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78 rows where experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL", experiment.platform = "ILLUMINA" and tissue_curation = "Tail"

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devstage_curation 3

technology 2

experiment.library_layout 2

devstage_curation_coarse 2

tissue_curation_coarse 1

tissue_curation 1

  • Tail · 78 ✖

experiment.platform 1

  • ILLUMINA · 78 ✖

experiment.library_strategy 1

experiment.library_source 1

  • TRANSCRIPTOMIC SINGLE CELL · 78 ✖

experiment.library_selection 1

Link 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
24790 24790 SRR25509944 SRX21240524 SRS18495447 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 prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf 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:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 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 5DPF_WT_plus_S17_L001_R2_001.fastq.gz 5DPF_WT_plus_S17_L001_R1_001.fastq.gz 5DPF_WT_plus_S17_L001_I1_001.fastq.gz fastq fastq fastq 5999080077.0 47236851.0 GSM7680083 r1 0:8 1:28 2:91 A:1212144705;C:959823109;G:1045323833;T:1081182723;N:79071 8 28 91   1212144705 959823109 1045323833 1081182723 79071 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91673   0.11695   0.77481   0.51165   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24791 24791 SRR25509945 SRX21240524 SRS18495447 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 prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf 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:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 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 5DPF_WT_plus_S17_L002_R2_001.fastq.gz 5DPF_WT_plus_S17_L002_R1_001.fastq.gz 5DPF_WT_plus_S17_L002_I1_001.fastq.gz fastq fastq fastq 6012350180.0 47341340.0 GSM7680083 r2 0:8 1:28 2:91 A:1215185110;C:961739027;G:1047332997;T:1083733742;N:71064 8 28 91   1215185110 961739027 1047332997 1083733742 71064 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91842   0.11714   0.7763   0.51731   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24792 24792 SRR25509946 SRX21240524 SRS18495447 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 prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf 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:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 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 5DPF_WT_plus_S18_L001_R2_001.fastq.gz 5DPF_WT_plus_S18_L001_R1_001.fastq.gz 5DPF_WT_plus_S18_L001_I1_001.fastq.gz fastq fastq fastq 4990947473.0 39298799.0 GSM7680083 r3 0:8 1:28 2:91 A:1007619958;C:800073636;G:871756682;T:896670984;N:69449 8 28 91   1007619958 800073636 871756682 896670984 69449 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91717   0.11737   0.7767   0.51879   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24793 24793 SRR25509947 SRX21240524 SRS18495447 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 prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf 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:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 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 5DPF_WT_plus_S18_L002_I1_001.fastq.gz 5DPF_WT_plus_S18_L002_R1_001.fastq.gz 5DPF_WT_plus_S18_L002_R2_001.fastq.gz fastq fastq fastq 4994343707.0 39325541.0 GSM7680083 r4 0:8 1:28 2:91 A:1008545361;C:800479170;G:872044753;T:897494026;N:60921 8 28 91   1008545361 800479170 872044753 897494026 60921 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.9173   0.11671   0.778   0.51414   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24794 24794 SRR25509948 SRX21240524 SRS18495447 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 prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf 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:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 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 5DPF_WT_plus_S20_L001_R2_001.fastq.gz 5DPF_WT_plus_S20_L001_R1_001.fastq.gz 5DPF_WT_plus_S20_L001_I1_001.fastq.gz fastq fastq fastq 4150807675.0 32683525.0 GSM7680083 r7 0:8 1:28 2:91 A:839301254;C:665476121;G:723277159;T:746089009;N:57232 8 28 91   839301254 665476121 723277159 746089009 57232 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91704   0.11665   0.77589   0.51231   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24795 24795 SRR25509949 SRX21240524 SRS18495447 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 prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf 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:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 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 5DPF_WT_plus_S20_L002_R2_001.fastq.gz 5DPF_WT_plus_S20_L002_R1_001.fastq.gz 5DPF_WT_plus_S20_L002_I1_001.fastq.gz fastq fastq fastq 4152701499.0 32698437.0 GSM7680083 r8 0:8 1:28 2:91 A:839837413;C:665793367;G:723399518;T:746476220;N:51249 8 28 91   839837413 665793367 723399518 746476220 51249 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91769   0.11677   0.77473   0.5172   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24796 24796 SRR25510006 SRX21240524 SRS18495447 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 prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf 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:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 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 5DPF_WT_plus_S19_L001_I1_001.fastq.gz 5DPF_WT_plus_S19_L001_R1_001.fastq.gz 5DPF_WT_plus_S19_L001_R2_001.fastq.gz fastq fastq fastq 5570139228.0 43859364.0 GSM7680083 r5 0:8 1:28 2:91 A:1124433319;C:892106407;G:974065175;T:1000519772;N:77451 8 28 91   1124433319 892106407 974065175 1000519772 77451 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.9181   0.11708   0.77725   0.506   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24797 24797 SRR25510007 SRX21240524 SRS18495447 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 prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf 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:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 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 5DPF_WT_plus_S19_L002_R2_001.fastq.gz 5DPF_WT_plus_S19_L002_R1_001.fastq.gz 5DPF_WT_plus_S19_L002_I1_001.fastq.gz fastq fastq fastq 5568879134.0 43849442.0 GSM7680083 r6 0:8 1:28 2:91 A:1124462080;C:891765530;G:973382320;T:1000621312;N:67980 8 28 91   1124462080 891765530 973382320 1000621312 67980 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91836   0.11752   0.77786   0.49118   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24798 24798 SRR25509950 SRX21240523 SRS18495446 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 prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 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 MECOM_minus_S29_L001_I1_001.fastq.gz MECOM_minus_S29_L001_R1_001.fastq.gz MECOM_minus_S29_L001_R2_001.fastq.gz fastq fastq fastq 6472457718.0 50964234.0 GSM7680088 r1 0:8 1:28 2:91 A:1374177983;C:969847712;G:1063043909;T:1230585953;N:89737 8 28 91   1374177983 969847712 1063043909 1230585953 89737 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91899   0.23002   0.75597   0.50918   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24799 24799 SRR25509951 SRX21240523 SRS18495446 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 prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 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 MECOM_minus_S29_L002_I1_001.fastq.gz MECOM_minus_S29_L002_R1_001.fastq.gz MECOM_minus_S29_L002_R2_001.fastq.gz fastq fastq fastq 6479801747.0 51022061.0 GSM7680088 r2 0:8 1:28 2:91 A:1375879660;C:970771702;G:1064110805;T:1232166662;N:78722 8 28 91   1375879660 970771702 1064110805 1232166662 78722 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91932   0.23011   0.75666   0.50726   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24800 24800 SRR25509952 SRX21240523 SRS18495446 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 prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 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 MECOM_minus_S30_L001_I1_001.fastq.gz MECOM_minus_S30_L001_R1_001.fastq.gz MECOM_minus_S30_L001_R2_001.fastq.gz fastq fastq fastq 6055044278.0 47677514.0 GSM7680088 r3 0:8 1:28 2:91 A:1285162347;C:907248700;G:995411468;T:1150745942;N:85317 8 28 91   1285162347 907248700 995411468 1150745942 85317 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91771   0.2306   0.75799   0.51641   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24801 24801 SRR25509953 SRX21240523 SRS18495446 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 prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 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 MECOM_minus_S30_L002_I1_001.fastq.gz MECOM_minus_S30_L002_R1_001.fastq.gz MECOM_minus_S30_L002_R2_001.fastq.gz fastq fastq fastq 6065969453.0 47763539.0 GSM7680088 r4 0:8 1:28 2:91 A:1287814805;C:908939739;G:996849881;T:1152803356;N:74268 8 28 91   1287814805 908939739 996849881 1152803356 74268 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91856   0.23244   0.75844   0.51273   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24802 24802 SRR25509954 SRX21240523 SRS18495446 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 prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 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 MECOM_minus_S31_L001_I1_001.fastq.gz MECOM_minus_S31_L001_R1_001.fastq.gz MECOM_minus_S31_L001_R2_001.fastq.gz fastq fastq fastq 5279309101.0 41569363.0 GSM7680088 r5 0:8 1:28 2:91 A:1122213686;C:789300425;G:868235888;T:1002988275;N:73759 8 28 91   1122213686 789300425 868235888 1002988275 73759 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91638   0.23107   0.75795   0.51508   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24803 24803 SRR25509955 SRX21240523 SRS18495446 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 prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 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 MECOM_minus_S31_L002_I1_001.fastq.gz MECOM_minus_S31_L002_R1_001.fastq.gz MECOM_minus_S31_L002_R2_001.fastq.gz fastq fastq fastq 5282579605.0 41595115.0 GSM7680088 r6 0:8 1:28 2:91 A:1123052612;C:789776127;G:868371205;T:1003891470;N:64051 8 28 91   1123052612 789776127 868371205 1003891470 64051 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91687   0.23155   0.75653   0.51167   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24804 24804 SRR25509956 SRX21240523 SRS18495446 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 prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 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 MECOM_minus_S32_L001_I1_001.fastq.gz MECOM_minus_S32_L001_R1_001.fastq.gz MECOM_minus_S32_L001_R2_001.fastq.gz fastq fastq fastq 5155833986.0 40597118.0 GSM7680088 r7 0:8 1:28 2:91 A:1096166065;C:771837218;G:846468036;T:979794053;N:72366 8 28 91   1096166065 771837218 846468036 979794053 72366 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91864   0.23062   0.75783   0.5144   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24805 24805 SRR25509957 SRX21240523 SRS18495446 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 prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 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 MECOM_minus_S32_L002_I1_001.fastq.gz MECOM_minus_S32_L002_R1_001.fastq.gz MECOM_minus_S32_L002_R2_001.fastq.gz fastq fastq fastq 5158852395.0 40620885.0 GSM7680088 r8 0:8 1:28 2:91 A:1096925078;C:772260867;G:846795917;T:980455576;N:63097 8 28 91   1096925078 772260867 846795917 980455576 63097 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91859   0.23143   0.75921   0.51192   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24806 24806 SRR25509958 SRX21240522 SRS18495445 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 prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 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 PRDM16-GFP_S1_L001_I1_001.fastq.gz PRDM16-GFP_S1_L001_R1_001.fastq.gz PRDM16-GFP_S1_L001_R2_001.fastq.gz fastq fastq fastq 7339736654.0 57793202.0 GSM7680087 r1 0:8 1:28 2:91 A:1557377528;C:1077119414;G:1156228317;T:1468352980;N:103143 8 28 91   1557377528 1077119414 1156228317 1468352980 103143 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91516   0.25902   0.74255   0.49922   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24807 24807 SRR25509959 SRX21240522 SRS18495445 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 prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 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 PRDM16-GFP_S1_L002_I1_001.fastq.gz PRDM16-GFP_S1_L002_R1_001.fastq.gz PRDM16-GFP_S1_L002_R2_001.fastq.gz fastq fastq fastq 7410090336.0 58347168.0 GSM7680087 r2 0:8 1:28 2:91 A:1569421640;C:1090998538;G:1171253819;T:1477822651;N:95640 8 28 91   1569421640 1090998538 1171253819 1477822651 95640 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91462   0.25846   0.74215   0.49672   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24808 24808 SRR25509960 SRX21240522 SRS18495445 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 prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 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 PRDM16-GFP_S2_L001_I1_001.fastq.gz PRDM16-GFP_S2_L001_R1_001.fastq.gz PRDM16-GFP_S2_L001_R2_001.fastq.gz fastq fastq fastq 7620847217.0 60006671.0 GSM7680087 r3 0:8 1:28 2:91 A:1615026295;C:1121044318;G:1201364994;T:1523062938;N:108516 8 28 91   1615026295 1121044318 1201364994 1523062938 108516 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91495   0.26021   0.74188   0.49871   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24809 24809 SRR25509961 SRX21240522 SRS18495445 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 prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 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 PRDM16-GFP_S2_L002_I1_001.fastq.gz PRDM16-GFP_S2_L002_R1_001.fastq.gz PRDM16-GFP_S2_L002_R2_001.fastq.gz fastq fastq fastq 7658170739.0 60300557.0 GSM7680087 r4 0:8 1:28 2:91 A:1620018228;C:1130072970;G:1211145212;T:1526013817;N:100460 8 28 91   1620018228 1130072970 1211145212 1526013817 100460 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.9153   0.25733   0.74406   0.49822   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24810 24810 SRR25509962 SRX21240522 SRS18495445 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 prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 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 PRDM16-GFP_S3_L001_I1_001.fastq.gz PRDM16-GFP_S3_L001_R1_001.fastq.gz PRDM16-GFP_S3_L001_R2_001.fastq.gz fastq fastq fastq 7520150568.0 59213784.0 GSM7680087 r5 0:8 1:28 2:91 A:1592224470;C:1104917106;G:1187483622;T:1503722424;N:106722 8 28 91   1592224470 1104917106 1187483622 1503722424 106722 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91528   0.25852   0.74168   0.50087   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24811 24811 SRR25509963 SRX21240522 SRS18495445 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 prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 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 PRDM16-GFP_S3_L002_I1_001.fastq.gz PRDM16-GFP_S3_L002_R1_001.fastq.gz PRDM16-GFP_S3_L002_R2_001.fastq.gz fastq fastq fastq 7547416198.0 59428474.0 GSM7680087 r6 0:8 1:28 2:91 A:1595335949;C:1112405532;G:1195632258;T:1504519719;N:97676 8 28 91   1595335949 1112405532 1195632258 1504519719 97676 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91572   0.25684   0.74227   0.49429   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24812 24812 SRR25509964 SRX21240522 SRS18495445 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 prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 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 PRDM16-GFP_S4_L001_I1_001.fastq.gz PRDM16-GFP_S4_L001_R1_001.fastq.gz PRDM16-GFP_S4_L001_R2_001.fastq.gz fastq fastq fastq 6203887389.0 48849507.0 GSM7680087 r7 0:8 1:28 2:91 A:1315023626;C:910416020;G:979167464;T:1240610297;N:87730 8 28 91   1315023626 910416020 979167464 1240610297 87730 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91294   0.25905   0.74426   0.49642   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24813 24813 SRR25509965 SRX21240522 SRS18495445 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 prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 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 PRDM16-GFP_S4_L002_I1_001.fastq.gz PRDM16-GFP_S4_L002_R1_001.fastq.gz PRDM16-GFP_S4_L002_R2_001.fastq.gz fastq fastq fastq 6164249419.0 48537397.0 GSM7680087 r8 0:8 1:28 2:91 A:1303982345;C:907803673;G:976227040;T:1228810005;N:80064 8 28 91   1303982345 907803673 976227040 1228810005 80064 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91422   0.25666   0.74383   0.49596   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24814 24814 SRR25509966 SRX21240521 SRS18495444 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 prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 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 MECOM_plus_S25_L001_I1_001.fastq.gz MECOM_plus_S25_L001_R1_001.fastq.gz MECOM_plus_S25_L001_R2_001.fastq.gz fastq fastq fastq 2154821446.0 16967098.0 GSM7680086 r1 0:8 1:28 2:91 A:451330902;C:339756831;G:379343350;T:373544930;N:29905 8 28 91   451330902 339756831 379343350 373544930 29905 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91882   0.142   0.78299   0.51956   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24815 24815 SRR25509967 SRX21240521 SRS18495444 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 prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 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 MECOM_plus_S25_L002_I1_001.fastq.gz MECOM_plus_S25_L002_R1_001.fastq.gz MECOM_plus_S25_L002_R2_001.fastq.gz fastq fastq fastq 2158219204.0 16993852.0 GSM7680086 r2 0:8 1:28 2:91 A:452280625;C:340228509;G:379707034;T:374197697;N:26667 8 28 91   452280625 340228509 379707034 374197697 26667 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91895   0.1417   0.78279   0.51981   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24816 24816 SRR25509968 SRX21240521 SRS18495444 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 prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 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 MECOM_plus_S26_L001_I1_001.fastq.gz MECOM_plus_S26_L001_R1_001.fastq.gz MECOM_plus_S26_L001_R2_001.fastq.gz fastq fastq fastq 2361287251.0 18592813.0 GSM7680086 r3 0:8 1:28 2:91 A:492891294;C:373079069;G:416862992;T:409079819;N:32809 8 28 91   492891294 373079069 416862992 409079819 32809 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.92068   0.13997   0.78516   0.50532   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24817 24817 SRR25509969 SRX21240521 SRS18495444 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 prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 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 MECOM_plus_S26_L002_I1_001.fastq.gz MECOM_plus_S26_L002_R1_001.fastq.gz MECOM_plus_S26_L002_R2_001.fastq.gz fastq fastq fastq 2362115545.0 18599335.0 GSM7680086 r4 0:8 1:28 2:91 A:493282758;C:373220256;G:416785305;T:409222388;N:28778 8 28 91   493282758 373220256 416785305 409222388 28778 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.92013   0.14129   0.78468   0.52049   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24818 24818 SRR25509970 SRX21240521 SRS18495444 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 prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 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 MECOM_plus_S27_L001_I1_001.fastq.gz MECOM_plus_S27_L001_R1_001.fastq.gz MECOM_plus_S27_L001_R2_001.fastq.gz fastq fastq fastq 2093107066.0 16481158.0 GSM7680086 r5 0:8 1:28 2:91 A:438295698;C:330083473;G:369094473;T:362282989;N:28745 8 28 91   438295698 330083473 369094473 362282989 28745 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91759   0.13991   0.78354   0.51917   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24819 24819 SRR25509971 SRX21240521 SRS18495444 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 prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 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 MECOM_plus_S27_L002_R2_001.fastq.gz MECOM_plus_S27_L002_R1_001.fastq.gz MECOM_plus_S27_L002_I1_001.fastq.gz fastq fastq fastq 2095025401.0 16496263.0 GSM7680086 r6 0:8 1:28 2:91 A:438926470;C:330300198;G:369243520;T:362664613;N:25132 8 28 91   438926470 330300198 369243520 362664613 25132 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91795   0.14216   0.78151   0.5067   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24820 24820 SRR25509972 SRX21240521 SRS18495444 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 prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 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 MECOM_plus_S28_L001_R2_001.fastq.gz MECOM_plus_S28_L001_R1_001.fastq.gz MECOM_plus_S28_L001_I1_001.fastq.gz fastq fastq fastq 1722573390.0 13563570.0 GSM7680086 r7 0:8 1:28 2:91 A:360865837;C:272246731;G:303643951;T:297504190;N:24161 8 28 91   360865837 272246731 303643951 297504190 24161 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91897   0.13999   0.78648   0.49913   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24821 24821 SRR25509973 SRX21240521 SRS18495444 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 prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 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 MECOM_plus_S28_L002_I1_001.fastq.gz MECOM_plus_S28_L002_R1_001.fastq.gz MECOM_plus_S28_L002_R2_001.fastq.gz fastq fastq fastq 1724036303.0 13575089.0 GSM7680086 r8 0:8 1:28 2:91 A:361391368;C:272402118;G:303699423;T:297819212;N:20978 8 28 91   361391368 272402118 303699423 297819212 20978 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.92182   0.14094   0.78326   0.50699   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24822 24822 SRR25509974 SRX21240520 SRS18495443 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 prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 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 PRDM16plusGFP_S5_L001_R2_001.fastq.gz PRDM16plusGFP_S5_L001_R1_001.fastq.gz PRDM16plusGFP_S5_L001_I1_001.fastq.gz fastq fastq fastq 8567717053.0 67462339.0 GSM7680085 r1 0:8 1:28 2:91 A:1758073165;C:1341216272;G:1446728174;T:1592934812;N:120426 8 28 91   1758073165 1341216272 1446728174 1592934812 120426 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.90663   0.17669   0.75812   0.50234   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24823 24823 SRR25509975 SRX21240520 SRS18495443 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 prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 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 PRDM16plusGFP_S5_L002_R2_001.fastq.gz PRDM16plusGFP_S5_L002_R1_001.fastq.gz PRDM16plusGFP_S5_L002_I1_001.fastq.gz fastq fastq fastq 8694310526.0 68459138.0 GSM7680085 r2 0:8 1:28 2:91 A:1780912602;C:1365177337;G:1472402153;T:1611176829;N:112637 8 28 91   1780912602 1365177337 1472402153 1611176829 112637 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.90543   0.17508   0.76019   0.51005   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24824 24824 SRR25509976 SRX21240520 SRS18495443 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 prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 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 PRDM16plusGFP_S6_L001_R2_001.fastq.gz PRDM16plusGFP_S6_L001_R1_001.fastq.gz PRDM16plusGFP_S6_L001_I1_001.fastq.gz fastq fastq fastq 9112215456.0 71749728.0 GSM7680085 r3 0:8 1:28 2:91 A:1868388882;C:1426817380;G:1540502920;T:1693385950;N:130116 8 28 91   1868388882 1426817380 1540502920 1693385950 130116 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.90763   0.17756   0.76102   0.50457   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24825 24825 SRR25509977 SRX21240520 SRS18495443 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 prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 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 PRDM16plusGFP_S6_L002_I1_001.fastq.gz PRDM16plusGFP_S6_L002_R1_001.fastq.gz PRDM16plusGFP_S6_L002_R2_001.fastq.gz fastq fastq fastq 9170568781.0 72209203.0 GSM7680085 r4 0:8 1:28 2:91 A:1876786596;C:1440704341;G:1555176461;T:1698251178;N:118897 8 28 91   1876786596 1440704341 1555176461 1698251178 118897 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.9062   0.17617   0.76203   0.49732   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24826 24826 SRR25509978 SRX21240520 SRS18495443 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 prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 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 PRDM16plusGFP_S7_L001_R2_001.fastq.gz PRDM16plusGFP_S7_L001_R1_001.fastq.gz PRDM16plusGFP_S7_L001_I1_001.fastq.gz fastq fastq fastq 96282510.0 758130.0 GSM7680085 r5 0:8 1:28 2:91 A:19884451;C:15070058;G:16206702;T:17827293;N:1326 8 28 91   19884451 15070058 16206702 17827293 1326 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.76071   0.14671   0.78064   0.49267   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24827 24827 SRR25509979 SRX21240520 SRS18495443 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 prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 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 PRDM16plusGFP_S7_L002_I1_001.fastq.gz PRDM16plusGFP_S7_L002_R2_001.fastq.gz PRDM16plusGFP_S7_L002_R1_001.fastq.gz fastq fastq fastq 96503236.0 759868.0 GSM7680085 r6 0:8 1:28 2:91 A:19898524;C:15152212;G:16290226;T:17805918;N:1108 8 28 91   19898524 15152212 16290226 17805918 1108 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.76382   0.1467   0.78508   0.48995   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24828 24828 SRR25509980 SRX21240520 SRS18495443 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 prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 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 PRDM16plusGFP_S8_L001_I1_001.fastq.gz PRDM16plusGFP_S8_L001_R1_001.fastq.gz PRDM16plusGFP_S8_L001_R2_001.fastq.gz fastq fastq fastq 8873313978.0 69868614.0 GSM7680085 r7 0:8 1:28 2:91 A:1820893372;C:1390912026;G:1498935631;T:1647176605;N:126240 8 28 91   1820893372 1390912026 1498935631 1647176605 126240 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.90718   0.17603   0.76211   0.50458   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24829 24829 SRR25509981 SRX21240520 SRS18495443 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 prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 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 PRDM16plusGFP_S8_L002_I1_001.fastq.gz PRDM16plusGFP_S8_L002_R1_001.fastq.gz PRDM16plusGFP_S8_L002_R2_001.fastq.gz fastq fastq fastq 8980314526.0 70711138.0 GSM7680085 r8 0:8 1:28 2:91 A:1839681468;C:1412028536;G:1521396962;T:1661490212;N:116380 8 28 91   1839681468 1412028536 1521396962 1661490212 116380 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.9078   0.17604   0.76037   0.47729   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24830 24830 SRR25509982 SRX21240519 SRS18495442 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 prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf 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:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 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 5DPF_WT_minus_S21_L001_I1_001.fastq.gz 5DPF_WT_minus_S21_L001_R1_001.fastq.gz 5DPF_WT_minus_S21_L001_R2_001.fastq.gz fastq fastq fastq 8634577600.0 67988800.0 GSM7680084 r1 0:8 1:28 2:91 A:1833391508;C:1279550998;G:1408086737;T:1665829499;N:122058 8 28 91   1833391508 1279550998 1408086737 1665829499 122058 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.92   0.2485   0.75552   0.51753   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24831 24831 SRR25509983 SRX21240519 SRS18495442 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 prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf 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:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 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 5DPF_WT_minus_S21_L002_I1_001.fastq.gz 5DPF_WT_minus_S21_L002_R1_001.fastq.gz 5DPF_WT_minus_S21_L002_R2_001.fastq.gz fastq fastq fastq 8644279892.0 68065196.0 GSM7680084 r2 0:8 1:28 2:91 A:1835831383;C:1280886675;G:1409188624;T:1667919807;N:106347 8 28 91   1835831383 1280886675 1409188624 1667919807 106347 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91942   0.24867   0.75396   0.52058   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24832 24832 SRR25509984 SRX21240519 SRS18495442 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 prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf 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:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 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 5DPF_WT_minus_S22_L001_R2_001.fastq.gz 5DPF_WT_minus_S22_L001_R1_001.fastq.gz 5DPF_WT_minus_S22_L001_I1_001.fastq.gz fastq fastq fastq 6144243998.0 48379874.0 GSM7680084 r3 0:8 1:28 2:91 A:1307018689;C:910675193;G:999334562;T:1185454346;N:85744 8 28 91   1307018689 910675193 999334562 1185454346 85744 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91944   0.2505   0.75538   0.5154   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24833 24833 SRR25509985 SRX21240519 SRS18495442 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 prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf 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:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 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 5DPF_WT_minus_S22_L002_I1_001.fastq.gz 5DPF_WT_minus_S22_L002_R1_001.fastq.gz 5DPF_WT_minus_S22_L002_R2_001.fastq.gz fastq fastq fastq 6161162938.0 48513094.0 GSM7680084 r4 0:8 1:28 2:91 A:1310818438;C:913067206;G:1001801994;T:1188928241;N:75675 8 28 91   1310818438 913067206 1001801994 1188928241 75675 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91847   0.24895   0.75483   0.52092   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24834 24834 SRR25509986 SRX21240519 SRS18495442 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 prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf 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:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 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 5DPF_WT_minus_S23_L001_I1_001.fastq.gz 5DPF_WT_minus_S23_L001_R1_001.fastq.gz 5DPF_WT_minus_S23_L001_R2_001.fastq.gz fastq fastq fastq 6893652075.0 54280725.0 GSM7680084 r5 0:8 1:28 2:91 A:1466387768;C:1021460104;G:1123606745;T:1327994370;N:96988 8 28 91   1466387768 1021460104 1123606745 1327994370 96988 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.92042   0.24759   0.75663   0.51662   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24835 24835 SRR25509987 SRX21240519 SRS18495442 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 prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf 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:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 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 5DPF_WT_minus_S23_L002_R1_001.fastq.gz 5DPF_WT_minus_S23_L002_R2_001.fastq.gz 5DPF_WT_minus_S23_L002_I1_001.fastq.gz fastq fastq fastq 6907881409.0 54392767.0 GSM7680084 r6 0:8 1:28 2:91 A:1469526451;C:1023529399;G:1125771813;T:1330830542;N:83592 8 28 91   1469526451 1023529399 1125771813 1330830542 83592 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91879   0.24904   0.75479   0.52175   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24836 24836 SRR25509988 SRX21240519 SRS18495442 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 prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf 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:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 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 5DPF_WT_minus_S24_L001_R2_001.fastq.gz 5DPF_WT_minus_S24_L001_R1_001.fastq.gz 5DPF_WT_minus_S24_L001_I1_001.fastq.gz fastq fastq fastq 6155284362.0 48466806.0 GSM7680084 r7 0:8 1:28 2:91 A:1309788155;C:909805561;G:1001863122;T:1188939208;N:83300 8 28 91   1309788155 909805561 1001863122 1188939208 83300 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91932   0.252   0.7541   0.52096   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24837 24837 SRR25509989 SRX21240519 SRS18495442 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 prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf 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:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 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 5DPF_WT_minus_S24_L002_I1_001.fastq.gz 5DPF_WT_minus_S24_L002_R1_001.fastq.gz 5DPF_WT_minus_S24_L002_R2_001.fastq.gz fastq fastq fastq 6165991605.0 48551115.0 GSM7680084 r8 0:8 1:28 2:91 A:1312424825;C:911081786;G:1003163970;T:1191408145;N:72739 8 28 91   1312424825 911081786 1003163970 1191408145 72739 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91842   0.24989   0.75542   0.51918   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24838 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
29031 29031 SRR26989303 SRX22682429 SRS19676381 SRP474934 PRJNA1046494 Cohesin composition and dosage independently affect early development in zebrafish GSE248952 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   pubmed:38975838   TB dissected stag2b NZ207 scRNA seq GSM7923481   source name:tailbud|tissue:tailbud|age:16 hpf|genotype:stag2b NZ207|geo loc name:missing|collection date:missing TB dissected stag2b NZ207 scRNA seq FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files tailbud   Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   tissue:tailbud|age:16 hpf|genotype:stag2b NZ207 GSM7923481 GSM7923481: TB dissected stag2b NZ207 scRNA seq; Danio rerio; RNA Seq GSM7923481 r1 GSM7923481 1 Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP474934   loader:fastq load.py S2B_bamtofastq_S1_L003_I1_001.fastq.gz S2B_bamtofastq_S1_L003_R1_001.fastq.gz S2B_bamtofastq_S1_L003_R2_001.fastq.gz fastq fastq fastq 31750000000.0 250000000.0 GSM7923481 r1 0:8 1:28 2:91 A:6537438301;C:4417903496;G:5047922141;T:6745922724;N:813338 8 28 91   6537438301 4417903496 5047922141 6745922724 813338 SRX22682429 SRS19676381 SRA1760034 Chromosome structure and development group, Pathology, University of Otago Chromosome structure and development group, Pathology, University of Otago 1 0.93608   0.14792   0.92462   0.51672   91   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   New Zealand 2023-11-29 Segmentation Embryo Tail Multi-system
29032 29032 SRR26989304 SRX22682429 SRS19676381 SRP474934 PRJNA1046494 Cohesin composition and dosage independently affect early development in zebrafish GSE248952 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   pubmed:38975838   TB dissected stag2b NZ207 scRNA seq GSM7923481   source name:tailbud|tissue:tailbud|age:16 hpf|genotype:stag2b NZ207|geo loc name:missing|collection date:missing TB dissected stag2b NZ207 scRNA seq FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files tailbud   Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   tissue:tailbud|age:16 hpf|genotype:stag2b NZ207 GSM7923481 GSM7923481: TB dissected stag2b NZ207 scRNA seq; Danio rerio; RNA Seq GSM7923481 r1 GSM7923481 1 Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP474934   loader:fastq load.py S2B_bamtofastq_S1_L003_I1_002.fastq.gz S2B_bamtofastq_S1_L003_R1_002.fastq.gz S2B_bamtofastq_S1_L003_R2_002.fastq.gz fastq fastq fastq 31750000000.0 250000000.0 GSM7923481 r2 0:8 1:28 2:91 A:6518388158;C:4725153194;G:5205254633;T:6300375689;N:828326 8 28 91   6518388158 4725153194 5205254633 6300375689 828326 SRX22682429 SRS19676381 SRA1760034 Chromosome structure and development group, Pathology, University of Otago Chromosome structure and development group, Pathology, University of Otago 1 0.95154   0.12683   0.92429   0.45021   91   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   New Zealand 2023-11-29 Segmentation Embryo Tail Multi-system
29033 29033 SRR26989305 SRX22682429 SRS19676381 SRP474934 PRJNA1046494 Cohesin composition and dosage independently affect early development in zebrafish GSE248952 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   pubmed:38975838   TB dissected stag2b NZ207 scRNA seq GSM7923481   source name:tailbud|tissue:tailbud|age:16 hpf|genotype:stag2b NZ207|geo loc name:missing|collection date:missing TB dissected stag2b NZ207 scRNA seq FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files tailbud   Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   tissue:tailbud|age:16 hpf|genotype:stag2b NZ207 GSM7923481 GSM7923481: TB dissected stag2b NZ207 scRNA seq; Danio rerio; RNA Seq GSM7923481 r1 GSM7923481 1 Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP474934   loader:fastq load.py S2B_bamtofastq_S1_L003_I1_003.fastq.gz S2B_bamtofastq_S1_L003_R1_003.fastq.gz S2B_bamtofastq_S1_L003_R2_003.fastq.gz fastq fastq fastq 31750000000.0 250000000.0 GSM7923481 r3 0:8 1:28 2:91 A:6383119961;C:4804063495;G:5444337911;T:6117664552;N:814081 8 28 91   6383119961 4804063495 5444337911 6117664552 814081 SRX22682429 SRS19676381 SRA1760034 Chromosome structure and development group, Pathology, University of Otago Chromosome structure and development group, Pathology, University of Otago 1 0.94222   0.11028   0.93052   0.61281   91   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   New Zealand 2023-11-29 Segmentation Embryo Tail Multi-system
29034 29034 SRR26989306 SRX22682429 SRS19676381 SRP474934 PRJNA1046494 Cohesin composition and dosage independently affect early development in zebrafish GSE248952 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   pubmed:38975838   TB dissected stag2b NZ207 scRNA seq GSM7923481   source name:tailbud|tissue:tailbud|age:16 hpf|genotype:stag2b NZ207|geo loc name:missing|collection date:missing TB dissected stag2b NZ207 scRNA seq FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files tailbud   Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   tissue:tailbud|age:16 hpf|genotype:stag2b NZ207 GSM7923481 GSM7923481: TB dissected stag2b NZ207 scRNA seq; Danio rerio; RNA Seq GSM7923481 r1 GSM7923481 1 Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP474934   loader:fastq load.py S2B_bamtofastq_S1_L003_I1_004.fastq.gz S2B_bamtofastq_S1_L003_R1_004.fastq.gz S2B_bamtofastq_S1_L003_R2_004.fastq.gz fastq fastq fastq 31750000000.0 250000000.0 GSM7923481 r4 0:8 1:28 2:91 A:6402125828;C:4842822163;G:5314139669;T:6190088524;N:823816 8 28 91   6402125828 4842822163 5314139669 6190088524 823816 SRX22682429 SRS19676381 SRA1760034 Chromosome structure and development group, Pathology, University of Otago Chromosome structure and development group, Pathology, University of Otago 1 0.94588   0.13163   0.91747   0.45552   91   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   New Zealand 2023-11-29 Segmentation Embryo Tail Multi-system
29035 29035 SRR26989307 SRX22682429 SRS19676381 SRP474934 PRJNA1046494 Cohesin composition and dosage independently affect early development in zebrafish GSE248952 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   pubmed:38975838   TB dissected stag2b NZ207 scRNA seq GSM7923481   source name:tailbud|tissue:tailbud|age:16 hpf|genotype:stag2b NZ207|geo loc name:missing|collection date:missing TB dissected stag2b NZ207 scRNA seq FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files tailbud   Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   tissue:tailbud|age:16 hpf|genotype:stag2b NZ207 GSM7923481 GSM7923481: TB dissected stag2b NZ207 scRNA seq; Danio rerio; RNA Seq GSM7923481 r1 GSM7923481 1 Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP474934   loader:fastq load.py S2B_bamtofastq_S1_L003_I1_005.fastq.gz S2B_bamtofastq_S1_L003_R1_005.fastq.gz S2B_bamtofastq_S1_L003_R2_005.fastq.gz fastq fastq fastq 21091269095.0 166072985.0 GSM7923481 r5 0:8 1:28 2:91 A:4762107201;C:2885106776;G:3288050363;T:4175805779;N:1571516 8 28 91   4762107201 2885106776 3288050363 4175805779 1571516 SRX22682429 SRS19676381 SRA1760034 Chromosome structure and development group, Pathology, University of Otago Chromosome structure and development group, Pathology, University of Otago 1 0.85155   0.18636   0.94314   0.62392   91   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   New Zealand 2023-11-29 Segmentation Embryo Tail Multi-system
29036 29036 SRR26989308 SRX22682428 SRS19676380 SRP474934 PRJNA1046494 Cohesin composition and dosage independently affect early development in zebrafish GSE248952 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   pubmed:38975838   TB dissected wild type scRNA seq GSM7923480   source name:tailbud|tissue:tailbud|age:16 hpf|genotype:AB wild type|geo loc name:missing|collection date:missing TB dissected wild type scRNA seq FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files tailbud   Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   tissue:tailbud|age:16 hpf|genotype:AB wild type GSM7923480 GSM7923480: TB dissected wild type scRNA seq; Danio rerio; RNA Seq GSM7923480 r1 GSM7923480 1 Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP474934   loader:fastq load.py WT_bamtofastq_S1_L003_I1_001.fastq.gz WT_bamtofastq_S1_L003_R1_001.fastq.gz WT_bamtofastq_S1_L003_R2_001.fastq.gz fastq fastq fastq 31750000000.0 250000000.0 GSM7923480 r1 0:8 1:28 2:91 A:6487643595;C:4511110883;G:5076824945;T:6673593696;N:826881 8 28 91   6487643595 4511110883 5076824945 6673593696 826881 SRX22682428 SRS19676380 SRA1760034 Chromosome structure and development group, Pathology, University of Otago Chromosome structure and development group, Pathology, University of Otago 1 0.95134   0.14233   0.91816   0.48251   91   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   New Zealand 2023-11-29 Segmentation Embryo Tail Multi-system
29037 29037 SRR26989309 SRX22682428 SRS19676380 SRP474934 PRJNA1046494 Cohesin composition and dosage independently affect early development in zebrafish GSE248952 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   pubmed:38975838   TB dissected wild type scRNA seq GSM7923480   source name:tailbud|tissue:tailbud|age:16 hpf|genotype:AB wild type|geo loc name:missing|collection date:missing TB dissected wild type scRNA seq FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files tailbud   Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   tissue:tailbud|age:16 hpf|genotype:AB wild type GSM7923480 GSM7923480: TB dissected wild type scRNA seq; Danio rerio; RNA Seq GSM7923480 r1 GSM7923480 1 Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP474934   loader:fastq load.py WT_bamtofastq_S1_L003_I1_002.fastq.gz WT_bamtofastq_S1_L003_R1_002.fastq.gz WT_bamtofastq_S1_L003_R2_002.fastq.gz fastq fastq fastq 31750000000.0 250000000.0 GSM7923480 r2 0:8 1:28 2:91 A:6572631256;C:4794881740;G:5255235646;T:6126414633;N:836725 8 28 91   6572631256 4794881740 5255235646 6126414633 836725 SRX22682428 SRS19676380 SRA1760034 Chromosome structure and development group, Pathology, University of Otago Chromosome structure and development group, Pathology, University of Otago 1 0.96222   0.11199   0.92332   0.50319   91   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   New Zealand 2023-11-29 Segmentation Embryo Tail Multi-system
29038 29038 SRR26989310 SRX22682428 SRS19676380 SRP474934 PRJNA1046494 Cohesin composition and dosage independently affect early development in zebrafish GSE248952 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   pubmed:38975838   TB dissected wild type scRNA seq GSM7923480   source name:tailbud|tissue:tailbud|age:16 hpf|genotype:AB wild type|geo loc name:missing|collection date:missing TB dissected wild type scRNA seq FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files tailbud   Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   tissue:tailbud|age:16 hpf|genotype:AB wild type GSM7923480 GSM7923480: TB dissected wild type scRNA seq; Danio rerio; RNA Seq GSM7923480 r1 GSM7923480 1 Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP474934   loader:fastq load.py WT_bamtofastq_S1_L003_I1_003.fastq.gz WT_bamtofastq_S1_L003_R1_003.fastq.gz WT_bamtofastq_S1_L003_R2_003.fastq.gz fastq fastq fastq 31750000000.0 250000000.0 GSM7923480 r3 0:8 1:28 2:91 A:6367741226;C:4801321001;G:5377991533;T:6202112567;N:833673 8 28 91   6367741226 4801321001 5377991533 6202112567 833673 SRX22682428 SRS19676380 SRA1760034 Chromosome structure and development group, Pathology, University of Otago Chromosome structure and development group, Pathology, University of Otago 1 0.95193   0.10884   0.91362   0.55405   91   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   New Zealand 2023-11-29 Segmentation Embryo Tail Multi-system
29039 29039 SRR26989311 SRX22682428 SRS19676380 SRP474934 PRJNA1046494 Cohesin composition and dosage independently affect early development in zebrafish GSE248952 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   pubmed:38975838   TB dissected wild type scRNA seq GSM7923480   source name:tailbud|tissue:tailbud|age:16 hpf|genotype:AB wild type|geo loc name:missing|collection date:missing TB dissected wild type scRNA seq FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files tailbud   Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   tissue:tailbud|age:16 hpf|genotype:AB wild type GSM7923480 GSM7923480: TB dissected wild type scRNA seq; Danio rerio; RNA Seq GSM7923480 r1 GSM7923480 1 Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP474934   loader:fastq load.py WT_bamtofastq_S1_L003_I1_004.fastq.gz WT_bamtofastq_S1_L003_R1_004.fastq.gz WT_bamtofastq_S1_L003_R2_004.fastq.gz fastq fastq fastq 31750000000.0 250000000.0 GSM7923480 r4 0:8 1:28 2:91 A:6643013514;C:4783035829;G:5148972841;T:6173682231;N:1295585 8 28 91   6643013514 4783035829 5148972841 6173682231 1295585 SRX22682428 SRS19676380 SRA1760034 Chromosome structure and development group, Pathology, University of Otago Chromosome structure and development group, Pathology, University of Otago 1 0.9356   0.12122   0.92084   0.52901   91   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   New Zealand 2023-11-29 Segmentation Embryo Tail Multi-system
29040 29040 SRR26989312 SRX22682428 SRS19676380 SRP474934 PRJNA1046494 Cohesin composition and dosage independently affect early development in zebrafish GSE248952 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: Tailbuds obtained from wild type and stag2bnz207 were manually dissected and then dissociated using collagenase P and trypsin. Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   pubmed:38975838   TB dissected wild type scRNA seq GSM7923480   source name:tailbud|tissue:tailbud|age:16 hpf|genotype:AB wild type|geo loc name:missing|collection date:missing TB dissected wild type scRNA seq FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRangerv7.1.0 filtered for empty droplets. Assembly: GRCz11 Supplementary files format and content: Tab separated value files and matrix files tailbud   Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   tissue:tailbud|age:16 hpf|genotype:AB wild type GSM7923480 GSM7923480: TB dissected wild type scRNA seq; Danio rerio; RNA Seq GSM7923480 r1 GSM7923480 1 Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP474934   loader:fastq load.py WT_bamtofastq_S1_L003_I1_005.fastq.gz WT_bamtofastq_S1_L003_R1_005.fastq.gz WT_bamtofastq_S1_L003_R2_005.fastq.gz fastq fastq fastq 3129498186.0 24641718.0 GSM7923480 r5 0:8 1:28 2:91 A:797078402;C:362323092;G:517613944;T:564921437;N:459463 8 28 91   797078402 362323092 517613944 564921437 459463 SRX22682428 SRS19676380 SRA1760034 Chromosome structure and development group, Pathology, University of Otago Chromosome structure and development group, Pathology, University of Otago 1 0.65184   0.40446   0.95262   0.62704   91   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   New Zealand 2023-11-29 Segmentation Embryo Tail Multi-system
74460 74460 SRR23802569 SRX19634451 SRS17003621 SRP426621 PRJNA943252 Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail] GSE227118 Other We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized filtered and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing. parent bioproject:PRJNA510836     Whole tail 72 hpf GSM7091920   source name:transgenic zebrafish embryos wild type|tissue:Whole tail|developmental stage:72 hpf Whole tail 72 hpf the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode transgenic zebrafish embryos wild type No treatments Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were bisected on the axial plane towards the caudal end of the yolk extension tail tissues were then homogenized filtered and viable cells sorted using live dead staining FACS into PBS collecting at least 25 000 cells. tissue:Whole tail|developmental stage:72 hpf GSM7091920 GSM7091920: Whole tail 72 hpf; Danio rerio; RNA Seq GSM7091920 r1 GSM7091920 1 Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP426621     EH_Tails_Single_Cell_GAGACGGA_L001.fastq.sorted.fastq.gz fastq 715456535.0 12017381.0 GSM7091920 r1 0:59.54 A:205982879;C:141307848;G:135221384;T:232940601;N:3823 59       205982879 141307848 135221384 232940601 3823 SRX19634451 SRS17003621     Oncology/Hematology, Boston Children's Hospital 1 0.88315   0.14516   0.78257   0.49661   61   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet indrops   United States 2023-03-10 Larval Larval Tail Multi-system
74461 74461 SRR23802570 SRX19634451 SRS17003621 SRP426621 PRJNA943252 Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail] GSE227118 Other We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized filtered and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing. parent bioproject:PRJNA510836     Whole tail 72 hpf GSM7091920   source name:transgenic zebrafish embryos wild type|tissue:Whole tail|developmental stage:72 hpf Whole tail 72 hpf the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode transgenic zebrafish embryos wild type No treatments Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were bisected on the axial plane towards the caudal end of the yolk extension tail tissues were then homogenized filtered and viable cells sorted using live dead staining FACS into PBS collecting at least 25 000 cells. tissue:Whole tail|developmental stage:72 hpf GSM7091920 GSM7091920: Whole tail 72 hpf; Danio rerio; RNA Seq GSM7091920 r1 GSM7091920 1 Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP426621     EH_Tails_Single_Cell_GAGACGGA_L002.fastq.sorted.fastq.gz fastq 589786185.0 9927008.0 GSM7091920 r2 0:59.41 A:170171480;C:115960508;G:111370241;T:192283114;N:842 59       170171480 115960508 111370241 192283114 842 SRX19634451 SRS17003621     Oncology/Hematology, Boston Children's Hospital 1 0.88418   0.1452   0.78173   0.48617   61   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet indrops   United States 2023-03-10 Larval Larval Tail Multi-system
74462 74462 SRR23802571 SRX19634451 SRS17003621 SRP426621 PRJNA943252 Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail] GSE227118 Other We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized filtered and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing. parent bioproject:PRJNA510836     Whole tail 72 hpf GSM7091920   source name:transgenic zebrafish embryos wild type|tissue:Whole tail|developmental stage:72 hpf Whole tail 72 hpf the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode transgenic zebrafish embryos wild type No treatments Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were bisected on the axial plane towards the caudal end of the yolk extension tail tissues were then homogenized filtered and viable cells sorted using live dead staining FACS into PBS collecting at least 25 000 cells. tissue:Whole tail|developmental stage:72 hpf GSM7091920 GSM7091920: Whole tail 72 hpf; Danio rerio; RNA Seq GSM7091920 r1 GSM7091920 1 Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP426621     EH_Tails_Single_Cell_GAGACGGA_L003.fastq.sorted.fastq.gz fastq 683131915.0 11477240.0 GSM7091920 r3 0:59.52 A:196805573;C:134822600;G:129142852;T:222358115;N:2775 59       196805573 134822600 129142852 222358115 2775 SRX19634451 SRS17003621     Oncology/Hematology, Boston Children's Hospital 1 0.88169   0.14457   0.78054   0.49459   61   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet indrops   United States 2023-03-10 Larval Larval Tail Multi-system
74463 74463 SRR23802572 SRX19634451 SRS17003621 SRP426621 PRJNA943252 Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail] GSE227118 Other We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized filtered and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing. parent bioproject:PRJNA510836     Whole tail 72 hpf GSM7091920   source name:transgenic zebrafish embryos wild type|tissue:Whole tail|developmental stage:72 hpf Whole tail 72 hpf the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode transgenic zebrafish embryos wild type No treatments Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were bisected on the axial plane towards the caudal end of the yolk extension tail tissues were then homogenized filtered and viable cells sorted using live dead staining FACS into PBS collecting at least 25 000 cells. tissue:Whole tail|developmental stage:72 hpf GSM7091920 GSM7091920: Whole tail 72 hpf; Danio rerio; RNA Seq GSM7091920 r1 GSM7091920 1 Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al. 2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al. 2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP426621     EH_Tails_Single_Cell_GAGACGGA_L004.fastq.sorted.fastq.gz fastq 584432554.0 9840065.0 GSM7091920 r4 0:59.39 A:168684456;C:114891950;G:110562368;T:190292465;N:1315 59       168684456 114891950 110562368 190292465 1315 SRX19634451 SRS17003621     Oncology/Hematology, Boston Children's Hospital 1 0.88266   0.14397   0.78001   0.49223   61   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet indrops   United States 2023-03-10 Larval Larval Tail Multi-system

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