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
24838,SRR25509990,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S65_L001_I1_001.fastq.gz Kristen_10X_101620_S65_L001_R1_001.fastq.gz Kristen_10X_101620_S65_L001_R2_001.fastq.gz,fastq fastq fastq,3327423622.0,26200186.0,GSM7680082 r1,0:8 1:28 2:91,A:693698335;C:494975421;G:540414923;T:654926705;N:201542,8,28,91,,693698335,494975421,540414923,654926705,201542,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91351,,0.22865,,0.77723,,0.49805,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24839,SRR25509991,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S67_L002_I1_001.fastq.gz Kristen_10X_101620_S67_L002_R1_001.fastq.gz Kristen_10X_101620_S67_L002_R2_001.fastq.gz,fastq fastq fastq,4430975390.0,34889570.0,GSM7680082 r10,0:8 1:28 2:91,A:923557751;C:658731986;G:718325003;T:874072049;N:264081,8,28,91,,923557751,658731986,718325003,874072049,264081,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91797,,0.22868,,0.77863,,0.50737,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24840,SRR25509992,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S67_L003_I1_001.fastq.gz Kristen_10X_101620_S67_L003_R1_001.fastq.gz Kristen_10X_101620_S67_L003_R2_001.fastq.gz,fastq fastq fastq,4429223552.0,34875776.0,GSM7680082 r11,0:8 1:28 2:91,A:923277621;C:658440918;G:718036099;T:873676803;N:264175,8,28,91,,923277621,658440918,718036099,873676803,264175,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91753,,0.22978,,0.77942,,0.50977,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24841,SRR25509993,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S67_L004_I1_001.fastq.gz Kristen_10X_101620_S67_L004_R1_001.fastq.gz Kristen_10X_101620_S67_L004_R2_001.fastq.gz,fastq fastq fastq,4549656890.0,35824070.0,GSM7680082 r12,0:8 1:28 2:91,A:950423951;C:673969790;G:734760168;T:900554096;N:282365,8,28,91,,950423951,673969790,734760168,900554096,282365,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91687,,0.23323,,0.77932,,0.50984,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24842,SRR25509994,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S68_L001_I1_001.fastq.gz Kristen_10X_101620_S68_L001_R1_001.fastq.gz Kristen_10X_101620_S68_L001_R2_001.fastq.gz,fastq fastq fastq,2696456634.0,21231942.0,GSM7680082 r13,0:8 1:28 2:91,A:562209710;C:401113540;G:437836456;T:530785441;N:161575,8,28,91,,562209710,401113540,437836456,530785441,161575,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91384,,0.22885,,0.77912,,0.50672,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24843,SRR25509995,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S68_L002_I1_001.fastq.gz Kristen_10X_101620_S68_L002_R1_001.fastq.gz Kristen_10X_101620_S68_L002_R2_001.fastq.gz,fastq fastq fastq,2735162932.0,21536716.0,GSM7680082 r14,0:8 1:28 2:91,A:570169460;C:406846839;G:443964376;T:538696359;N:164122,8,28,91,,570169460,406846839,443964376,538696359,164122,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91691,,0.22998,,0.77942,,0.51035,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24844,SRR25509996,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S68_L003_I1_001.fastq.gz Kristen_10X_101620_S68_L003_R1_001.fastq.gz Kristen_10X_101620_S68_L003_R2_001.fastq.gz,fastq fastq fastq,2739703563.0,21572469.0,GSM7680082 r15,0:8 1:28 2:91,A:571283074;C:407511119;G:444574049;T:539563747;N:162690,8,28,91,,571283074,407511119,444574049,539563747,162690,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91526,,0.22747,,0.7793,,0.51387,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24845,SRR25509997,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S68_L004_I1_001.fastq.gz Kristen_10X_101620_S68_L004_R1_001.fastq.gz Kristen_10X_101620_S68_L004_R2_001.fastq.gz,fastq fastq fastq,2828960433.0,22275279.0,GSM7680082 r16,0:8 1:28 2:91,A:591166850;C:419193897;G:457332081;T:559181603;N:175958,8,28,91,,591166850,419193897,457332081,559181603,175958,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91651,,0.23126,,0.77613,,0.50223,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24846,SRR25509998,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S65_L002_I1_001.fastq.gz Kristen_10X_101620_S65_L002_R1_001.fastq.gz Kristen_10X_101620_S65_L002_R2_001.fastq.gz,fastq fastq fastq,3374189340.0,26568420.0,GSM7680082 r2,0:8 1:28 2:91,A:703424426;C:501911907;G:547786373;T:664402117;N:201397,8,28,91,,703424426,501911907,547786373,664402117,201397,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91522,,0.22812,,0.77753,,0.50208,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24847,SRR25509999,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S65_L003_I1_001.fastq.gz Kristen_10X_101620_S65_L003_R1_001.fastq.gz Kristen_10X_101620_S65_L003_R2_001.fastq.gz,fastq fastq fastq,3383217516.0,26639508.0,GSM7680082 r3,0:8 1:28 2:91,A:705514047;C:503189161;G:549089218;T:666200894;N:201908,8,28,91,,705514047,503189161,549089218,666200894,201908,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91535,,0.23036,,0.78078,,0.50202,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24848,SRR25510000,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S65_L004_I1_001.fastq.gz Kristen_10X_101620_S65_L004_R1_001.fastq.gz Kristen_10X_101620_S65_L004_R2_001.fastq.gz,fastq fastq fastq,3493154050.0,27505150.0,GSM7680082 r4,0:8 1:28 2:91,A:729910298;C:517582902;G:564926384;T:690333365;N:215701,8,28,91,,729910298,517582902,564926384,690333365,215701,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91569,,0.22913,,0.77873,,0.50186,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24849,SRR25510001,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S66_L001_I1_001.fastq.gz Kristen_10X_101620_S66_L001_R1_001.fastq.gz Kristen_10X_101620_S66_L001_R2_001.fastq.gz,fastq fastq fastq,3237456187.0,25491781.0,GSM7680082 r5,0:8 1:28 2:91,A:674885196;C:481871349;G:525642933;T:637154812;N:197781,8,28,91,,674885196,481871349,525642933,637154812,197781,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91378,,0.22852,,0.77843,,0.50985,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24850,SRR25510002,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S66_L002_I1_001.fastq.gz Kristen_10X_101620_S66_L002_R1_001.fastq.gz Kristen_10X_101620_S66_L002_R2_001.fastq.gz,fastq fastq fastq,3287789081.0,25888103.0,GSM7680082 r6,0:8 1:28 2:91,A:685408765;C:489232060;G:533550966;T:647427897;N:197685,8,28,91,,685408765,489232060,533550966,647427897,197685,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91484,,0.22872,,0.78001,,0.49909,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24851,SRR25510003,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S66_L003_I1_001.fastq.gz Kristen_10X_101620_S66_L003_R1_001.fastq.gz Kristen_10X_101620_S66_L003_R2_001.fastq.gz,fastq fastq fastq,3298207145.0,25970135.0,GSM7680082 r7,0:8 1:28 2:91,A:687621787;C:490851045;G:535230137;T:649382247;N:197069,8,28,91,,687621787,490851045,535230137,649382247,197069,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91559,,0.2268,,0.77766,,0.50935,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24852,SRR25510004,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S66_L004_I1_001.fastq.gz Kristen_10X_101620_S66_L004_R1_001.fastq.gz Kristen_10X_101620_S66_L004_R2_001.fastq.gz,fastq fastq fastq,3377888088.0,26597544.0,GSM7680082 r8,0:8 1:28 2:91,A:705624374;C:500985504;G:546306692;T:667248332;N:211602,8,28,91,,705624374,500985504,546306692,667248332,211602,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91679,,0.22965,,0.77837,,0.51495,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24853,SRR25510005,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S67_L001_I1_001.fastq.gz Kristen_10X_101620_S67_L001_R1_001.fastq.gz Kristen_10X_101620_S67_L001_R2_001.fastq.gz,fastq fastq fastq,4346114117.0,34221371.0,GSM7680082 r9,0:8 1:28 2:91,A:905838814;C:646261347;G:704993570;T:856789016;N:262014,8,28,91,,905838814,646261347,704993570,856789016,262014,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91558,,0.22834,,0.7783,,0.49972,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
63887,SRR14202114,SRX10569027,SRS8675160,SRP314271,PRJNA720970,Single cell transcriptional profiles of islet1 derived ECs and the other ECs in the tail of 48 hpf zebrafish embryos,GSE171822,Transcriptome Analysis,We report transcriptional heterogeneity of venous endothelial cells ECs in the tail of zebrafish embryos  which consist of HSPC niche constituting ECs and caudal vessel CV constituting ECs. To characterize isl1 derived ECs which derive from the endoderm and mainly constitute the HSPC niche in the caudal hematopoietic tissue CHT  we performed single cell RNA sequencing scRNA seq of isl1 derived ECs and the other ECs separately isolated from the tails of zebrafish embryos. Our analyses revealed that tail venous ECs were split into 5 distinct sub clusters where isl1 derived ECs and the other ECs were similarly distributed to all venous EC clusters  and further revealed that genes whose expression levels are different between isl1 derived ECs and the other ECs tend to show similar changes across all of the clusters even post their diversification. Overall design: We isolated live TagRFP+/EGFP+ cells for isl1 derived ECs and TagRFP /EGFP+ cells for the other ECs separately by FACS sorting from the tails of TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf. Then  barcoded single cell cDNA libraries were prepared using the Chromium Single Cell three prime Reagents Kits v3.1 and were then sequenced using Illumina NovaSeq6000.,,pubmed:36693371,,RNA seq the other ECs,GSM5235246,,source name:resected tails posterior to the yolk end|strain:AB|genotype:TgBACisl1:TagRFP;Tgdab2:EGFP|developmental stage:48 hpf|tissue:Tail|cell type:other ECs TagRFP /EGFP+,RNA seq the other ECs,The 10x Genomics Cell Ranger pipeline version 5.0.0 was used to perform sample demultiplexing  alignment to the reference genome Danio rerio GRCz11 and reporter sequences EGFP and RFP with the gene annotation file Danio rerio.GRCz11.99.chr.gtf.gz  barcode/UMI processing  and gene counting for each cell. Genome build: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample  mtx files count gene UMI counts for each sample.,resected tails posterior to the yolk end,,Tails resected from TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf were subjected to mechanical and enzymatic dissociation by pipetting every 5 minutes in 1 ml of protease solution TrypLE Express with 2.7 mg/ml Collagenase P and incubated at 28 °C until full dissociation 15 min. Cells were pelleted 3000 rpm  5 minutes at 4 °C and resuspended in suspension medium phenol red free Dulbecco’s modified Eagle’s medium with 1% FBS and 0.8 mM calcium chloride twice. Resuspended cells were passed through a cell strainer and subjected to cell sorting using a FACS Aria III cell sorter to isolate live TagRFP+/EGFP+ cells and TagRFP /EGFP+ cells separately. For scRNA seq  single cell suspensions were resuspended with the suspension medium and barcoded with a 10x Chromium Controller 10x Genomics. RNA from the barcoded cells for each sample was subsequently reverse transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v3.1 reagent kit 10x Genomics. Sequencing was performed with Illumina NovaSeq6000.,,strain:AB|genotype:TgBACisl1:TagRFP;Tgdab2:EGFP|developmental stage:48 hpf|tissue:Tail|cell type:other ECs TagRFP /EGFP+,GSM5235246,GSM5235246: RNA seq the other ECs; Danio rerio; RNA Seq,GSM5235246,,1,Tails resected from TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf were subjected to mechanical and enzymatic dissociation by pipetting every 5 minutes in 1 ml of protease solution TrypLE Express with 2.7 mg/ml Collagenase P and incubated at 28 °C until full dissociation 15 min. Cells were pelleted 3000 rpm  5 minutes at 4 °C and resuspended in suspension medium phenol red free Dulbecco's modified Eagle's medium with 1% FBS and 0.8 mM calcium chloride twice. Resuspended cells were passed through a cell strainer and subjected to cell sorting using a FACS Aria III cell sorter to isolate live TagRFP+/EGFP+ cells and TagRFP /EGFP+ cells separately. For scRNA seq  single cell suspensions were resuspended with the suspension medium and barcoded with a 10x Chromium Controller 10x Genomics. RNA from the barcoded cells for each sample was subsequently reverse transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v3.1 reagent kit 10x Genomics. Sequencing was performed with Illumina NovaSeq6000.,GEO Accession:GSM5235246,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP314271,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTTB   read1PairFiles=ZebEmb GFP RFP I1.fastq.gz   read2PairFiles=ZebEmb GFP RFP I2.fastq.gz   read3PairFiles=ZebEmb GFP RFP R1.fastq.gz   read4PairFiles=ZebEmb GFP RFP R2.fastq.gz,ZebEmb_GFP_RFP_I1.fastq.gz ZebEmb_GFP_RFP_I2.fastq.gz ZebEmb_GFP_RFP_R1.fastq.gz ZebEmb_GFP_RFP_R2.fastq.gz,fastq fastq fastq fastq,46144044078.0,334377131.0,GSM5235246 r1,0:10 1:10 2:28 3:90,A:12365801825;C:10786766050;G:11098071597;T:11890763395;N:2641211,10,10,28,90,12365801825,10786766050,11098071597,11890763395,2641211,SRX10569027,SRS8675160,SRA1217192,GEO,"Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute",1,0.93604,,0.14513,,0.79038,,0.50811,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2021-04-09,Hatching,Embryo,Tail,Multi-system
63888,SRR14202113,SRX10569026,SRS8675161,SRP314271,PRJNA720970,Single cell transcriptional profiles of islet1 derived ECs and the other ECs in the tail of 48 hpf zebrafish embryos,GSE171822,Transcriptome Analysis,We report transcriptional heterogeneity of venous endothelial cells ECs in the tail of zebrafish embryos  which consist of HSPC niche constituting ECs and caudal vessel CV constituting ECs. To characterize isl1 derived ECs which derive from the endoderm and mainly constitute the HSPC niche in the caudal hematopoietic tissue CHT  we performed single cell RNA sequencing scRNA seq of isl1 derived ECs and the other ECs separately isolated from the tails of zebrafish embryos. Our analyses revealed that tail venous ECs were split into 5 distinct sub clusters where isl1 derived ECs and the other ECs were similarly distributed to all venous EC clusters  and further revealed that genes whose expression levels are different between isl1 derived ECs and the other ECs tend to show similar changes across all of the clusters even post their diversification. Overall design: We isolated live TagRFP+/EGFP+ cells for isl1 derived ECs and TagRFP /EGFP+ cells for the other ECs separately by FACS sorting from the tails of TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf. Then  barcoded single cell cDNA libraries were prepared using the Chromium Single Cell three prime Reagents Kits v3.1 and were then sequenced using Illumina NovaSeq6000.,,pubmed:36693371,,RNA seq isl1 derived ECs,GSM5235245,,source name:resected tails posterior to the yolk end|strain:AB|genotype:TgBACisl1:TagRFP;Tgdab2:EGFP|developmental stage:48 hpf|tissue:Tail|cell type:isl1 derived ECs TagRFP+/EGFP+,RNA seq isl1 derived ECs,The 10x Genomics Cell Ranger pipeline version 5.0.0 was used to perform sample demultiplexing  alignment to the reference genome Danio rerio GRCz11 and reporter sequences EGFP and RFP with the gene annotation file Danio rerio.GRCz11.99.chr.gtf.gz  barcode/UMI processing  and gene counting for each cell. Genome build: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample  mtx files count gene UMI counts for each sample.,resected tails posterior to the yolk end,,Tails resected from TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf were subjected to mechanical and enzymatic dissociation by pipetting every 5 minutes in 1 ml of protease solution TrypLE Express with 2.7 mg/ml Collagenase P and incubated at 28 °C until full dissociation 15 min. Cells were pelleted 3000 rpm  5 minutes at 4 °C and resuspended in suspension medium phenol red free Dulbecco’s modified Eagle’s medium with 1% FBS and 0.8 mM calcium chloride twice. Resuspended cells were passed through a cell strainer and subjected to cell sorting using a FACS Aria III cell sorter to isolate live TagRFP+/EGFP+ cells and TagRFP /EGFP+ cells separately. For scRNA seq  single cell suspensions were resuspended with the suspension medium and barcoded with a 10x Chromium Controller 10x Genomics. RNA from the barcoded cells for each sample was subsequently reverse transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v3.1 reagent kit 10x Genomics. Sequencing was performed with Illumina NovaSeq6000.,,strain:AB|genotype:TgBACisl1:TagRFP;Tgdab2:EGFP|developmental stage:48 hpf|tissue:Tail|cell type:isl1 derived ECs TagRFP+/EGFP+,GSM5235245,GSM5235245: RNA seq isl1 derived ECs; Danio rerio; RNA Seq,GSM5235245,,1,Tails resected from TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf were subjected to mechanical and enzymatic dissociation by pipetting every 5 minutes in 1 ml of protease solution TrypLE Express with 2.7 mg/ml Collagenase P and incubated at 28 °C until full dissociation 15 min. Cells were pelleted 3000 rpm  5 minutes at 4 °C and resuspended in suspension medium phenol red free Dulbecco's modified Eagle's medium with 1% FBS and 0.8 mM calcium chloride twice. Resuspended cells were passed through a cell strainer and subjected to cell sorting using a FACS Aria III cell sorter to isolate live TagRFP+/EGFP+ cells and TagRFP /EGFP+ cells separately. For scRNA seq  single cell suspensions were resuspended with the suspension medium and barcoded with a 10x Chromium Controller 10x Genomics. RNA from the barcoded cells for each sample was subsequently reverse transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v3.1 reagent kit 10x Genomics. Sequencing was performed with Illumina NovaSeq6000.,GEO Accession:GSM5235245,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP314271,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTTB   read1PairFiles=ZebEmb GFP I1.fastq.gz   read2PairFiles=ZebEmb GFP I2.fastq.gz   read3PairFiles=ZebEmb GFP R1.fastq.gz   read4PairFiles=ZebEmb GFP R2.fastq.gz,ZebEmb_GFP_I1.fastq.gz ZebEmb_GFP_I2.fastq.gz ZebEmb_GFP_R1.fastq.gz ZebEmb_GFP_R2.fastq.gz,fastq fastq fastq fastq,53036547366.0,384322807.0,GSM5235245 r1,0:10 1:10 2:28 3:90,A:14610188978;C:12169986421;G:12283689207;T:13969658178;N:3024582,10,10,28,90,14610188978,12169986421,12283689207,13969658178,3024582,SRX10569026,SRS8675161,SRA1217192,GEO,"Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute",1,0.94469,,0.10454,,0.79133,,0.51214,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2021-04-09,Hatching,Embryo,Tail,Multi-system