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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,SRR25509990,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S65_L001_I1_001.fastq.gz Kristen_10X_101620_S65_L001_R1_001.fastq.gz Kristen_10X_101620_S65_L001_R2_001.fastq.gz,fastq fastq fastq,3327423622.0,26200186.0,GSM7680082 r1,0:8 1:28 2:91,A:693698335;C:494975421;G:540414923;T:654926705;N:201542,8,28,91,,693698335,494975421,540414923,654926705,201542,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91351,,0.22865,,0.77723,,0.49805,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24839,SRR25509991,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S67_L002_I1_001.fastq.gz Kristen_10X_101620_S67_L002_R1_001.fastq.gz Kristen_10X_101620_S67_L002_R2_001.fastq.gz,fastq fastq fastq,4430975390.0,34889570.0,GSM7680082 r10,0:8 1:28 2:91,A:923557751;C:658731986;G:718325003;T:874072049;N:264081,8,28,91,,923557751,658731986,718325003,874072049,264081,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91797,,0.22868,,0.77863,,0.50737,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24840,SRR25509992,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S67_L003_I1_001.fastq.gz Kristen_10X_101620_S67_L003_R1_001.fastq.gz Kristen_10X_101620_S67_L003_R2_001.fastq.gz,fastq fastq fastq,4429223552.0,34875776.0,GSM7680082 r11,0:8 1:28 2:91,A:923277621;C:658440918;G:718036099;T:873676803;N:264175,8,28,91,,923277621,658440918,718036099,873676803,264175,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91753,,0.22978,,0.77942,,0.50977,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24841,SRR25509993,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S67_L004_I1_001.fastq.gz Kristen_10X_101620_S67_L004_R1_001.fastq.gz Kristen_10X_101620_S67_L004_R2_001.fastq.gz,fastq fastq fastq,4549656890.0,35824070.0,GSM7680082 r12,0:8 1:28 2:91,A:950423951;C:673969790;G:734760168;T:900554096;N:282365,8,28,91,,950423951,673969790,734760168,900554096,282365,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91687,,0.23323,,0.77932,,0.50984,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24842,SRR25509994,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S68_L001_I1_001.fastq.gz Kristen_10X_101620_S68_L001_R1_001.fastq.gz Kristen_10X_101620_S68_L001_R2_001.fastq.gz,fastq fastq fastq,2696456634.0,21231942.0,GSM7680082 r13,0:8 1:28 2:91,A:562209710;C:401113540;G:437836456;T:530785441;N:161575,8,28,91,,562209710,401113540,437836456,530785441,161575,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91384,,0.22885,,0.77912,,0.50672,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24843,SRR25509995,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S68_L002_I1_001.fastq.gz Kristen_10X_101620_S68_L002_R1_001.fastq.gz Kristen_10X_101620_S68_L002_R2_001.fastq.gz,fastq fastq fastq,2735162932.0,21536716.0,GSM7680082 r14,0:8 1:28 2:91,A:570169460;C:406846839;G:443964376;T:538696359;N:164122,8,28,91,,570169460,406846839,443964376,538696359,164122,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91691,,0.22998,,0.77942,,0.51035,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24844,SRR25509996,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S68_L003_I1_001.fastq.gz Kristen_10X_101620_S68_L003_R1_001.fastq.gz Kristen_10X_101620_S68_L003_R2_001.fastq.gz,fastq fastq fastq,2739703563.0,21572469.0,GSM7680082 r15,0:8 1:28 2:91,A:571283074;C:407511119;G:444574049;T:539563747;N:162690,8,28,91,,571283074,407511119,444574049,539563747,162690,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91526,,0.22747,,0.7793,,0.51387,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24845,SRR25509997,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S68_L004_I1_001.fastq.gz Kristen_10X_101620_S68_L004_R1_001.fastq.gz Kristen_10X_101620_S68_L004_R2_001.fastq.gz,fastq fastq fastq,2828960433.0,22275279.0,GSM7680082 r16,0:8 1:28 2:91,A:591166850;C:419193897;G:457332081;T:559181603;N:175958,8,28,91,,591166850,419193897,457332081,559181603,175958,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91651,,0.23126,,0.77613,,0.50223,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24846,SRR25509998,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S65_L002_I1_001.fastq.gz Kristen_10X_101620_S65_L002_R1_001.fastq.gz Kristen_10X_101620_S65_L002_R2_001.fastq.gz,fastq fastq fastq,3374189340.0,26568420.0,GSM7680082 r2,0:8 1:28 2:91,A:703424426;C:501911907;G:547786373;T:664402117;N:201397,8,28,91,,703424426,501911907,547786373,664402117,201397,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91522,,0.22812,,0.77753,,0.50208,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24847,SRR25509999,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S65_L003_I1_001.fastq.gz Kristen_10X_101620_S65_L003_R1_001.fastq.gz Kristen_10X_101620_S65_L003_R2_001.fastq.gz,fastq fastq fastq,3383217516.0,26639508.0,GSM7680082 r3,0:8 1:28 2:91,A:705514047;C:503189161;G:549089218;T:666200894;N:201908,8,28,91,,705514047,503189161,549089218,666200894,201908,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91535,,0.23036,,0.78078,,0.50202,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24848,SRR25510000,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S65_L004_I1_001.fastq.gz Kristen_10X_101620_S65_L004_R1_001.fastq.gz Kristen_10X_101620_S65_L004_R2_001.fastq.gz,fastq fastq fastq,3493154050.0,27505150.0,GSM7680082 r4,0:8 1:28 2:91,A:729910298;C:517582902;G:564926384;T:690333365;N:215701,8,28,91,,729910298,517582902,564926384,690333365,215701,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91569,,0.22913,,0.77873,,0.50186,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24849,SRR25510001,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S66_L001_I1_001.fastq.gz Kristen_10X_101620_S66_L001_R1_001.fastq.gz Kristen_10X_101620_S66_L001_R2_001.fastq.gz,fastq fastq fastq,3237456187.0,25491781.0,GSM7680082 r5,0:8 1:28 2:91,A:674885196;C:481871349;G:525642933;T:637154812;N:197781,8,28,91,,674885196,481871349,525642933,637154812,197781,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91378,,0.22852,,0.77843,,0.50985,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24850,SRR25510002,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S66_L002_I1_001.fastq.gz Kristen_10X_101620_S66_L002_R1_001.fastq.gz Kristen_10X_101620_S66_L002_R2_001.fastq.gz,fastq fastq fastq,3287789081.0,25888103.0,GSM7680082 r6,0:8 1:28 2:91,A:685408765;C:489232060;G:533550966;T:647427897;N:197685,8,28,91,,685408765,489232060,533550966,647427897,197685,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91484,,0.22872,,0.78001,,0.49909,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24851,SRR25510003,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S66_L003_I1_001.fastq.gz Kristen_10X_101620_S66_L003_R1_001.fastq.gz Kristen_10X_101620_S66_L003_R2_001.fastq.gz,fastq fastq fastq,3298207145.0,25970135.0,GSM7680082 r7,0:8 1:28 2:91,A:687621787;C:490851045;G:535230137;T:649382247;N:197069,8,28,91,,687621787,490851045,535230137,649382247,197069,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91559,,0.2268,,0.77766,,0.50935,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24852,SRR25510004,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S66_L004_I1_001.fastq.gz Kristen_10X_101620_S66_L004_R1_001.fastq.gz Kristen_10X_101620_S66_L004_R2_001.fastq.gz,fastq fastq fastq,3377888088.0,26597544.0,GSM7680082 r8,0:8 1:28 2:91,A:705624374;C:500985504;G:546306692;T:667248332;N:211602,8,28,91,,705624374,500985504,546306692,667248332,211602,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91679,,0.22965,,0.77837,,0.51495,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
24853,SRR25510005,SRX21240518,SRS18495441,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,GSM7680082,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  2dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs,GSM7680082,GSM7680082: Spinal cord MNs  olig2dsRed  2dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680082 r1,GSM7680082,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,Kristen_10X_101620_S67_L001_I1_001.fastq.gz Kristen_10X_101620_S67_L001_R1_001.fastq.gz Kristen_10X_101620_S67_L001_R2_001.fastq.gz,fastq fastq fastq,4346114117.0,34221371.0,GSM7680082 r9,0:8 1:28 2:91,A:905838814;C:646261347;G:704993570;T:856789016;N:262014,8,28,91,,905838814,646261347,704993570,856789016,262014,SRX21240518,SRS18495441,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91558,,0.22834,,0.7783,,0.49972,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Hatching,Embryo,Tail,Multi-system
25133,SRR25634296,SRX21361065,SRS18605555,SRP454944,PRJNA1005241,Nkx2.7 is a Conserved Regulator of Craniofacial Development,GSE240780,Transcriptome Analysis,Pharyngeal arch cells are comprised of endoderm  mesoderm  and neural crest layers. We used single cell RNA sequencing scRNA seq to analyze the genetic differences in pharyngeal arch cell types between wild type and nkx2.7 /  samples. Overall design: Pharyngeal arch cells were obtained through manual dissection of wild type and nkx2.7 /  embryos at 26 hpf. All embryos were positive for TgBACtcf21:mcherry NTR  which was used as a visual guide for dissection. Cells were FACS sorted to eliminate dead cells from sequencing. 2 wild type embryos and 2 nkx2.7 /  samples were pooled for submission.,,pubmed:40268889,,KC002  scRNAseq,GSM7709162,,source name:Pharyngeal arches|genotype:nkx2.7 / |tissue:Pharyngeal arches|strain:AB|developmental stage:26 hpf|geo loc name:missing|collection date:missing,KC002  scRNAseq,The read alignment and gene counting were made using the Cell Ranger software v6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 version 105 Supplementary files format and content: Tab separated values files and matrix files,Pharyngeal arches,,From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108  two wild type and two nkx2.7 /  embryos were identified by genotyping.  The pharyngeal arches and surrounding tissue were dissected  dissociated  and submitted for flow cytometry.  Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution.  Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C.  The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer.  Finally  DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI.  NERL Diluent 2 Thermo Fisher  DIL5522 solution was used for sheath fluid.  The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences  655051  SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m  5 mL Spherotech  RCP 30 5A  followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences  345249. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,genotype:nkx2.7 / |tissue:Pharyngeal arches|strain:AB|developmental stage:26 hpf,GSM7709162,GSM7709162: KC002  scRNAseq; Danio rerio; RNA Seq,GSM7709162 r1,GSM7709162,1,From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108  two wild type and two nkx2.7 /  embryos were identified by genotyping.  The pharyngeal arches and surrounding tissue were dissected  dissociated  and submitted for flow cytometry.  Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution.  Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C.  The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer.  Finally  DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI.  NERL Diluent 2 Thermo Fisher  DIL5522 solution was used for sheath fluid.  The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences  655051  SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m  5 mL Spherotech  RCP 30 5A  followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences  345249. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454944,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=KC002 S1 L004 I1 001.fastq.gz   read2PairFiles=KC002 S1 L004 I2 001.fastq.gz   read3PairFiles=KC002 S1 L004 R1 001.fastq.gz   read4PairFiles=KC002 S1 L004 R2 001.fastq.gz,KC002_S1_L004_I1_001.fastq.gz KC002_S1_L004_I2_001.fastq.gz KC002_S1_L004_R1_001.fastq.gz KC002_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,65825988564.0,296513462.0,GSM7709162 r1,0:10 1:10 2:101 3:101,A:14990994149;C:11485312838;G:11921291570;T:21497933732;N:187035,10,10,101,101,14990994149,11485312838,11921291570,21497933732,187035,SRX21361065,SRS18605555,SRA1692494,"SangesLab Computational Genomics, NEUROSCIENCE, SISSA","SangesLab Computational Genomics, NEUROSCIENCE, SISSA",2,0.00059,0.93473,2e-05,0.14487,0.99949,0.78364,0.5,0.52799,101,101,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Italy,2023-08-14,Pharyngula,Embryo,Pharyngeal Arch,Multi-system
25134,SRR25634297,SRX21361064,SRS18605556,SRP454944,PRJNA1005241,Nkx2.7 is a Conserved Regulator of Craniofacial Development,GSE240780,Transcriptome Analysis,Pharyngeal arch cells are comprised of endoderm  mesoderm  and neural crest layers. We used single cell RNA sequencing scRNA seq to analyze the genetic differences in pharyngeal arch cell types between wild type and nkx2.7 /  samples. Overall design: Pharyngeal arch cells were obtained through manual dissection of wild type and nkx2.7 /  embryos at 26 hpf. All embryos were positive for TgBACtcf21:mcherry NTR  which was used as a visual guide for dissection. Cells were FACS sorted to eliminate dead cells from sequencing. 2 wild type embryos and 2 nkx2.7 /  samples were pooled for submission.,,pubmed:40268889,,KC001  scRNAseq,GSM7709161,,source name:Pharyngeal arches|genotype:wild type|tissue:Pharyngeal arches|strain:AB|developmental stage:26 hpf|geo loc name:missing|collection date:missing,KC001  scRNAseq,The read alignment and gene counting were made using the Cell Ranger software v6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 version 105 Supplementary files format and content: Tab separated values files and matrix files,Pharyngeal arches,,From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108  two wild type and two nkx2.7 /  embryos were identified by genotyping.  The pharyngeal arches and surrounding tissue were dissected  dissociated  and submitted for flow cytometry.  Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution.  Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C.  The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer.  Finally  DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI.  NERL Diluent 2 Thermo Fisher  DIL5522 solution was used for sheath fluid.  The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences  655051  SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m  5 mL Spherotech  RCP 30 5A  followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences  345249. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,genotype:wild type|tissue:Pharyngeal arches|strain:AB|developmental stage:26 hpf,GSM7709161,GSM7709161: KC001  scRNAseq; Danio rerio; RNA Seq,GSM7709161 r1,GSM7709161,1,From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108  two wild type and two nkx2.7 /  embryos were identified by genotyping.  The pharyngeal arches and surrounding tissue were dissected  dissociated  and submitted for flow cytometry.  Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution.  Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C.  The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer.  Finally  DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI.  NERL Diluent 2 Thermo Fisher  DIL5522 solution was used for sheath fluid.  The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences  655051  SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m  5 mL Spherotech  RCP 30 5A  followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences  345249. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454944,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=KC001 S1 L004 I1 001.fastq.gz   read2PairFiles=KC001 S1 L004 I2 001.fastq.gz   read3PairFiles=KC001 S1 L004 R1 001.fastq.gz   read4PairFiles=KC001 S1 L004 R2 001.fastq.gz,KC001_S1_L004_I1_001.fastq.gz KC001_S1_L004_I2_001.fastq.gz KC001_S1_L004_R1_001.fastq.gz KC001_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,69380677872.0,312525576.0,GSM7709161 r1,0:10 1:10 2:101 3:101,A:16018222868;C:11704492905;G:12161620273;T:23245625739;N:204567,10,10,101,101,16018222868,11704492905,12161620273,23245625739,204567,SRX21361064,SRS18605556,SRA1692494,"SangesLab Computational Genomics, NEUROSCIENCE, SISSA","SangesLab Computational Genomics, NEUROSCIENCE, SISSA",2,0.00071,0.93976,0.0001,0.12725,0.99945,0.78457,0.75,0.50121,101,101,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Italy,2023-08-14,Pharyngula,Embryo,Pharyngeal Arch,Multi-system
25237,SRR25721801,SRX21445937,SRS18680715,SRP456253,PRJNA1007646,Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival [larva],GSE241296,Other,Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish  this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation  making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however  the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach  we demonstrate that larval RBs in zebrafish fall into three  largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities  including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover  this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib  which is used in clinic and causes peripheral neuropathy. Importantly  dovitinib mediated axon loss can be suppressed by loss of Sarm1  a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 µm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 µl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 µl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 µm opening. The solution was filtered through a 35 µm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing,,,,zebrafish larva  neurons and glia  scRNAseq,GSM7720759,,source name:zebrafish larva|cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf loc name:missing|collection date:missing,zebrafish larva  neurons and glia  scRNAseq,using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files,zebrafish larva,,About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 μm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol  10x Genomics.,,cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf,GSM7720759,GSM7720759: zebrafish larva  neurons and glia  scRNAseq; Danio rerio; RNA Seq,GSM7720759 r1,GSM7720759,1,About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 μm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456253,,loader:fastq load.py,CEL210928PB_HW1008_SAIG_D7_S1_L002_I1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L002_I2_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L002_R1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,55936355640.0,254256162.0,GSM7720759 r1,0:10 1:10 2:100 3:100,A:13207297968;C:10496996981;G:10989402500;T:16156355819;N:1179132,10,10,100,100,13207297968,10496996981,10989402500,16156355819,1179132,SRX21445937,SRS18680715,SRA1696793,Oregon Health and Science Univ,Oregon Health and Science Univ,2,0.0,0.81961,0.0,0.19165,1.0,0.8508,,0.59575,100,100,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-21,Larval,Larval,Multi-tissue,Multi-system
25238,SRR25721802,SRX21445937,SRS18680715,SRP456253,PRJNA1007646,Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival [larva],GSE241296,Other,Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish  this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation  making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however  the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach  we demonstrate that larval RBs in zebrafish fall into three  largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities  including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover  this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib  which is used in clinic and causes peripheral neuropathy. Importantly  dovitinib mediated axon loss can be suppressed by loss of Sarm1  a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 µm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 µl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 µl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 µm opening. The solution was filtered through a 35 µm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing,,,,zebrafish larva  neurons and glia  scRNAseq,GSM7720759,,source name:zebrafish larva|cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf loc name:missing|collection date:missing,zebrafish larva  neurons and glia  scRNAseq,using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files,zebrafish larva,,About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 μm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol  10x Genomics.,,cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf,GSM7720759,GSM7720759: zebrafish larva  neurons and glia  scRNAseq; Danio rerio; RNA Seq,GSM7720759 r1,GSM7720759,1,About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 μm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456253,,loader:fastq load.py,CEL210928PB_HW1008_SAIG_D7_S1_L001_I1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_I2_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_R1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,54474841080.0,247612914.0,GSM7720759 r2,0:10 1:10 2:100 3:100,A:12887048507;C:10210716068;G:10683375130;T:15740176261;N:1266834,10,10,100,100,12887048507,10210716068,10683375130,15740176261,1266834,SRX21445937,SRS18680715,SRA1696793,Oregon Health and Science Univ,Oregon Health and Science Univ,2,0.0,0.82189,0.0,0.19349,1.0,0.85025,,0.6092,100,100,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-21,Larval,Larval,Multi-tissue,Multi-system
28707,SRR26588119,SRX22289209,SRS19340293,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 5.8 mm,GSM7871949,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871949,GSM7871949: WT 5.8 mm; Danio rerio; RNA Seq,GSM7871949 r1,GSM7871949,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0628_S3_L001_R2_001.fastq.gz FS_WT0628_S3_L001_R1_001.fastq.gz FS_WT0628_S3_L001_I1_001.fastq.gz,fastq fastq fastq,3515731348.0,27682924.0,GSM7871949 r1,0:8 1:28 2:91,A:723968955;C:551528974;G:650193733;T:593113624;N:340798,8,28,91,,723968955,551528974,650193733,593113624,340798,SRX22289209,SRS19340293,SRA1742079,Boston University,Boston University,1,0.8674,,0.17534,,0.84098,,0.62971,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28708,SRR26588120,SRX22289209,SRS19340293,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 5.8 mm,GSM7871949,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871949,GSM7871949: WT 5.8 mm; Danio rerio; RNA Seq,GSM7871949 r1,GSM7871949,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0628_S3_L002_R2_001.fastq.gz FS_WT0628_S3_L002_R1_001.fastq.gz FS_WT0628_S3_L002_I1_001.fastq.gz,fastq fastq fastq,3453128095.0,27189985.0,GSM7871949 r2,0:8 1:28 2:91,A:711376907;C:541911169;G:638181451;T:582510928;N:308180,8,28,91,,711376907,541911169,638181451,582510928,308180,SRX22289209,SRS19340293,SRA1742079,Boston University,Boston University,1,0.86684,,0.17663,,0.84108,,0.64294,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28709,SRR26588121,SRX22289209,SRS19340293,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 5.8 mm,GSM7871949,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871949,GSM7871949: WT 5.8 mm; Danio rerio; RNA Seq,GSM7871949 r1,GSM7871949,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0628_S3_L003_R2_001.fastq.gz FS_WT0628_S3_L003_R1_001.fastq.gz FS_WT0628_S3_L003_I1_001.fastq.gz,fastq fastq fastq,3525654366.0,27761058.0,GSM7871949 r3,0:8 1:28 2:91,A:725811733;C:554304351;G:651619754;T:593988032;N:532408,8,28,91,,725811733,554304351,651619754,593988032,532408,SRX22289209,SRS19340293,SRA1742079,Boston University,Boston University,1,0.86621,,0.17459,,0.83936,,0.63657,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28710,SRR26588122,SRX22289209,SRS19340293,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 5.8 mm,GSM7871949,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871949,GSM7871949: WT 5.8 mm; Danio rerio; RNA Seq,GSM7871949 r1,GSM7871949,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0628_S3_L004_R2_001.fastq.gz FS_WT0628_S3_L004_R1_001.fastq.gz FS_WT0628_S3_L004_I1_001.fastq.gz,fastq fastq fastq,3476431706.0,27373478.0,GSM7871949 r4,0:8 1:28 2:91,A:715940083;C:546111535;G:642639757;T:585816460;N:478663,8,28,91,,715940083,546111535,642639757,585816460,478663,SRX22289209,SRS19340293,SRA1742079,Boston University,Boston University,1,0.86857,,0.17561,,0.84094,,0.63847,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28711,SRR26588123,SRX22289208,SRS19340290,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 7.0 mm,GSM7871948,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871948,GSM7871948: WT 7.0 mm; Danio rerio; RNA Seq,GSM7871948 r1,GSM7871948,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0621_S1_L001_R2_001.fastq.gz FS_WT0621_S1_L001_R1_001.fastq.gz FS_WT0621_S1_L001_I1_001.fastq.gz,fastq fastq fastq,4296091865.0,33827495.0,GSM7871948 r1,0:8 1:28 2:91,A:873692918;C:671758488;G:778592608;T:753844494;N:413537,8,28,91,,873692918,671758488,778592608,753844494,413537,SRX22289208,SRS19340290,SRA1742079,Boston University,Boston University,1,0.88226,,0.23142,,0.80811,,0.58869,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28712,SRR26588124,SRX22289208,SRS19340290,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 7.0 mm,GSM7871948,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871948,GSM7871948: WT 7.0 mm; Danio rerio; RNA Seq,GSM7871948 r1,GSM7871948,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0621_S1_L002_R2_001.fastq.gz FS_WT0621_S1_L002_R1_001.fastq.gz FS_WT0621_S1_L002_I1_001.fastq.gz,fastq fastq fastq,4219879546.0,33227398.0,GSM7871948 r2,0:8 1:28 2:91,A:858665689;C:660231321;G:764062561;T:740359496;N:374151,8,28,91,,858665689,660231321,764062561,740359496,374151,SRX22289208,SRS19340290,SRA1742079,Boston University,Boston University,1,0.8833,,0.23028,,0.80734,,0.5998,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28713,SRR26588125,SRX22289208,SRS19340290,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 7.0 mm,GSM7871948,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871948,GSM7871948: WT 7.0 mm; Danio rerio; RNA Seq,GSM7871948 r1,GSM7871948,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0621_S1_L003_R2_001.fastq.gz FS_WT0621_S1_L003_R1_001.fastq.gz FS_WT0621_S1_L003_I1_001.fastq.gz,fastq fastq fastq,4341378795.0,34184085.0,GSM7871948 r3,0:8 1:28 2:91,A:882850653;C:681021491;G:786172206;T:760063970;N:643415,8,28,91,,882850653,681021491,786172206,760063970,643415,SRX22289208,SRS19340290,SRA1742079,Boston University,Boston University,1,0.88158,,0.23138,,0.80921,,0.5997,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28714,SRR26588126,SRX22289208,SRS19340290,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 7.0 mm,GSM7871948,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871948,GSM7871948: WT 7.0 mm; Danio rerio; RNA Seq,GSM7871948 r1,GSM7871948,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0621_S1_L004_R2_001.fastq.gz FS_WT0621_S1_L004_R1_001.fastq.gz FS_WT0621_S1_L004_I1_001.fastq.gz,fastq fastq fastq,4270514446.0,33626098.0,GSM7871948 r4,0:8 1:28 2:91,A:868634109;C:669284353;G:773305808;T:748175261;N:575387,8,28,91,,868634109,669284353,773305808,748175261,575387,SRX22289208,SRS19340290,SRA1742079,Boston University,Boston University,1,0.8822,,0.23032,,0.80695,,0.58745,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28715,SRR26588127,SRX22289207,SRS19340289,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 5.8 mm,GSM7871947,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871947,GSM7871947: sp7 mutant 5.8 mm; Danio rerio; RNA Seq,GSM7871947 r1,GSM7871947,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0628_S4_L001_R2_001.fastq.gz FS_Mutant0628_S4_L001_R1_001.fastq.gz FS_Mutant0628_S4_L001_I1_001.fastq.gz,fastq fastq fastq,3870633229.0,30477427.0,GSM7871947 r1,0:8 1:28 2:91,A:784323459;C:609892390;G:730737771;T:648119651;N:372586,8,28,91,,784323459,609892390,730737771,648119651,372586,SRX22289207,SRS19340289,SRA1742079,Boston University,Boston University,1,0.83967,,0.19678,,0.84027,,0.62798,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28716,SRR26588128,SRX22289207,SRS19340289,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 5.8 mm,GSM7871947,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871947,GSM7871947: sp7 mutant 5.8 mm; Danio rerio; RNA Seq,GSM7871947 r1,GSM7871947,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0628_S4_L002_R2_001.fastq.gz FS_Mutant0628_S4_L002_R1_001.fastq.gz FS_Mutant0628_S4_L002_I1_001.fastq.gz,fastq fastq fastq,3795705896.0,29887448.0,GSM7871947 r2,0:8 1:28 2:91,A:769584134;C:598310890;G:715720368;T:635803045;N:339331,8,28,91,,769584134,598310890,715720368,635803045,339331,SRX22289207,SRS19340289,SRA1742079,Boston University,Boston University,1,0.83992,,0.199,,0.84094,,0.63528,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28717,SRR26588129,SRX22289207,SRS19340289,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 5.8 mm,GSM7871947,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871947,GSM7871947: sp7 mutant 5.8 mm; Danio rerio; RNA Seq,GSM7871947 r1,GSM7871947,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0628_S4_L003_I1_001.fastq.gz FS_Mutant0628_S4_L003_R1_001.fastq.gz FS_Mutant0628_S4_L003_R2_001.fastq.gz,fastq fastq fastq,3882075802.0,30567526.0,GSM7871947 r3,0:8 1:28 2:91,A:786373431;C:613286785;G:731993747;T:649408434;N:582469,8,28,91,,786373431,613286785,731993747,649408434,582469,SRX22289207,SRS19340289,SRA1742079,Boston University,Boston University,1,0.83867,,0.19884,,0.83826,,0.63213,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28718,SRR26588130,SRX22289207,SRS19340289,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 5.8 mm,GSM7871947,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871947,GSM7871947: sp7 mutant 5.8 mm; Danio rerio; RNA Seq,GSM7871947 r1,GSM7871947,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0628_S4_L004_R2_001.fastq.gz FS_Mutant0628_S4_L004_R1_001.fastq.gz FS_Mutant0628_S4_L004_I1_001.fastq.gz,fastq fastq fastq,3821331575.0,30089225.0,GSM7871947 r4,0:8 1:28 2:91,A:774445827;C:603171063;G:720511073;T:639476444;N:515068,8,28,91,,774445827,603171063,720511073,639476444,515068,SRX22289207,SRS19340289,SRA1742079,Boston University,Boston University,1,0.84008,,0.19754,,0.84076,,0.63418,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28719,SRR26588131,SRX22289206,SRS19340291,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 7.0 mm,GSM7871946,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant  7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871946,GSM7871946: sp7 mutant  7.0 mm; Danio rerio; RNA Seq,GSM7871946 r1,GSM7871946,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0621_S2_L001_I1_001.fastq.gz FS_Mutant0621_S2_L001_R1_001.fastq.gz FS_Mutant0621_S2_L001_R2_001.fastq.gz,fastq fastq fastq,4256651761.0,33516943.0,GSM7871946 r1,0:8 1:28 2:91,A:862245132;C:673711733;G:766388204;T:747287820;N:408924,8,28,91,,862245132,673711733,766388204,747287820,408924,SRX22289206,SRS19340291,SRA1742079,Boston University,Boston University,1,0.89937,,0.20157,,0.80691,,0.60147,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28720,SRR26588132,SRX22289206,SRS19340291,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 7.0 mm,GSM7871946,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant  7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871946,GSM7871946: sp7 mutant  7.0 mm; Danio rerio; RNA Seq,GSM7871946 r1,GSM7871946,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0621_S2_L002_I1_001.fastq.gz FS_Mutant0621_S2_L002_R1_001.fastq.gz FS_Mutant0621_S2_L002_R2_001.fastq.gz,fastq fastq fastq,4173795437.0,32864531.0,GSM7871946 r2,0:8 1:28 2:91,A:846056609;C:660910650;G:750849639;T:732486246;N:369177,8,28,91,,846056609,660910650,750849639,732486246,369177,SRX22289206,SRS19340291,SRA1742079,Boston University,Boston University,1,0.89896,,0.20107,,0.80415,,0.60881,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28721,SRR26588133,SRX22289206,SRS19340291,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 7.0 mm,GSM7871946,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant  7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871946,GSM7871946: sp7 mutant  7.0 mm; Danio rerio; RNA Seq,GSM7871946 r1,GSM7871946,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0621_S2_L003_I1_001.fastq.gz FS_Mutant0621_S2_L003_R1_001.fastq.gz FS_Mutant0621_S2_L003_R2_001.fastq.gz,fastq fastq fastq,4291089081.0,33788103.0,GSM7871946 r3,0:8 1:28 2:91,A:869084749;C:681276277;G:772278057;T:751443489;N:634801,8,28,91,,869084749,681276277,772278057,751443489,634801,SRX22289206,SRS19340291,SRA1742079,Boston University,Boston University,1,0.89995,,0.20079,,0.80505,,0.60752,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28722,SRR26588134,SRX22289206,SRS19340291,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 7.0 mm,GSM7871946,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant  7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871946,GSM7871946: sp7 mutant  7.0 mm; Danio rerio; RNA Seq,GSM7871946 r1,GSM7871946,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0621_S2_L004_I1_001.fastq.gz FS_Mutant0621_S2_L004_R1_001.fastq.gz FS_Mutant0621_S2_L004_R2_001.fastq.gz,fastq fastq fastq,4221057598.0,33236674.0,GSM7871946 r4,0:8 1:28 2:91,A:855377679;C:669535108;G:759458317;T:739600774;N:565456,8,28,91,,855377679,669535108,759458317,739600774,565456,SRX22289206,SRS19340291,SRA1742079,Boston University,Boston University,1,0.90012,,0.20095,,0.80562,,0.60729,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
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,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,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,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,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,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,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,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,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,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
29812,SRR27466771,SRX23138319,SRS20089385,SRP482605,PRJNA1062705,Comparative transcriptomics coupled to developmental grading via transgenic Zebrafish reporter strains identifies conserved features in neutrophil maturation,GSE252788,Transcriptome Analysis,Neutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defence. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized  which limits their applicability to studying human disease. Here we show  by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages  a high resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors  including C/ebp ß  which is important for late neutrophil maturation. Cross species comparison of zebrafish  mouse  and human samples confirms high molecular similarity of immature stages and discriminates zebrafish specific from pan species gene signatures. Applying the pan species neutrophil maturation signature to RNA sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease. Overall design: Kidney marrow from 2 adult  six mpf  male zebrafish was isolated  labelled using lipid tagged following MULTI seq protocol  for scRNA seq using 10x Genomics.,,pubmed:38413586,,MF317 A2 GEX zebrafish multiseq,GSM8007850,,source name:Kidney marrow|tissue:Kidney marrow|cell type:Whole kidney marrow PBMCs|geo loc name:missing|collection date:missing,MF317 A2 GEX zebrafish multiseq,We used the CellRanger v3.1.0 software 10x Genomics for cell demultiplexing and alignment and loaded the counts into Seurat v4.0.2. Assembly: GRCz11 3.1.0 zebrafish reference transcriptome that had been expanded to include the sequences of reporter genes Citrine and CFPNTR  sequences from snapgene.com. Supplementary files format and content: compressed matrix files of CellRanger outputs Supplementary files format and content: rds file containting Seurat object Supplementary files format and content: hd5a file containting Seurat object,Kidney marrow,,Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 μM for 5’ on ice and then incubated with lipid co anchor 2 μM for 5’ on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell 3’ Library & Gel Bead Kit v3.1 10x Genomics  Pleasanton  CA  according to the manufacturer’s protocols 10x Genomics and sequenced by protocol.,,tissue:Kidney marrow|cell type:Whole kidney marrow PBMCs,GSM8007850,GSM8007850: MF317 A2 GEX zebrafish multiseq; Danio rerio; RNA Seq,GSM8007850 r1,GSM8007850,1,Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 μM for five prime on ice and then incubated with lipid co anchor 2 μM for five prime on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell three prime Library & Gel Bead Kit v3.1 10x Genomics  Pleasanton  CA  according to the manufacturer's protocols 10x Genomics and sequenced by protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP482605,,loader:fastq load.py,MF317_A2_GEX_zebrafish_multiseq_S3_L004_I1_001.fastq.gz MF317_A2_GEX_zebrafish_multiseq_S3_L004_R1_001.fastq.gz MF317_A2_GEX_zebrafish_multiseq_S3_L004_R2_001.fastq.gz,fastq fastq fastq,20397464955.0,151092333.0,GSM8007850 r1,0:8 1:29 2:98,A:4317555978;C:3264550330;G:3319063129;T:3903632022;N:2247175,8,29,98,,4317555978,3264550330,3319063129,3903632022,2247175,SRX23138319,SRS20089385,,,"Developmental Cancer Genomics, St. Anna Children's Cancer Research Institute (CCRI)",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Austria,2024-01-09,Undetermined,Adult,Multi-tissue,Multi-system
29813,SRR27466772,SRX23138319,SRS20089385,SRP482605,PRJNA1062705,Comparative transcriptomics coupled to developmental grading via transgenic Zebrafish reporter strains identifies conserved features in neutrophil maturation,GSE252788,Transcriptome Analysis,Neutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defence. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized  which limits their applicability to studying human disease. Here we show  by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages  a high resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors  including C/ebp ß  which is important for late neutrophil maturation. Cross species comparison of zebrafish  mouse  and human samples confirms high molecular similarity of immature stages and discriminates zebrafish specific from pan species gene signatures. Applying the pan species neutrophil maturation signature to RNA sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease. Overall design: Kidney marrow from 2 adult  six mpf  male zebrafish was isolated  labelled using lipid tagged following MULTI seq protocol  for scRNA seq using 10x Genomics.,,pubmed:38413586,,MF317 A2 GEX zebrafish multiseq,GSM8007850,,source name:Kidney marrow|tissue:Kidney marrow|cell type:Whole kidney marrow PBMCs|geo loc name:missing|collection date:missing,MF317 A2 GEX zebrafish multiseq,We used the CellRanger v3.1.0 software 10x Genomics for cell demultiplexing and alignment and loaded the counts into Seurat v4.0.2. Assembly: GRCz11 3.1.0 zebrafish reference transcriptome that had been expanded to include the sequences of reporter genes Citrine and CFPNTR  sequences from snapgene.com. Supplementary files format and content: compressed matrix files of CellRanger outputs Supplementary files format and content: rds file containting Seurat object Supplementary files format and content: hd5a file containting Seurat object,Kidney marrow,,Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 μM for 5’ on ice and then incubated with lipid co anchor 2 μM for 5’ on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell 3’ Library & Gel Bead Kit v3.1 10x Genomics  Pleasanton  CA  according to the manufacturer’s protocols 10x Genomics and sequenced by protocol.,,tissue:Kidney marrow|cell type:Whole kidney marrow PBMCs,GSM8007850,GSM8007850: MF317 A2 GEX zebrafish multiseq; Danio rerio; RNA Seq,GSM8007850 r1,GSM8007850,1,Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 μM for five prime on ice and then incubated with lipid co anchor 2 μM for five prime on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell three prime Library & Gel Bead Kit v3.1 10x Genomics  Pleasanton  CA  according to the manufacturer's protocols 10x Genomics and sequenced by protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP482605,,loader:fastq load.py,MF317_A2_barcode_zebrafish_multiseq_S68024_S10_L004_I1_001.fastq.gz MF317_A2_barcode_zebrafish_multiseq_S68024_S10_L004_R1_001.fastq.gz MF317_A2_barcode_zebrafish_multiseq_S68024_S10_L004_R2_001.fastq.gz,fastq fastq fastq,609557670.0,4515242.0,GSM8007850 r2,0:8 1:29 2:98,A:288037892;C:47138905;G:85961330;T:21289087;N:66502,8,29,98,,288037892,47138905,85961330,21289087,66502,SRX23138319,SRS20089385,,,"Developmental Cancer Genomics, St. Anna Children's Cancer Research Institute (CCRI)",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Austria,2024-01-09,Undetermined,Adult,Multi-tissue,Multi-system
29814,SRR27466773,SRX23138318,SRS20089387,SRP482605,PRJNA1062705,Comparative transcriptomics coupled to developmental grading via transgenic Zebrafish reporter strains identifies conserved features in neutrophil maturation,GSE252788,Transcriptome Analysis,Neutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defence. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized  which limits their applicability to studying human disease. Here we show  by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages  a high resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors  including C/ebp ß  which is important for late neutrophil maturation. Cross species comparison of zebrafish  mouse  and human samples confirms high molecular similarity of immature stages and discriminates zebrafish specific from pan species gene signatures. Applying the pan species neutrophil maturation signature to RNA sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease. Overall design: Kidney marrow from 2 adult  six mpf  male zebrafish was isolated  labelled using lipid tagged following MULTI seq protocol  for scRNA seq using 10x Genomics.,,pubmed:38413586,,MF317 A1 GEX zebrafish multiseq,GSM8007849,,source name:Kidney marrow|tissue:Kidney marrow|cell type:Neutrophils|geo loc name:missing|collection date:missing,MF317 A1 GEX zebrafish multiseq,We used the CellRanger v3.1.0 software 10x Genomics for cell demultiplexing and alignment and loaded the counts into Seurat v4.0.2. Assembly: GRCz11 3.1.0 zebrafish reference transcriptome that had been expanded to include the sequences of reporter genes Citrine and CFPNTR  sequences from snapgene.com. Supplementary files format and content: compressed matrix files of CellRanger outputs Supplementary files format and content: rds file containting Seurat object Supplementary files format and content: hd5a file containting Seurat object,Kidney marrow,,Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 μM for 5’ on ice and then incubated with lipid co anchor 2 μM for 5’ on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell 3’ Library & Gel Bead Kit v3.1 10x Genomics  Pleasanton  CA  according to the manufacturer’s protocols 10x Genomics and sequenced by protocol.,,tissue:Kidney marrow|cell type:Neutrophils,GSM8007849,GSM8007849: MF317 A1 GEX zebrafish multiseq; Danio rerio; RNA Seq,GSM8007849 r1,GSM8007849,1,Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 μM for five prime on ice and then incubated with lipid co anchor 2 μM for five prime on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell three prime Library & Gel Bead Kit v3.1 10x Genomics  Pleasanton  CA  according to the manufacturer's protocols 10x Genomics and sequenced by protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP482605,,loader:fastq load.py,MF317_A1_GEX_zebrafish_multiseq_S1_L004_I1_001.fastq.gz MF317_A1_GEX_zebrafish_multiseq_S1_L004_R1_001.fastq.gz MF317_A1_GEX_zebrafish_multiseq_S1_L004_R2_001.fastq.gz,fastq fastq fastq,20471343840.0,151639584.0,GSM8007849 r1,0:8 1:29 2:98,A:4574898668;C:2902052527;G:3115258212;T:4266202403;N:2267422,8,29,98,,4574898668,2902052527,3115258212,4266202403,2267422,SRX23138318,SRS20089387,,,"Developmental Cancer Genomics, St. Anna Children's Cancer Research Institute (CCRI)",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Austria,2024-01-09,Undetermined,Adult,Multi-tissue,Multi-system
29815,SRR27466774,SRX23138318,SRS20089387,SRP482605,PRJNA1062705,Comparative transcriptomics coupled to developmental grading via transgenic Zebrafish reporter strains identifies conserved features in neutrophil maturation,GSE252788,Transcriptome Analysis,Neutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defence. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized  which limits their applicability to studying human disease. Here we show  by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages  a high resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors  including C/ebp ß  which is important for late neutrophil maturation. Cross species comparison of zebrafish  mouse  and human samples confirms high molecular similarity of immature stages and discriminates zebrafish specific from pan species gene signatures. Applying the pan species neutrophil maturation signature to RNA sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease. Overall design: Kidney marrow from 2 adult  six mpf  male zebrafish was isolated  labelled using lipid tagged following MULTI seq protocol  for scRNA seq using 10x Genomics.,,pubmed:38413586,,MF317 A1 GEX zebrafish multiseq,GSM8007849,,source name:Kidney marrow|tissue:Kidney marrow|cell type:Neutrophils|geo loc name:missing|collection date:missing,MF317 A1 GEX zebrafish multiseq,We used the CellRanger v3.1.0 software 10x Genomics for cell demultiplexing and alignment and loaded the counts into Seurat v4.0.2. Assembly: GRCz11 3.1.0 zebrafish reference transcriptome that had been expanded to include the sequences of reporter genes Citrine and CFPNTR  sequences from snapgene.com. Supplementary files format and content: compressed matrix files of CellRanger outputs Supplementary files format and content: rds file containting Seurat object Supplementary files format and content: hd5a file containting Seurat object,Kidney marrow,,Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 μM for 5’ on ice and then incubated with lipid co anchor 2 μM for 5’ on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell 3’ Library & Gel Bead Kit v3.1 10x Genomics  Pleasanton  CA  according to the manufacturer’s protocols 10x Genomics and sequenced by protocol.,,tissue:Kidney marrow|cell type:Neutrophils,GSM8007849,GSM8007849: MF317 A1 GEX zebrafish multiseq; Danio rerio; RNA Seq,GSM8007849 r1,GSM8007849,1,Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 μM for five prime on ice and then incubated with lipid co anchor 2 μM for five prime on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell three prime Library & Gel Bead Kit v3.1 10x Genomics  Pleasanton  CA  according to the manufacturer's protocols 10x Genomics and sequenced by protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP482605,,loader:fastq load.py,MF317_A1_barcode_zebrafish_multiseq_S68025_S5_L004_I1_001.fastq.gz MF317_A1_barcode_zebrafish_multiseq_S68025_S5_L004_R1_001.fastq.gz MF317_A1_barcode_zebrafish_multiseq_S68025_S5_L004_R2_001.fastq.gz,fastq fastq fastq,205092135.0,1519201.0,GSM8007849 r2,0:8 1:29 2:98,A:96315447;C:12651302;G:31425404;T:8467378;N:22167,8,29,98,,96315447,12651302,31425404,8467378,22167,SRX23138318,SRS20089387,,,"Developmental Cancer Genomics, St. Anna Children's Cancer Research Institute (CCRI)",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Austria,2024-01-09,Undetermined,Adult,Multi-tissue,Multi-system
33900,SRR30879294,SRX26276609,SRS22814231,SRP536515,PRJNA1168532,scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf,GSE278733,Transcriptome Analysis,The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions  they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however  the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal  and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf  and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.,,,,dsRED+ TKO 4 dpf,GSM8553899,,tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO|geo loc name:missing|collection date:missing,dsRED+ TKO 4 dpf,Following sequencing  an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ  aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples  while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files,4 dpf,,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO,GSM8553899,GSM8553899: dsRED+ TKO 4 dpf; Danio rerio; RNA Seq,GSM8553899 r1,GSM8553899,1,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP536515,,loader:fastq load.py,TKO_dsRED_S2_L001_I1_001.fastq.gz TKO_dsRED_S2_L001_I2_001.fastq.gz TKO_dsRED_S2_L001_R1_001.fastq.gz TKO_dsRED_S2_L001_R2_001.fastq.gz,fastq fastq fastq fastq,3764848932.0,27281514.0,GSM8553899 r1,0:10 1:10 2:28 3:90,A:692470222;C:567540605;G:576111845;T:618305574;N:908014,10,10,28,90,692470222,567540605,576111845,618305574,908014,SRX26276609,SRS22814231,SRA1985700,nih,nih,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-03,Larval,Larval,Multi-tissue,Multi-system
33901,SRR30879295,SRX26276609,SRS22814231,SRP536515,PRJNA1168532,scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf,GSE278733,Transcriptome Analysis,The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions  they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however  the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal  and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf  and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.,,,,dsRED+ TKO 4 dpf,GSM8553899,,tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO|geo loc name:missing|collection date:missing,dsRED+ TKO 4 dpf,Following sequencing  an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ  aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples  while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files,4 dpf,,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO,GSM8553899,GSM8553899: dsRED+ TKO 4 dpf; Danio rerio; RNA Seq,GSM8553899 r1,GSM8553899,1,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP536515,,loader:fastq load.py,TKO_dsRED_S2_L002_I1_001.fastq.gz TKO_dsRED_S2_L002_I2_001.fastq.gz TKO_dsRED_S2_L002_R1_001.fastq.gz TKO_dsRED_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,3726674544.0,27004888.0,GSM8553899 r2,0:10 1:10 2:28 3:90,A:685914766;C:561837246;G:569990126;T:611748773;N:949009,10,10,28,90,685914766,561837246,569990126,611748773,949009,SRX26276609,SRS22814231,SRA1985700,nih,nih,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-03,Larval,Larval,Multi-tissue,Multi-system