907	GEO	Molecular Neurobiology, MBB, Karolinska Institutet	1	0.87693		0.21094		0.92602		0.51892		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

Advanced export

JSON shape: default, array, newline-delimited

CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;