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