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147 rows where experiment.library_layout = "PAIRED", technology = "10x" and tissue_curation = "Tail"

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devstage_curation 3

experiment.library_source 2

devstage_curation_coarse 2

tissue_curation_coarse 1

tissue_curation 1

  • Tail · 147 ✖

technology 1

  • 10x · 147 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_selection 1

experiment.library_layout 1

  • PAIRED · 147 ✖
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
52243 52243 SRR9050632 SRX5827023 SRS4754837 SRP198298 PRJNA542704 Thyroid hormone regulates distinct paths to maturation in pigment cell lineages GSE131136 Transcriptome Analysis Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.   pubmed:31140974;pubmed:33933422   Neural crest derived cells from 5 dpf euthyroid zebrafish tails GSM3764579   tissue:sox10:Cre+ cells from 5 dpf zebrafish tail tissue|cell type:2154 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from tails of 5 dpf zebrafish.|treatment:Untreated Neural crest derived cells from 5 dpf euthyroid zebrafish tails Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files. sox10:Cre+ cells from 5 dpf zebrafish tail tissue Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms. cell type:2154 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from tails of 5 dpf zebrafish.|treatment:Untreated GSM3764579 GSM3764579: Neural crest derived cells from 5 dpf euthyroid zebrafish tails; Danio rerio; RNA Seq GSM3764579   1 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP198298   dangling references:treat as unmapped 5dpf_possorted_genome_bam.bam 10X Genomics bam file 6566978892.0 115210156.0 GSM3764579 r1 0:57 A:1984051591;C:1302406550;G:1514564296;T:1762601545;N:3354910 57       1984051591 1302406550 1514564296 1762601545 3354910 SRX5827023 SRS4754837 SRA886020 GEO Biology, University of Virginia 1 0.9291   0.194   0.81466   0.53116   57   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-05-13 Larval Larval Tail Multi-system
56820 56820 SRR15414667 SRX11716797 SRS9747215 SRP249927 PRJNA607316 The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration GSE145497 Transcriptome Analysis Throughout their lifetime fish maintain a high capacity for regenerating complex xxx post injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio which serves as an ideal model of appendage regeneration due to its easy manipulation relatively simple mixture of cell types and superior imaging properties. Regeneration of the embryonic zebrafish tail requires development of a blastema a mass of dedifferentiated cells capable of replacing lost tissue a crucial step in all known examples of appendage regeneration. Using this model we show that tail amputation triggers an obligate metabolic shift to promote glucose metabolism during early regeneration similar to the Warburg effect observed in tumor forming cells. Inhibition of glucose metabolism did not affect the overall health of the embryo but completely blocked the fin from regenerating post amputation due to the failure to form a functional blastema. We performed a time series of single cell RNA sequencing on regenerating tails with and without xxx of glucose metabolism. We demonstrated that metabolic reprogramming is required for sustained TGF ß signaling and blocking glucose metabolism largely mimicked inhibition of TGF ß receptors both resulting in an aberrant blastema. Finally we showed using genetic ablation of three possible metabolic pathways for glucose that metabolic reprogramming is required to provide glucose specifically to the hexosamine biosynthetic pathway while neither glycolysis nor the pentose phosphate pathway were necessary for regeneration. Overall design: Single cell RNAseq data was generated from uninjured or regenerating embryonic zebrafish tails at 24 and 48 hours post amputation with and without xxx deoxyglucose. Please note that the UI ctrl.cloupe is a single sample from uninjured untreated embryo tails and the ctrl cloupe.cloupe is an aggregate file of all non 2DG treated samples UI ctrl 24hpa ctrl and 48hpa ctrl.   pubmed:34518542   UI 2DG GSM5513441   tissue:Developing embryonic zebrafish tail|strain:TAB 5|embryo age:3 dpf mM 2 deoxyglucose UI 2DG Binary Base Call BCL files generated from an Illumina 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics Cell Ranger Version 3.0.2. was used to demultiplex for barcode processing for single cell gene counts and aggregating files. Further analyses of the samples was performed using Loupe Cell Browser 10x Genomics Genome build: Danio Rerio 11 Supplementary files format and content: clouple files are provided which can be visiualized with the Loupe Cell Browser 10x Genomics Developing embryonic zebrafish tail   Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries was generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics   strain:TAB 5|embryo age:3 dpf mM 2 deoxyglucose GSM5513441 GSM5513441: UI 2DG; Danio rerio; RNA Seq GSM5513441   1 Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries was generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics GEO Accession:GSM5513441 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249927   assembly:Danio Rerio 11|intentional duplicate UI_2DG.bam 10X Genomics bam file 7617244817.0 83705987.0 GSM5513441 r1 0:91 A:2234691645;C:1513876602;G:1889440050;T:1970597369;N:8639151 91       2234691645 1513876602 1889440050 1970597369 8639151 SRX11716797 SRS9747215 SRA1044429 GEO National Human Genome Research Institute, National Institutes of Health 1 0.93814   0.15677   0.8254   0.52455   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-08-11 Larval Larval Tail Multi-system
56821 56821 SRR15414666 SRX11716796 SRS9747214 SRP249927 PRJNA607316 The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration GSE145497 Transcriptome Analysis Throughout their lifetime fish maintain a high capacity for regenerating complex xxx post injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio which serves as an ideal model of appendage regeneration due to its easy manipulation relatively simple mixture of cell types and superior imaging properties. Regeneration of the embryonic zebrafish tail requires development of a blastema a mass of dedifferentiated cells capable of replacing lost tissue a crucial step in all known examples of appendage regeneration. Using this model we show that tail amputation triggers an obligate metabolic shift to promote glucose metabolism during early regeneration similar to the Warburg effect observed in tumor forming cells. Inhibition of glucose metabolism did not affect the overall health of the embryo but completely blocked the fin from regenerating post amputation due to the failure to form a functional blastema. We performed a time series of single cell RNA sequencing on regenerating tails with and without xxx of glucose metabolism. We demonstrated that metabolic reprogramming is required for sustained TGF ß signaling and blocking glucose metabolism largely mimicked inhibition of TGF ß receptors both resulting in an aberrant blastema. Finally we showed using genetic ablation of three possible metabolic pathways for glucose that metabolic reprogramming is required to provide glucose specifically to the hexosamine biosynthetic pathway while neither glycolysis nor the pentose phosphate pathway were necessary for regeneration. Overall design: Single cell RNAseq data was generated from uninjured or regenerating embryonic zebrafish tails at 24 and 48 hours post amputation with and without xxx deoxyglucose. Please note that the UI ctrl.cloupe is a single sample from uninjured untreated embryo tails and the ctrl cloupe.cloupe is an aggregate file of all non 2DG treated samples UI ctrl 24hpa ctrl and 48hpa ctrl.   pubmed:34518542   UI ctrl GSM5513440   tissue:Regenerating embryonic zebrafish tail|strain:TAB 5|embryo age:3 dpf UI ctrl Binary Base Call BCL files generated from an Illumina 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics Cell Ranger Version 3.0.2. was used to demultiplex for barcode processing for single cell gene counts and aggregating files. Further analyses of the samples was performed using Loupe Cell Browser 10x Genomics Genome build: Danio Rerio 11 Supplementary files format and content: clouple files are provided which can be visiualized with the Loupe Cell Browser 10x Genomics Regenerating embryonic zebrafish tail   Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries was generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics   strain:TAB 5|embryo age:3 dpf GSM5513440 GSM5513440: UI ctrl; Danio rerio; RNA Seq GSM5513440   1 Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries was generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics GEO Accession:GSM5513440 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249927   assembly:Danio Rerio 11|intentional duplicate UI_ctrl.bam 10X Genomics bam file 8002896265.0 87943915.0 GSM5513440 r1 0:91 A:2325005630;C:1613869115;G:2033844364;T:2021144325;N:9032831 91       2325005630 1613869115 2033844364 2021144325 9032831 SRX11716796 SRS9747214 SRA1044429 GEO National Human Genome Research Institute, National Institutes of Health 1 0.93599   0.15189   0.83603   0.50802   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-08-11 Larval Larval Tail Multi-system
56822 56822 SRR11107235 SRX7744906 SRS6164695 SRP249927 PRJNA607316 The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration GSE145497 Transcriptome Analysis Throughout their lifetime fish maintain a high capacity for regenerating complex xxx post injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio which serves as an ideal model of appendage regeneration due to its easy manipulation relatively simple mixture of cell types and superior imaging properties. Regeneration of the embryonic zebrafish tail requires development of a blastema a mass of dedifferentiated cells capable of replacing lost tissue a crucial step in all known examples of appendage regeneration. Using this model we show that tail amputation triggers an obligate metabolic shift to promote glucose metabolism during early regeneration similar to the Warburg effect observed in tumor forming cells. Inhibition of glucose metabolism did not affect the overall health of the embryo but completely blocked the fin from regenerating post amputation due to the failure to form a functional blastema. We performed a time series of single cell RNA sequencing on regenerating tails with and without xxx of glucose metabolism. We demonstrated that metabolic reprogramming is required for sustained TGF ß signaling and blocking glucose metabolism largely mimicked inhibition of TGF ß receptors both resulting in an aberrant blastema. Finally we showed using genetic ablation of three possible metabolic pathways for glucose that metabolic reprogramming is required to provide glucose specifically to the hexosamine biosynthetic pathway while neither glycolysis nor the pentose phosphate pathway were necessary for regeneration. Overall design: Single cell RNAseq data was generated from uninjured or regenerating embryonic zebrafish tails at 24 and 48 hours post amputation with and without xxx deoxyglucose. Please note that the UI ctrl.cloupe is a single sample from uninjured untreated embryo tails and the ctrl cloupe.cloupe is an aggregate file of all non 2DG treated samples UI ctrl 24hpa ctrl and 48hpa ctrl.   pubmed:34518542   48hpa 2DG GSM4319213   source name:Regenerating embryonic zebrafish tail|strain:TAB 5|tissue:Regenerating embryonic tail|embryo age:5 dpf mM 2 deoxyglucose|time point:48hpa 48hpa 2DG Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2. was used to demultiplex for barcode processing for single cell gene counts and aggregating files. Further analyses of the samples was performed using Loupe Cell Browser 10x Genomics. Genome build: Danio Rerio 11 danRer11 GRCz11 Supplementary files format and content: cloupe files are provided which can be visualized with the Loupe Cell Browser 10x Genomics. Supplementary files format and content: hd5 files. Regenerating embryonic zebrafish tail   Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics.   strain:TAB 5|tissue:Regenerating embryonic tail|embryo age:5 dpf mM 2 deoxyglucose|time point:48hpa GSM4319213 GSM4319213: 48hpa 2DG; Danio rerio; RNA Seq GSM4319213   1 Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. GEO Accession:GSM4319213 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249927   intentional duplicate 48hpa_2DG.bam 10X Genomics bam file 6786532025.0 74577275.0 GSM4319213 r1 0:91 A:1972992538;C:1368168542;G:1707658855;T:1729990330;N:7721760 91       1972992538 1368168542 1707658855 1729990330 7721760 SRX7744906 SRS6164695 SRA1044429 GEO National Human Genome Research Institute, National Institutes of Health 1 0.9456   0.16065   0.80852   0.56712   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-02-18 Larval Larval Tail Multi-system
56823 56823 SRR11107234 SRX7744905 SRS6165316 SRP249927 PRJNA607316 The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration GSE145497 Transcriptome Analysis Throughout their lifetime fish maintain a high capacity for regenerating complex xxx post injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio which serves as an ideal model of appendage regeneration due to its easy manipulation relatively simple mixture of cell types and superior imaging properties. Regeneration of the embryonic zebrafish tail requires development of a blastema a mass of dedifferentiated cells capable of replacing lost tissue a crucial step in all known examples of appendage regeneration. Using this model we show that tail amputation triggers an obligate metabolic shift to promote glucose metabolism during early regeneration similar to the Warburg effect observed in tumor forming cells. Inhibition of glucose metabolism did not affect the overall health of the embryo but completely blocked the fin from regenerating post amputation due to the failure to form a functional blastema. We performed a time series of single cell RNA sequencing on regenerating tails with and without xxx of glucose metabolism. We demonstrated that metabolic reprogramming is required for sustained TGF ß signaling and blocking glucose metabolism largely mimicked inhibition of TGF ß receptors both resulting in an aberrant blastema. Finally we showed using genetic ablation of three possible metabolic pathways for glucose that metabolic reprogramming is required to provide glucose specifically to the hexosamine biosynthetic pathway while neither glycolysis nor the pentose phosphate pathway were necessary for regeneration. Overall design: Single cell RNAseq data was generated from uninjured or regenerating embryonic zebrafish tails at 24 and 48 hours post amputation with and without xxx deoxyglucose. Please note that the UI ctrl.cloupe is a single sample from uninjured untreated embryo tails and the ctrl cloupe.cloupe is an aggregate file of all non 2DG treated samples UI ctrl 24hpa ctrl and 48hpa ctrl.   pubmed:34518542   48hpa ctrl GSM4319212   source name:Regenerating embryonic zebrafish tail|strain:TAB 5|tissue:Regenerating embryonic tail|embryo age:5 dpf point:48hpa 48hpa ctrl Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2. was used to demultiplex for barcode processing for single cell gene counts and aggregating files. Further analyses of the samples was performed using Loupe Cell Browser 10x Genomics. Genome build: Danio Rerio 11 danRer11 GRCz11 Supplementary files format and content: cloupe files are provided which can be visualized with the Loupe Cell Browser 10x Genomics. Supplementary files format and content: hd5 files. Regenerating embryonic zebrafish tail   Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics.   strain:TAB 5|tissue:Regenerating embryonic tail|embryo age:5 dpf point:48hpa GSM4319212 GSM4319212: 48hpa ctrl; Danio rerio; RNA Seq GSM4319212   1 Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. GEO Accession:GSM4319212 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249927   intentional duplicate 48hpa_ctrl.bam 10X Genomics bam file 6315141924.0 69397164.0 GSM4319212 r1 0:91 A:1820671652;C:1274680094;G:1600555332;T:1612090454;N:7144392 91       1820671652 1274680094 1600555332 1612090454 7144392 SRX7744905 SRS6165316 SRA1044429 GEO National Human Genome Research Institute, National Institutes of Health 1 0.94831   0.155   0.80866   0.5428   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-02-18 Larval Larval Tail Multi-system
56824 56824 SRR11107233 SRX7744904 SRS6165317 SRP249927 PRJNA607316 The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration GSE145497 Transcriptome Analysis Throughout their lifetime fish maintain a high capacity for regenerating complex xxx post injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio which serves as an ideal model of appendage regeneration due to its easy manipulation relatively simple mixture of cell types and superior imaging properties. Regeneration of the embryonic zebrafish tail requires development of a blastema a mass of dedifferentiated cells capable of replacing lost tissue a crucial step in all known examples of appendage regeneration. Using this model we show that tail amputation triggers an obligate metabolic shift to promote glucose metabolism during early regeneration similar to the Warburg effect observed in tumor forming cells. Inhibition of glucose metabolism did not affect the overall health of the embryo but completely blocked the fin from regenerating post amputation due to the failure to form a functional blastema. We performed a time series of single cell RNA sequencing on regenerating tails with and without xxx of glucose metabolism. We demonstrated that metabolic reprogramming is required for sustained TGF ß signaling and blocking glucose metabolism largely mimicked inhibition of TGF ß receptors both resulting in an aberrant blastema. Finally we showed using genetic ablation of three possible metabolic pathways for glucose that metabolic reprogramming is required to provide glucose specifically to the hexosamine biosynthetic pathway while neither glycolysis nor the pentose phosphate pathway were necessary for regeneration. Overall design: Single cell RNAseq data was generated from uninjured or regenerating embryonic zebrafish tails at 24 and 48 hours post amputation with and without xxx deoxyglucose. Please note that the UI ctrl.cloupe is a single sample from uninjured untreated embryo tails and the ctrl cloupe.cloupe is an aggregate file of all non 2DG treated samples UI ctrl 24hpa ctrl and 48hpa ctrl.   pubmed:34518542   24hpa 2DG GSM4319211   source name:Regenerating embryonic zebrafish tail|strain:TAB 5|tissue:Regenerating embryonic tail|embryo age:4 dpf mM 2 deoxyglucose|time point:24hpa 24hpa 2DG Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2. was used to demultiplex for barcode processing for single cell gene counts and aggregating files. Further analyses of the samples was performed using Loupe Cell Browser 10x Genomics. Genome build: Danio Rerio 11 danRer11 GRCz11 Supplementary files format and content: cloupe files are provided which can be visualized with the Loupe Cell Browser 10x Genomics. Supplementary files format and content: hd5 files. Regenerating embryonic zebrafish tail   Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics.   strain:TAB 5|tissue:Regenerating embryonic tail|embryo age:4 dpf mM 2 deoxyglucose|time point:24hpa GSM4319211 GSM4319211: 24hpa 2DG; Danio rerio; RNA Seq GSM4319211   1 Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. GEO Accession:GSM4319211 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249927   intentional duplicate 24hpa_2DG.bam 10X Genomics bam file 4751770569.0 52217259.0 GSM4319211 r1 0:91 A:1367937805;C:991264209;G:1237114736;T:1153230321;N:2223498 91       1367937805 991264209 1237114736 1153230321 2223498 SRX7744904 SRS6165317 SRA1044429 GEO National Human Genome Research Institute, National Institutes of Health 1 0.8338   0.14372   0.82108   0.57161   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-02-18 Larval Larval Tail Multi-system
56825 56825 SRR11107232 SRX7744903 SRS6164694 SRP249927 PRJNA607316 The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration GSE145497 Transcriptome Analysis Throughout their lifetime fish maintain a high capacity for regenerating complex xxx post injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio which serves as an ideal model of appendage regeneration due to its easy manipulation relatively simple mixture of cell types and superior imaging properties. Regeneration of the embryonic zebrafish tail requires development of a blastema a mass of dedifferentiated cells capable of replacing lost tissue a crucial step in all known examples of appendage regeneration. Using this model we show that tail amputation triggers an obligate metabolic shift to promote glucose metabolism during early regeneration similar to the Warburg effect observed in tumor forming cells. Inhibition of glucose metabolism did not affect the overall health of the embryo but completely blocked the fin from regenerating post amputation due to the failure to form a functional blastema. We performed a time series of single cell RNA sequencing on regenerating tails with and without xxx of glucose metabolism. We demonstrated that metabolic reprogramming is required for sustained TGF ß signaling and blocking glucose metabolism largely mimicked inhibition of TGF ß receptors both resulting in an aberrant blastema. Finally we showed using genetic ablation of three possible metabolic pathways for glucose that metabolic reprogramming is required to provide glucose specifically to the hexosamine biosynthetic pathway while neither glycolysis nor the pentose phosphate pathway were necessary for regeneration. Overall design: Single cell RNAseq data was generated from uninjured or regenerating embryonic zebrafish tails at 24 and 48 hours post amputation with and without xxx deoxyglucose. Please note that the UI ctrl.cloupe is a single sample from uninjured untreated embryo tails and the ctrl cloupe.cloupe is an aggregate file of all non 2DG treated samples UI ctrl 24hpa ctrl and 48hpa ctrl.   pubmed:34518542   24hpa ctrl GSM4319210   source name:Regenerating embryonic zebrafish tail|strain:TAB 5|tissue:Regenerating embryonic tail|embryo age:4 dpf point:24hpa 24hpa ctrl Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2. was used to demultiplex for barcode processing for single cell gene counts and aggregating files. Further analyses of the samples was performed using Loupe Cell Browser 10x Genomics. Genome build: Danio Rerio 11 danRer11 GRCz11 Supplementary files format and content: cloupe files are provided which can be visualized with the Loupe Cell Browser 10x Genomics. Supplementary files format and content: hd5 files. Regenerating embryonic zebrafish tail   Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics.   strain:TAB 5|tissue:Regenerating embryonic tail|embryo age:4 dpf point:24hpa GSM4319210 GSM4319210: 24hpa ctrl; Danio rerio; RNA Seq GSM4319210   1 Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. GEO Accession:GSM4319210 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249927   intentional duplicate 24hpa_ctrl.bam 10X Genomics bam file 5461996085.0 60021935.0 GSM4319210 r1 0:91 A:1578516213;C:1146696708;G:1390321964;T:1344258467;N:2202733 91       1578516213 1146696708 1390321964 1344258467 2202733 SRX7744903 SRS6164694 SRA1044429 GEO National Human Genome Research Institute, National Institutes of Health 1 0.83781   0.14102   0.81264   0.58676   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-02-18 Larval Larval Tail Multi-system
63865 63865 SRR14143478 SRX10512841 SRS8636598 SRP313475 PRJNA719789 scRNA seq of tailbud development in zebrafish GSE171482 Other We have performed single cell RNA seq of whole tailbuds in WT zebrafish at 16 hpf. Overall design: Single cells were captured via 10X Chromium platform at 16 hpf from whole tailbuds.       Tailbud single cells at 16 hpf GSM5226215   source name:Dissociated tailbuds from 30 hpf 16 hpf embryos|transgenic:AB wildtypes|age:16 hpf embryo|tissue:dissociated tailbuds Tailbud single cells at 16 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: .csv file contains counts matrix for each cell that met quality thresholds Dissociated tailbuds from 30 hpf 16 hpf embryos   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. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   transgenic:AB wildtypes|age:16 hpf embryo|tissue:dissociated tailbuds GSM5226215 GSM5226215: Tailbud single cells at 16 hpf; Danio rerio; RNA Seq GSM5226215   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. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5226215 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP313475   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=WT tailbud S1 L003 I1 001.fastq.gz read2PairFiles=WT tailbud S1 L003 R1 001.fastq.gz read3PairFiles=WT tailbud S1 L003 R2 001.fastq.gz     31286394882.0 246349566.0 GSM5226215 r1 0:8 1:28 2:91 A:8483875403;C:6562544452;G:7703313223;T:8535328683;N:1333121 8 28 91   8483875403 6562544452 7703313223 8535328683 1333121 SRX10512841 SRS8636598 SRA1215249 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.94915   0.12419   0.79411   0.48155   91   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-04-05 Segmentation Embryo Tail Multi-system
63866 63866 SRR14143479 SRX10512841 SRS8636598 SRP313475 PRJNA719789 scRNA seq of tailbud development in zebrafish GSE171482 Other We have performed single cell RNA seq of whole tailbuds in WT zebrafish at 16 hpf. Overall design: Single cells were captured via 10X Chromium platform at 16 hpf from whole tailbuds.       Tailbud single cells at 16 hpf GSM5226215   source name:Dissociated tailbuds from 30 hpf 16 hpf embryos|transgenic:AB wildtypes|age:16 hpf embryo|tissue:dissociated tailbuds Tailbud single cells at 16 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: .csv file contains counts matrix for each cell that met quality thresholds Dissociated tailbuds from 30 hpf 16 hpf embryos   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. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   transgenic:AB wildtypes|age:16 hpf embryo|tissue:dissociated tailbuds GSM5226215 GSM5226215: Tailbud single cells at 16 hpf; Danio rerio; RNA Seq GSM5226215   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. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5226215 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP313475   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=WT tailbud S2 L003 I1 001.fastq.gz read2PairFiles=WT tailbud S2 L003 R1 001.fastq.gz read3PairFiles=WT tailbud S2 L003 R2 001.fastq.gz WT_tailbud_S2_L003_I1_001.fastq.gz WT_tailbud_S2_L003_R1_001.fastq.gz WT_tailbud_S2_L003_R2_001.fastq.gz fastq fastq fastq 34222167268.0 269465884.0 GSM5226215 r2 0:8 1:28 2:91 A:10380791879;C:7173180527;G:7598116520;T:9068620061;N:1458281 8 28 91   10380791879 7173180527 7598116520 9068620061 1458281 SRX10512841 SRS8636598 SRA1215249 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.94862   0.1236   0.79322   0.50153   91   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-04-05 Segmentation Embryo Tail Multi-system
63867 63867 SRR14143480 SRX10512841 SRS8636598 SRP313475 PRJNA719789 scRNA seq of tailbud development in zebrafish GSE171482 Other We have performed single cell RNA seq of whole tailbuds in WT zebrafish at 16 hpf. Overall design: Single cells were captured via 10X Chromium platform at 16 hpf from whole tailbuds.       Tailbud single cells at 16 hpf GSM5226215   source name:Dissociated tailbuds from 30 hpf 16 hpf embryos|transgenic:AB wildtypes|age:16 hpf embryo|tissue:dissociated tailbuds Tailbud single cells at 16 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: .csv file contains counts matrix for each cell that met quality thresholds Dissociated tailbuds from 30 hpf 16 hpf embryos   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. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   transgenic:AB wildtypes|age:16 hpf embryo|tissue:dissociated tailbuds GSM5226215 GSM5226215: Tailbud single cells at 16 hpf; Danio rerio; RNA Seq GSM5226215   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. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5226215 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP313475   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=WT tailbud S3 L003 I1 001.fastq.gz read2PairFiles=WT tailbud S3 L003 R1 001.fastq.gz read3PairFiles=WT tailbud S3 L003 R2 001.fastq.gz WT_tailbud_S3_L003_I1_001.fastq.gz WT_tailbud_S3_L003_R1_001.fastq.gz WT_tailbud_S3_L003_R2_001.fastq.gz fastq fastq fastq 33676411438.0 265168594.0 GSM5226215 r3 0:8 1:28 2:91 A:9145545141;C:7581198882;G:7228819079;T:9719412772;N:1435564 8 28 91   9145545141 7581198882 7228819079 9719412772 1435564 SRX10512841 SRS8636598 SRA1215249 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.94728   0.12372   0.79366   0.49386   91   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-04-05 Segmentation Embryo Tail Multi-system
63868 63868 SRR14143481 SRX10512841 SRS8636598 SRP313475 PRJNA719789 scRNA seq of tailbud development in zebrafish GSE171482 Other We have performed single cell RNA seq of whole tailbuds in WT zebrafish at 16 hpf. Overall design: Single cells were captured via 10X Chromium platform at 16 hpf from whole tailbuds.       Tailbud single cells at 16 hpf GSM5226215   source name:Dissociated tailbuds from 30 hpf 16 hpf embryos|transgenic:AB wildtypes|age:16 hpf embryo|tissue:dissociated tailbuds Tailbud single cells at 16 hpf FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: .csv file contains counts matrix for each cell that met quality thresholds Dissociated tailbuds from 30 hpf 16 hpf embryos   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. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3   transgenic:AB wildtypes|age:16 hpf embryo|tissue:dissociated tailbuds GSM5226215 GSM5226215: Tailbud single cells at 16 hpf; Danio rerio; RNA Seq GSM5226215   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. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3 GEO Accession:GSM5226215 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP313475   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=WT tailbud S4 L003 I1 001.fastq.gz read2PairFiles=WT tailbud S4 L003 R1 001.fastq.gz read3PairFiles=WT tailbud S4 L003 R2 001.fastq.gz WT_tailbud_S4_L003_I1_001.fastq.gz WT_tailbud_S4_L003_R1_001.fastq.gz WT_tailbud_S4_L003_R2_001.fastq.gz fastq fastq fastq 30944524598.0 243657674.0 GSM5226215 r4 0:8 1:28 2:91 A:8382983101;C:6979019830;G:7383731031;T:8197465285;N:1325351 8 28 91   8382983101 6979019830 7383731031 8197465285 1325351 SRX10512841 SRS8636598 SRA1215249 GEO Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine 1 0.94927   0.12443   0.79316   0.48307   91   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-04-05 Segmentation Embryo Tail Multi-system
63887 63887 SRR14202114 SRX10569027 SRS8675160 SRP314271 PRJNA720970 Single cell transcriptional profiles of islet1 derived ECs and the other ECs in the tail of 48 hpf zebrafish embryos GSE171822 Transcriptome Analysis We report transcriptional heterogeneity of venous endothelial cells ECs in the tail of zebrafish embryos which consist of HSPC niche constituting ECs and caudal vessel CV constituting ECs. To characterize isl1 derived ECs which derive from the endoderm and mainly constitute the HSPC niche in the caudal hematopoietic tissue CHT we performed single cell RNA sequencing scRNA seq of isl1 derived ECs and the other ECs separately isolated from the tails of zebrafish embryos. Our analyses revealed that tail venous ECs were split into 5 distinct sub clusters where isl1 derived ECs and the other ECs were similarly distributed to all venous EC clusters and further revealed that genes whose expression levels are different between isl1 derived ECs and the other ECs tend to show similar changes across all of the clusters even post their diversification. Overall design: We isolated live TagRFP+/EGFP+ cells for isl1 derived ECs and TagRFP /EGFP+ cells for the other ECs separately by FACS sorting from the tails of TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf. Then barcoded single cell cDNA libraries were prepared using the Chromium Single Cell three prime Reagents Kits v3.1 and were then sequenced using Illumina NovaSeq6000.   pubmed:36693371   RNA seq the other ECs GSM5235246   source name:resected tails posterior to the yolk end|strain:AB|genotype:TgBACisl1:TagRFP;Tgdab2:EGFP|developmental stage:48 hpf|tissue:Tail|cell type:other ECs TagRFP /EGFP+ RNA seq the other ECs The 10x Genomics Cell Ranger pipeline version 5.0.0 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 and reporter sequences EGFP and RFP with the gene annotation file Danio rerio.GRCz11.99.chr.gtf.gz barcode/UMI processing and gene counting for each cell. Genome build: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI counts for each sample. resected tails posterior to the yolk end   Tails resected from TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf were subjected to mechanical and enzymatic dissociation by pipetting every 5 minutes in 1 ml of protease solution TrypLE Express with 2.7 mg/ml Collagenase P and incubated at 28 °C until full dissociation 15 min. Cells were pelleted 3000 rpm 5 minutes at 4 °C and resuspended in suspension medium phenol red free Dulbecco’s modified Eagle’s medium with 1% FBS and 0.8 mM calcium chloride twice. Resuspended cells were passed through a cell strainer and subjected to cell sorting using a FACS Aria III cell sorter to isolate live TagRFP+/EGFP+ cells and TagRFP /EGFP+ cells separately. For scRNA seq single cell suspensions were resuspended with the suspension medium and barcoded with a 10x Chromium Controller 10x Genomics. RNA from the barcoded cells for each sample was subsequently reverse transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v3.1 reagent kit 10x Genomics. Sequencing was performed with Illumina NovaSeq6000.   strain:AB|genotype:TgBACisl1:TagRFP;Tgdab2:EGFP|developmental stage:48 hpf|tissue:Tail|cell type:other ECs TagRFP /EGFP+ GSM5235246 GSM5235246: RNA seq the other ECs; Danio rerio; RNA Seq GSM5235246   1 Tails resected from TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf were subjected to mechanical and enzymatic dissociation by pipetting every 5 minutes in 1 ml of protease solution TrypLE Express with 2.7 mg/ml Collagenase P and incubated at 28 °C until full dissociation 15 min. Cells were pelleted 3000 rpm 5 minutes at 4 °C and resuspended in suspension medium phenol red free Dulbecco's modified Eagle's medium with 1% FBS and 0.8 mM calcium chloride twice. Resuspended cells were passed through a cell strainer and subjected to cell sorting using a FACS Aria III cell sorter to isolate live TagRFP+/EGFP+ cells and TagRFP /EGFP+ cells separately. For scRNA seq single cell suspensions were resuspended with the suspension medium and barcoded with a 10x Chromium Controller 10x Genomics. RNA from the barcoded cells for each sample was subsequently reverse transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v3.1 reagent kit 10x Genomics. Sequencing was performed with Illumina NovaSeq6000. GEO Accession:GSM5235246 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP314271   loader:fastq load.py|options: platform=Illumina readTypes=TTTB read1PairFiles=ZebEmb GFP RFP I1.fastq.gz read2PairFiles=ZebEmb GFP RFP I2.fastq.gz read3PairFiles=ZebEmb GFP RFP R1.fastq.gz read4PairFiles=ZebEmb GFP RFP R2.fastq.gz ZebEmb_GFP_RFP_I1.fastq.gz ZebEmb_GFP_RFP_I2.fastq.gz ZebEmb_GFP_RFP_R1.fastq.gz ZebEmb_GFP_RFP_R2.fastq.gz fastq fastq fastq fastq 46144044078.0 334377131.0 GSM5235246 r1 0:10 1:10 2:28 3:90 A:12365801825;C:10786766050;G:11098071597;T:11890763395;N:2641211 10 10 28 90 12365801825 10786766050 11098071597 11890763395 2641211 SRX10569027 SRS8675160 SRA1217192 GEO Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute 1 0.93604   0.14513   0.79038   0.50811   90   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Japan 2021-04-09 Hatching Embryo Tail Multi-system
63888 63888 SRR14202113 SRX10569026 SRS8675161 SRP314271 PRJNA720970 Single cell transcriptional profiles of islet1 derived ECs and the other ECs in the tail of 48 hpf zebrafish embryos GSE171822 Transcriptome Analysis We report transcriptional heterogeneity of venous endothelial cells ECs in the tail of zebrafish embryos which consist of HSPC niche constituting ECs and caudal vessel CV constituting ECs. To characterize isl1 derived ECs which derive from the endoderm and mainly constitute the HSPC niche in the caudal hematopoietic tissue CHT we performed single cell RNA sequencing scRNA seq of isl1 derived ECs and the other ECs separately isolated from the tails of zebrafish embryos. Our analyses revealed that tail venous ECs were split into 5 distinct sub clusters where isl1 derived ECs and the other ECs were similarly distributed to all venous EC clusters and further revealed that genes whose expression levels are different between isl1 derived ECs and the other ECs tend to show similar changes across all of the clusters even post their diversification. Overall design: We isolated live TagRFP+/EGFP+ cells for isl1 derived ECs and TagRFP /EGFP+ cells for the other ECs separately by FACS sorting from the tails of TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf. Then barcoded single cell cDNA libraries were prepared using the Chromium Single Cell three prime Reagents Kits v3.1 and were then sequenced using Illumina NovaSeq6000.   pubmed:36693371   RNA seq isl1 derived ECs GSM5235245   source name:resected tails posterior to the yolk end|strain:AB|genotype:TgBACisl1:TagRFP;Tgdab2:EGFP|developmental stage:48 hpf|tissue:Tail|cell type:isl1 derived ECs TagRFP+/EGFP+ RNA seq isl1 derived ECs The 10x Genomics Cell Ranger pipeline version 5.0.0 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 and reporter sequences EGFP and RFP with the gene annotation file Danio rerio.GRCz11.99.chr.gtf.gz barcode/UMI processing and gene counting for each cell. Genome build: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI counts for each sample. resected tails posterior to the yolk end   Tails resected from TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf were subjected to mechanical and enzymatic dissociation by pipetting every 5 minutes in 1 ml of protease solution TrypLE Express with 2.7 mg/ml Collagenase P and incubated at 28 °C until full dissociation 15 min. Cells were pelleted 3000 rpm 5 minutes at 4 °C and resuspended in suspension medium phenol red free Dulbecco’s modified Eagle’s medium with 1% FBS and 0.8 mM calcium chloride twice. Resuspended cells were passed through a cell strainer and subjected to cell sorting using a FACS Aria III cell sorter to isolate live TagRFP+/EGFP+ cells and TagRFP /EGFP+ cells separately. For scRNA seq single cell suspensions were resuspended with the suspension medium and barcoded with a 10x Chromium Controller 10x Genomics. RNA from the barcoded cells for each sample was subsequently reverse transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v3.1 reagent kit 10x Genomics. Sequencing was performed with Illumina NovaSeq6000.   strain:AB|genotype:TgBACisl1:TagRFP;Tgdab2:EGFP|developmental stage:48 hpf|tissue:Tail|cell type:isl1 derived ECs TagRFP+/EGFP+ GSM5235245 GSM5235245: RNA seq isl1 derived ECs; Danio rerio; RNA Seq GSM5235245   1 Tails resected from TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf were subjected to mechanical and enzymatic dissociation by pipetting every 5 minutes in 1 ml of protease solution TrypLE Express with 2.7 mg/ml Collagenase P and incubated at 28 °C until full dissociation 15 min. Cells were pelleted 3000 rpm 5 minutes at 4 °C and resuspended in suspension medium phenol red free Dulbecco's modified Eagle's medium with 1% FBS and 0.8 mM calcium chloride twice. Resuspended cells were passed through a cell strainer and subjected to cell sorting using a FACS Aria III cell sorter to isolate live TagRFP+/EGFP+ cells and TagRFP /EGFP+ cells separately. For scRNA seq single cell suspensions were resuspended with the suspension medium and barcoded with a 10x Chromium Controller 10x Genomics. RNA from the barcoded cells for each sample was subsequently reverse transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v3.1 reagent kit 10x Genomics. Sequencing was performed with Illumina NovaSeq6000. GEO Accession:GSM5235245 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP314271   loader:fastq load.py|options: platform=Illumina readTypes=TTTB read1PairFiles=ZebEmb GFP I1.fastq.gz read2PairFiles=ZebEmb GFP I2.fastq.gz read3PairFiles=ZebEmb GFP R1.fastq.gz read4PairFiles=ZebEmb GFP R2.fastq.gz ZebEmb_GFP_I1.fastq.gz ZebEmb_GFP_I2.fastq.gz ZebEmb_GFP_R1.fastq.gz ZebEmb_GFP_R2.fastq.gz fastq fastq fastq fastq 53036547366.0 384322807.0 GSM5235245 r1 0:10 1:10 2:28 3:90 A:14610188978;C:12169986421;G:12283689207;T:13969658178;N:3024582 10 10 28 90 14610188978 12169986421 12283689207 13969658178 3024582 SRX10569026 SRS8675161 SRA1217192 GEO Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute 1 0.94469   0.10454   0.79133   0.51214   90   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Japan 2021-04-09 Hatching Embryo Tail Multi-system
64263 64263 SRR14428602 SRX10779739 SRS8866172 SRP318543 PRJNA727493 Single cell gene expression analysis of zebrafish body elongation GSE173894 Transcriptome Analysis scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.   pubmed:37267354   scRNA seq of notum 1 treatment embryo replicate 4 GSM5282506   tissue:tail|treatment:notum 1 scRNA seq of notum 1 treatment embryo replicate 4 We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file. tail Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together. Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…   treatment:notum 1 GSM5282506 GSM5282506: scRNA seq of notum 1 treatment embryo replicate 4; Danio rerio; RNA Seq GSM5282506   1 Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr… GEO Accession:GSM5282506 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP318543     WNT_MG2_S40_L006_R1_001.fastq.gz WNT_MG2_S40_L006_R2_001.fastq.gz fastq fastq 59309016800.0 296545084.0 GSM5282506 r1 0:100 1:100 A:13101652467;C:9053865386;G:9914199388;T:27226829088;N:12470471 100 100     13101652467 9053865386 9914199388 27226829088 12470471 SRX10779739 SRS8866172 SRA1228423 GEO Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University 2 0.00907 0.91374 0.00232 0.07221 0.99293 0.82822 0.5 0.50749 100 100 T B mate1 technical by mapping diff illumina hiseq_era full_length poly_a unknown sc single_cell_droplet 10x   United States 2021-05-05 Segmentation Embryo Tail Multi-system
64264 64264 SRR14428601 SRX10779738 SRS8866171 SRP318543 PRJNA727493 Single cell gene expression analysis of zebrafish body elongation GSE173894 Transcriptome Analysis scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.   pubmed:37267354   scRNA seq of notum 1 treatment embryo replicate 3 GSM5282505   tissue:tail|treatment:notum 1 scRNA seq of notum 1 treatment embryo replicate 3 We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file. tail Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together. Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…   treatment:notum 1 GSM5282505 GSM5282505: scRNA seq of notum 1 treatment embryo replicate 3; Danio rerio; RNA Seq GSM5282505   1 Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr… GEO Accession:GSM5282505 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP318543     WNT_MG1_S39_L005_R1_001.fastq.gz WNT_MG1_S39_L005_R2_001.fastq.gz fastq fastq 75003307800.0 375016539.0 GSM5282505 r1 0:100 1:100 A:17011122660;C:12505646501;G:12322737410;T:33144126985;N:19674244 100 100     17011122660 12505646501 12322737410 33144126985 19674244 SRX10779738 SRS8866171 SRA1228423 GEO Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University 2 0.0068 0.94221 0.00175 0.08258 0.99608 0.82473 0.49289 0.52202 100 100 T B mate1 technical by mapping diff illumina hiseq_era full_length poly_a unknown sc single_cell_droplet 10x   United States 2021-05-05 Segmentation Embryo Tail Multi-system
64265 64265 SRR14428600 SRX10779737 SRS8866170 SRP318543 PRJNA727493 Single cell gene expression analysis of zebrafish body elongation GSE173894 Transcriptome Analysis scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.   pubmed:37267354   scRNA seq of notum 1 treatment embryo replicate 2 GSM5282504   tissue:tail|treatment:notum 1 scRNA seq of notum 1 treatment embryo replicate 2 We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file. tail Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together. Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…   treatment:notum 1 GSM5282504 GSM5282504: scRNA seq of notum 1 treatment embryo replicate 2; Danio rerio; RNA Seq GSM5282504   1 Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr… GEO Accession:GSM5282504 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP318543     WNT_DJ2_S42_L008_R1_001.fastq.gz WNT_DJ2_S42_L008_R2_001.fastq.gz fastq fastq 73921649200.0 369608246.0 GSM5282504 r1 0:100 1:100 A:16691509262;C:12147679273;G:12179457462;T:32881202116;N:21801087 100 100     16691509262 12147679273 12179457462 32881202116 21801087 SRX10779737 SRS8866170 SRA1228423 GEO Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University 2 0.00683 0.92595 0.00109 0.08047 0.99531 0.82558 0.5017 0.48675 100 100 T B mate1 technical by mapping diff illumina hiseq_era full_length poly_a unknown sc single_cell_droplet 10x   United States 2021-05-05 Segmentation Embryo Tail Multi-system
64266 64266 SRR14428599 SRX10779736 SRS8866169 SRP318543 PRJNA727493 Single cell gene expression analysis of zebrafish body elongation GSE173894 Transcriptome Analysis scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.   pubmed:37267354   scRNA seq of notum 1 treatment embryo replicate 1 GSM5282503   tissue:tail|treatment:notum 1 scRNA seq of notum 1 treatment embryo replicate 1 We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file. tail Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together. Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…   treatment:notum 1 GSM5282503 GSM5282503: scRNA seq of notum 1 treatment embryo replicate 1; Danio rerio; RNA Seq GSM5282503   1 Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr… GEO Accession:GSM5282503 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP318543     WNT_DJ1_S41_L007_R1_001.fastq.gz WNT_DJ1_S41_L007_R2_001.fastq.gz fastq fastq 72873756000.0 364368780.0 GSM5282503 r1 0:100 1:100 A:16621508845;C:12254073814;G:11510875104;T:32473791832;N:13506405 100 100     16621508845 12254073814 11510875104 32473791832 13506405 SRX10779736 SRS8866169 SRA1228423 GEO Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University 2 0.00358 0.94302 0.0008 0.08218 0.99803 0.82181 0.50485 0.51251 100 100 T B mate1 technical by mapping diff illumina hiseq_era full_length poly_a unknown sc single_cell_droplet 10x   United States 2021-05-05 Segmentation Embryo Tail Multi-system
64267 64267 SRR14428593 SRX10779735 SRS8866168 SRP318543 PRJNA727493 Single cell gene expression analysis of zebrafish body elongation GSE173894 Transcriptome Analysis scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.   pubmed:37267354   scRNA seq of SU5402 treatment embryo replicate 4 GSM5282502   tissue:tail|treatment:SU5402 scRNA seq of SU5402 treatment embryo replicate 4 We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file. tail Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together. Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…   treatment:SU5402 GSM5282502 GSM5282502: scRNA seq of SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq GSM5282502   1 Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr… GEO Accession:GSM5282502 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP318543   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=SU4 DRT S2 L001 I1 001.fastq.gz read2PairFiles=SU4 DRT S2 L001 R1 001.fastq.gz read3PairFiles=SU4 DRT S2 L001 R2 001.fastq.gz SU4_DRT_S2_L001_I1_001.fastq.gz SU4_DRT_S2_L001_R1_001.fastq.gz SU4_DRT_S2_L001_R2_001.fastq.gz fastq fastq fastq 6902983527.0 54354201.0 GSM5282502 r1 0:8 1:28 2:91 A:1904129671;C:1528133826;G:1597676497;T:1870308784;N:2734749 8 28 91   1904129671 1528133826 1597676497 1870308784 2734749 SRX10779735 SRS8866168 SRA1228423 GEO Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University 1 0.93834   0.14712   0.80097   0.53464   91   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_droplet 10x   United States 2021-05-05 Segmentation Embryo Tail Multi-system
64268 64268 SRR14428594 SRX10779735 SRS8866168 SRP318543 PRJNA727493 Single cell gene expression analysis of zebrafish body elongation GSE173894 Transcriptome Analysis scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.   pubmed:37267354   scRNA seq of SU5402 treatment embryo replicate 4 GSM5282502   tissue:tail|treatment:SU5402 scRNA seq of SU5402 treatment embryo replicate 4 We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file. tail Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together. Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…   treatment:SU5402 GSM5282502 GSM5282502: scRNA seq of SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq GSM5282502   1 Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr… GEO Accession:GSM5282502 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP318543   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=SU4 DRT S2 L002 I1 001.fastq.gz read2PairFiles=SU4 DRT S2 L002 R1 001.fastq.gz read3PairFiles=SU4 DRT S2 L002 R2 001.fastq.gz SU4_DRT_S2_L002_I1_001.fastq.gz SU4_DRT_S2_L002_R1_001.fastq.gz SU4_DRT_S2_L002_R2_001.fastq.gz fastq fastq fastq 7355984272.0 57921136.0 GSM5282502 r2 0:8 1:28 2:91 A:2029150464;C:1629831151;G:1703134376;T:1991639472;N:2228809 8 28 91   2029150464 1629831151 1703134376 1991639472 2228809 SRX10779735 SRS8866168 SRA1228423 GEO Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University 1 0.93751   0.14654   0.80048   0.53568   91   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_droplet 10x   United States 2021-05-05 Segmentation Embryo Tail Multi-system
64269 64269 SRR14428595 SRX10779735 SRS8866168 SRP318543 PRJNA727493 Single cell gene expression analysis of zebrafish body elongation GSE173894 Transcriptome Analysis scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.   pubmed:37267354   scRNA seq of SU5402 treatment embryo replicate 4 GSM5282502   tissue:tail|treatment:SU5402 scRNA seq of SU5402 treatment embryo replicate 4 We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file. tail Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together. Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…   treatment:SU5402 GSM5282502 GSM5282502: scRNA seq of SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq GSM5282502   1 Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr… GEO Accession:GSM5282502 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP318543   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=SU4 DRT S2 L003 I1 001.fastq.gz read2PairFiles=SU4 DRT S2 L003 R1 001.fastq.gz read3PairFiles=SU4 DRT S2 L003 R2 001.fastq.gz SU4_DRT_S2_L003_I1_001.fastq.gz SU4_DRT_S2_L003_R1_001.fastq.gz SU4_DRT_S2_L003_R2_001.fastq.gz fastq fastq fastq 6915051321.0 54449223.0 GSM5282502 r3 0:8 1:28 2:91 A:1907859125;C:1531399983;G:1600723047;T:1872767703;N:2301463 8 28 91   1907859125 1531399983 1600723047 1872767703 2301463 SRX10779735 SRS8866168 SRA1228423 GEO Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University 1 0.93859   0.14759   0.80075   0.53726   91   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_droplet 10x   United States 2021-05-05 Segmentation Embryo Tail Multi-system
64270 64270 SRR14428596 SRX10779735 SRS8866168 SRP318543 PRJNA727493 Single cell gene expression analysis of zebrafish body elongation GSE173894 Transcriptome Analysis scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.   pubmed:37267354   scRNA seq of SU5402 treatment embryo replicate 4 GSM5282502   tissue:tail|treatment:SU5402 scRNA seq of SU5402 treatment embryo replicate 4 We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file. tail Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together. Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…   treatment:SU5402 GSM5282502 GSM5282502: scRNA seq of SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq GSM5282502   1 Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr… GEO Accession:GSM5282502 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP318543   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=SU4 DRT S2 L004 I1 001.fastq.gz read2PairFiles=SU4 DRT S2 L004 R1 001.fastq.gz read3PairFiles=SU4 DRT S2 L004 R2 001.fastq.gz SU4_DRT_S2_L004_I1_001.fastq.gz SU4_DRT_S2_L004_R1_001.fastq.gz SU4_DRT_S2_L004_R2_001.fastq.gz fastq fastq fastq 6496116929.0 51150527.0 GSM5282502 r4 0:8 1:28 2:91 A:1791207713;C:1438082538;G:1503927125;T:1760463486;N:2436067 8 28 91   1791207713 1438082538 1503927125 1760463486 2436067 SRX10779735 SRS8866168 SRA1228423 GEO Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University 1 0.93855   0.14517   0.80142   0.51836   91   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_droplet 10x   United States 2021-05-05 Segmentation Embryo Tail Multi-system
64271 64271 SRR14428597 SRX10779735 SRS8866168 SRP318543 PRJNA727493 Single cell gene expression analysis of zebrafish body elongation GSE173894 Transcriptome Analysis scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.   pubmed:37267354   scRNA seq of SU5402 treatment embryo replicate 4 GSM5282502   tissue:tail|treatment:SU5402 scRNA seq of SU5402 treatment embryo replicate 4 We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file. tail Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together. Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…   treatment:SU5402 GSM5282502 GSM5282502: scRNA seq of SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq GSM5282502   1 Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr… GEO Accession:GSM5282502 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP318543   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=SU4 DRT S2 L005 I1 001.fastq.gz read2PairFiles=SU4 DRT S2 L005 R1 001.fastq.gz read3PairFiles=SU4 DRT S2 L005 R2 001.fastq.gz SU4_DRT_S2_L005_I1_001.fastq.gz SU4_DRT_S2_L005_R1_001.fastq.gz SU4_DRT_S2_L005_R2_001.fastq.gz fastq fastq fastq 6925225545.0 54529335.0 GSM5282502 r5 0:8 1:28 2:91 A:1908749610;C:1534337999;G:1604298047;T:1874791459;N:3048430 8 28 91   1908749610 1534337999 1604298047 1874791459 3048430 SRX10779735 SRS8866168 SRA1228423 GEO Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University 1 0.93705   0.14527   0.79811   0.49961   91   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_droplet 10x   United States 2021-05-05 Segmentation Embryo Tail Multi-system
64272 64272 SRR14428598 SRX10779735 SRS8866168 SRP318543 PRJNA727493 Single cell gene expression analysis of zebrafish body elongation GSE173894 Transcriptome Analysis scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.   pubmed:37267354   scRNA seq of SU5402 treatment embryo replicate 4 GSM5282502   tissue:tail|treatment:SU5402 scRNA seq of SU5402 treatment embryo replicate 4 We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file. tail Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together. Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…   treatment:SU5402 GSM5282502 GSM5282502: scRNA seq of SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq GSM5282502   1 Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr… GEO Accession:GSM5282502 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP318543   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=SU4 DRT S2 L006 I1 001.fastq.gz read2PairFiles=SU4 DRT S2 L006 R1 001.fastq.gz read3PairFiles=SU4 DRT S2 L006 R2 001.fastq.gz SU4_DRT_S2_L006_I1_001.fastq.gz SU4_DRT_S2_L006_R1_001.fastq.gz SU4_DRT_S2_L006_R2_001.fastq.gz fastq fastq fastq 5772764553.0 45454839.0 GSM5282502 r6 0:8 1:28 2:91 A:1592079310;C:1277414314;G:1335013911;T:1565676607;N:2580411 8 28 91   1592079310 1277414314 1335013911 1565676607 2580411 SRX10779735 SRS8866168 SRA1228423 GEO Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University 1 0.93895   0.1477   0.79772   0.52786   91   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_droplet 10x   United States 2021-05-05 Segmentation Embryo Tail Multi-system
64273 64273 SRR14428587 SRX10779734 SRS8866167 SRP318543 PRJNA727493 Single cell gene expression analysis of zebrafish body elongation GSE173894 Transcriptome Analysis scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.   pubmed:37267354   scRNA seq of SU5402 treatment embryo replicate 3 GSM5282501   tissue:tail|treatment:SU5402 scRNA seq of SU5402 treatment embryo replicate 3 We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file. tail Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together. Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…   treatment:SU5402 GSM5282501 GSM5282501: scRNA seq of SU5402 treatment embryo replicate 3; Danio rerio; RNA Seq GSM5282501   1 Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr… GEO Accession:GSM5282501 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP318543   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=SU3 DRT S1 L001 I1 001.fastq.gz read2PairFiles=SU3 DRT S1 L001 R1 001.fastq.gz read3PairFiles=SU3 DRT S1 L001 R2 001.fastq.gz SU3_DRT_S1_L001_I1_001.fastq.gz SU3_DRT_S1_L001_R1_001.fastq.gz SU3_DRT_S1_L001_R2_001.fastq.gz fastq fastq fastq 8251078748.0 64969124.0 GSM5282501 r1 0:8 1:28 2:91 A:2304710369;C:1797342936;G:1900704244;T:2245059790;N:3261409 8 28 91   2304710369 1797342936 1900704244 2245059790 3261409 SRX10779734 SRS8866167 SRA1228423 GEO Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University 1 0.92754   0.16532   0.81462   0.52604   91   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_droplet 10x   United States 2021-05-05 Segmentation Embryo Tail Multi-system
64274 64274 SRR14428588 SRX10779734 SRS8866167 SRP318543 PRJNA727493 Single cell gene expression analysis of zebrafish body elongation GSE173894 Transcriptome Analysis scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.   pubmed:37267354   scRNA seq of SU5402 treatment embryo replicate 3 GSM5282501   tissue:tail|treatment:SU5402 scRNA seq of SU5402 treatment embryo replicate 3 We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file. tail Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together. Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…   treatment:SU5402 GSM5282501 GSM5282501: scRNA seq of SU5402 treatment embryo replicate 3; Danio rerio; RNA Seq GSM5282501   1 Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr… GEO Accession:GSM5282501 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP318543   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=SU3 DRT S1 L002 I1 001.fastq.gz read2PairFiles=SU3 DRT S1 L002 R1 001.fastq.gz read3PairFiles=SU3 DRT S1 L002 R2 001.fastq.gz SU3_DRT_S1_L002_I1_001.fastq.gz SU3_DRT_S1_L002_R1_001.fastq.gz SU3_DRT_S1_L002_R2_001.fastq.gz fastq fastq fastq 8745931073.0 68865599.0 GSM5282501 r2 0:8 1:28 2:91 A:2444384848;C:1906587775;G:2015145654;T:2377159417;N:2653379 8 28 91   2444384848 1906587775 2015145654 2377159417 2653379 SRX10779734 SRS8866167 SRA1228423 GEO Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University 1 0.92881   0.16592   0.8132   0.53153   91   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_droplet 10x   United States 2021-05-05 Segmentation Embryo Tail Multi-system
64275 64275 SRR14428589 SRX10779734 SRS8866167 SRP318543 PRJNA727493 Single cell gene expression analysis of zebrafish body elongation GSE173894 Transcriptome Analysis scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.   pubmed:37267354   scRNA seq of SU5402 treatment embryo replicate 3 GSM5282501   tissue:tail|treatment:SU5402 scRNA seq of SU5402 treatment embryo replicate 3 We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file. tail Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together. Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…   treatment:SU5402 GSM5282501 GSM5282501: scRNA seq of SU5402 treatment embryo replicate 3; Danio rerio; RNA Seq GSM5282501   1 Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr… GEO Accession:GSM5282501 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP318543   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=SU3 DRT S1 L003 I1 001.fastq.gz read2PairFiles=SU3 DRT S1 L003 R1 001.fastq.gz read3PairFiles=SU3 DRT S1 L003 R2 001.fastq.gz SU3_DRT_S1_L003_I1_001.fastq.gz SU3_DRT_S1_L003_R1_001.fastq.gz SU3_DRT_S1_L003_R2_001.fastq.gz fastq fastq fastq 8264591040.0 65075520.0 GSM5282501 r3 0:8 1:28 2:91 A:2309308717;C:1801010847;G:1903956632;T:2247562936;N:2751908 8 28 91   2309308717 1801010847 1903956632 2247562936 2751908 SRX10779734 SRS8866167 SRA1228423 GEO Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University 1 0.92814   0.16403   0.81186   0.54282   91   B   usable mapping rate illumina hiseq_era full_length poly_a unknown sc single_cell_droplet 10x   United States 2021-05-05 Segmentation Embryo 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");;