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613 rows where devstage_curation_coarse = "Larval" and tissue_curation = "Tail"

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technology 7

experiment.platform 2

experiment.library_strategy 2

experiment.library_source 2

experiment.library_selection 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Tail · 613 ✖

devstage_curation_coarse 1

  • Larval · 613 ✖

devstage_curation 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
24790 24790 SRR25509944 SRX21240524 SRS18495447 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_plus_S17_L001_R2_001.fastq.gz 5DPF_WT_plus_S17_L001_R1_001.fastq.gz 5DPF_WT_plus_S17_L001_I1_001.fastq.gz fastq fastq fastq 5999080077.0 47236851.0 GSM7680083 r1 0:8 1:28 2:91 A:1212144705;C:959823109;G:1045323833;T:1081182723;N:79071 8 28 91   1212144705 959823109 1045323833 1081182723 79071 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91673   0.11695   0.77481   0.51165   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24791 24791 SRR25509945 SRX21240524 SRS18495447 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_plus_S17_L002_R2_001.fastq.gz 5DPF_WT_plus_S17_L002_R1_001.fastq.gz 5DPF_WT_plus_S17_L002_I1_001.fastq.gz fastq fastq fastq 6012350180.0 47341340.0 GSM7680083 r2 0:8 1:28 2:91 A:1215185110;C:961739027;G:1047332997;T:1083733742;N:71064 8 28 91   1215185110 961739027 1047332997 1083733742 71064 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91842   0.11714   0.7763   0.51731   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24792 24792 SRR25509946 SRX21240524 SRS18495447 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_plus_S18_L001_R2_001.fastq.gz 5DPF_WT_plus_S18_L001_R1_001.fastq.gz 5DPF_WT_plus_S18_L001_I1_001.fastq.gz fastq fastq fastq 4990947473.0 39298799.0 GSM7680083 r3 0:8 1:28 2:91 A:1007619958;C:800073636;G:871756682;T:896670984;N:69449 8 28 91   1007619958 800073636 871756682 896670984 69449 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91717   0.11737   0.7767   0.51879   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24793 24793 SRR25509947 SRX21240524 SRS18495447 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_plus_S18_L002_I1_001.fastq.gz 5DPF_WT_plus_S18_L002_R1_001.fastq.gz 5DPF_WT_plus_S18_L002_R2_001.fastq.gz fastq fastq fastq 4994343707.0 39325541.0 GSM7680083 r4 0:8 1:28 2:91 A:1008545361;C:800479170;G:872044753;T:897494026;N:60921 8 28 91   1008545361 800479170 872044753 897494026 60921 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.9173   0.11671   0.778   0.51414   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24794 24794 SRR25509948 SRX21240524 SRS18495447 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_plus_S20_L001_R2_001.fastq.gz 5DPF_WT_plus_S20_L001_R1_001.fastq.gz 5DPF_WT_plus_S20_L001_I1_001.fastq.gz fastq fastq fastq 4150807675.0 32683525.0 GSM7680083 r7 0:8 1:28 2:91 A:839301254;C:665476121;G:723277159;T:746089009;N:57232 8 28 91   839301254 665476121 723277159 746089009 57232 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91704   0.11665   0.77589   0.51231   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24795 24795 SRR25509949 SRX21240524 SRS18495447 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_plus_S20_L002_R2_001.fastq.gz 5DPF_WT_plus_S20_L002_R1_001.fastq.gz 5DPF_WT_plus_S20_L002_I1_001.fastq.gz fastq fastq fastq 4152701499.0 32698437.0 GSM7680083 r8 0:8 1:28 2:91 A:839837413;C:665793367;G:723399518;T:746476220;N:51249 8 28 91   839837413 665793367 723399518 746476220 51249 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91769   0.11677   0.77473   0.5172   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24796 24796 SRR25510006 SRX21240524 SRS18495447 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_plus_S19_L001_I1_001.fastq.gz 5DPF_WT_plus_S19_L001_R1_001.fastq.gz 5DPF_WT_plus_S19_L001_R2_001.fastq.gz fastq fastq fastq 5570139228.0 43859364.0 GSM7680083 r5 0:8 1:28 2:91 A:1124433319;C:892106407;G:974065175;T:1000519772;N:77451 8 28 91   1124433319 892106407 974065175 1000519772 77451 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.9181   0.11708   0.77725   0.506   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24797 24797 SRR25510007 SRX21240524 SRS18495447 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq GSM7680083   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680083 GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680083 r1 GSM7680083 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_plus_S19_L002_R2_001.fastq.gz 5DPF_WT_plus_S19_L002_R1_001.fastq.gz 5DPF_WT_plus_S19_L002_I1_001.fastq.gz fastq fastq fastq 5568879134.0 43849442.0 GSM7680083 r6 0:8 1:28 2:91 A:1124462080;C:891765530;G:973382320;T:1000621312;N:67980 8 28 91   1124462080 891765530 973382320 1000621312 67980 SRX21240524 SRS18495447 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91836   0.11752   0.77786   0.49118   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24798 24798 SRR25509950 SRX21240523 SRS18495446 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_minus_S29_L001_I1_001.fastq.gz MECOM_minus_S29_L001_R1_001.fastq.gz MECOM_minus_S29_L001_R2_001.fastq.gz fastq fastq fastq 6472457718.0 50964234.0 GSM7680088 r1 0:8 1:28 2:91 A:1374177983;C:969847712;G:1063043909;T:1230585953;N:89737 8 28 91   1374177983 969847712 1063043909 1230585953 89737 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91899   0.23002   0.75597   0.50918   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24799 24799 SRR25509951 SRX21240523 SRS18495446 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_minus_S29_L002_I1_001.fastq.gz MECOM_minus_S29_L002_R1_001.fastq.gz MECOM_minus_S29_L002_R2_001.fastq.gz fastq fastq fastq 6479801747.0 51022061.0 GSM7680088 r2 0:8 1:28 2:91 A:1375879660;C:970771702;G:1064110805;T:1232166662;N:78722 8 28 91   1375879660 970771702 1064110805 1232166662 78722 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91932   0.23011   0.75666   0.50726   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24800 24800 SRR25509952 SRX21240523 SRS18495446 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_minus_S30_L001_I1_001.fastq.gz MECOM_minus_S30_L001_R1_001.fastq.gz MECOM_minus_S30_L001_R2_001.fastq.gz fastq fastq fastq 6055044278.0 47677514.0 GSM7680088 r3 0:8 1:28 2:91 A:1285162347;C:907248700;G:995411468;T:1150745942;N:85317 8 28 91   1285162347 907248700 995411468 1150745942 85317 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91771   0.2306   0.75799   0.51641   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24801 24801 SRR25509953 SRX21240523 SRS18495446 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_minus_S30_L002_I1_001.fastq.gz MECOM_minus_S30_L002_R1_001.fastq.gz MECOM_minus_S30_L002_R2_001.fastq.gz fastq fastq fastq 6065969453.0 47763539.0 GSM7680088 r4 0:8 1:28 2:91 A:1287814805;C:908939739;G:996849881;T:1152803356;N:74268 8 28 91   1287814805 908939739 996849881 1152803356 74268 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91856   0.23244   0.75844   0.51273   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24802 24802 SRR25509954 SRX21240523 SRS18495446 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_minus_S31_L001_I1_001.fastq.gz MECOM_minus_S31_L001_R1_001.fastq.gz MECOM_minus_S31_L001_R2_001.fastq.gz fastq fastq fastq 5279309101.0 41569363.0 GSM7680088 r5 0:8 1:28 2:91 A:1122213686;C:789300425;G:868235888;T:1002988275;N:73759 8 28 91   1122213686 789300425 868235888 1002988275 73759 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91638   0.23107   0.75795   0.51508   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24803 24803 SRR25509955 SRX21240523 SRS18495446 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_minus_S31_L002_I1_001.fastq.gz MECOM_minus_S31_L002_R1_001.fastq.gz MECOM_minus_S31_L002_R2_001.fastq.gz fastq fastq fastq 5282579605.0 41595115.0 GSM7680088 r6 0:8 1:28 2:91 A:1123052612;C:789776127;G:868371205;T:1003891470;N:64051 8 28 91   1123052612 789776127 868371205 1003891470 64051 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91687   0.23155   0.75653   0.51167   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24804 24804 SRR25509956 SRX21240523 SRS18495446 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_minus_S32_L001_I1_001.fastq.gz MECOM_minus_S32_L001_R1_001.fastq.gz MECOM_minus_S32_L001_R2_001.fastq.gz fastq fastq fastq 5155833986.0 40597118.0 GSM7680088 r7 0:8 1:28 2:91 A:1096166065;C:771837218;G:846468036;T:979794053;N:72366 8 28 91   1096166065 771837218 846468036 979794053 72366 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91864   0.23062   0.75783   0.5144   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24805 24805 SRR25509957 SRX21240523 SRS18495446 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq GSM7680088   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680088 GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680088 r1 GSM7680088 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_minus_S32_L002_I1_001.fastq.gz MECOM_minus_S32_L002_R1_001.fastq.gz MECOM_minus_S32_L002_R2_001.fastq.gz fastq fastq fastq 5158852395.0 40620885.0 GSM7680088 r8 0:8 1:28 2:91 A:1096925078;C:772260867;G:846795917;T:980455576;N:63097 8 28 91   1096925078 772260867 846795917 980455576 63097 SRX21240523 SRS18495446 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91859   0.23143   0.75921   0.51192   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24806 24806 SRR25509958 SRX21240522 SRS18495445 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16-GFP_S1_L001_I1_001.fastq.gz PRDM16-GFP_S1_L001_R1_001.fastq.gz PRDM16-GFP_S1_L001_R2_001.fastq.gz fastq fastq fastq 7339736654.0 57793202.0 GSM7680087 r1 0:8 1:28 2:91 A:1557377528;C:1077119414;G:1156228317;T:1468352980;N:103143 8 28 91   1557377528 1077119414 1156228317 1468352980 103143 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91516   0.25902   0.74255   0.49922   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24807 24807 SRR25509959 SRX21240522 SRS18495445 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16-GFP_S1_L002_I1_001.fastq.gz PRDM16-GFP_S1_L002_R1_001.fastq.gz PRDM16-GFP_S1_L002_R2_001.fastq.gz fastq fastq fastq 7410090336.0 58347168.0 GSM7680087 r2 0:8 1:28 2:91 A:1569421640;C:1090998538;G:1171253819;T:1477822651;N:95640 8 28 91   1569421640 1090998538 1171253819 1477822651 95640 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91462   0.25846   0.74215   0.49672   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24808 24808 SRR25509960 SRX21240522 SRS18495445 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16-GFP_S2_L001_I1_001.fastq.gz PRDM16-GFP_S2_L001_R1_001.fastq.gz PRDM16-GFP_S2_L001_R2_001.fastq.gz fastq fastq fastq 7620847217.0 60006671.0 GSM7680087 r3 0:8 1:28 2:91 A:1615026295;C:1121044318;G:1201364994;T:1523062938;N:108516 8 28 91   1615026295 1121044318 1201364994 1523062938 108516 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91495   0.26021   0.74188   0.49871   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24809 24809 SRR25509961 SRX21240522 SRS18495445 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16-GFP_S2_L002_I1_001.fastq.gz PRDM16-GFP_S2_L002_R1_001.fastq.gz PRDM16-GFP_S2_L002_R2_001.fastq.gz fastq fastq fastq 7658170739.0 60300557.0 GSM7680087 r4 0:8 1:28 2:91 A:1620018228;C:1130072970;G:1211145212;T:1526013817;N:100460 8 28 91   1620018228 1130072970 1211145212 1526013817 100460 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.9153   0.25733   0.74406   0.49822   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24810 24810 SRR25509962 SRX21240522 SRS18495445 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16-GFP_S3_L001_I1_001.fastq.gz PRDM16-GFP_S3_L001_R1_001.fastq.gz PRDM16-GFP_S3_L001_R2_001.fastq.gz fastq fastq fastq 7520150568.0 59213784.0 GSM7680087 r5 0:8 1:28 2:91 A:1592224470;C:1104917106;G:1187483622;T:1503722424;N:106722 8 28 91   1592224470 1104917106 1187483622 1503722424 106722 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91528   0.25852   0.74168   0.50087   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24811 24811 SRR25509963 SRX21240522 SRS18495445 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16-GFP_S3_L002_I1_001.fastq.gz PRDM16-GFP_S3_L002_R1_001.fastq.gz PRDM16-GFP_S3_L002_R2_001.fastq.gz fastq fastq fastq 7547416198.0 59428474.0 GSM7680087 r6 0:8 1:28 2:91 A:1595335949;C:1112405532;G:1195632258;T:1504519719;N:97676 8 28 91   1595335949 1112405532 1195632258 1504519719 97676 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91572   0.25684   0.74227   0.49429   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24812 24812 SRR25509964 SRX21240522 SRS18495445 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16-GFP_S4_L001_I1_001.fastq.gz PRDM16-GFP_S4_L001_R1_001.fastq.gz PRDM16-GFP_S4_L001_R2_001.fastq.gz fastq fastq fastq 6203887389.0 48849507.0 GSM7680087 r7 0:8 1:28 2:91 A:1315023626;C:910416020;G:979167464;T:1240610297;N:87730 8 28 91   1315023626 910416020 979167464 1240610297 87730 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91294   0.25905   0.74426   0.49642   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24813 24813 SRR25509965 SRX21240522 SRS18495445 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq GSM7680087   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680087 GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680087 r1 GSM7680087 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16-GFP_S4_L002_I1_001.fastq.gz PRDM16-GFP_S4_L002_R1_001.fastq.gz PRDM16-GFP_S4_L002_R2_001.fastq.gz fastq fastq fastq 6164249419.0 48537397.0 GSM7680087 r8 0:8 1:28 2:91 A:1303982345;C:907803673;G:976227040;T:1228810005;N:80064 8 28 91   1303982345 907803673 976227040 1228810005 80064 SRX21240522 SRS18495445 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91422   0.25666   0.74383   0.49596   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24814 24814 SRR25509966 SRX21240521 SRS18495444 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_plus_S25_L001_I1_001.fastq.gz MECOM_plus_S25_L001_R1_001.fastq.gz MECOM_plus_S25_L001_R2_001.fastq.gz fastq fastq fastq 2154821446.0 16967098.0 GSM7680086 r1 0:8 1:28 2:91 A:451330902;C:339756831;G:379343350;T:373544930;N:29905 8 28 91   451330902 339756831 379343350 373544930 29905 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91882   0.142   0.78299   0.51956   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24815 24815 SRR25509967 SRX21240521 SRS18495444 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_plus_S25_L002_I1_001.fastq.gz MECOM_plus_S25_L002_R1_001.fastq.gz MECOM_plus_S25_L002_R2_001.fastq.gz fastq fastq fastq 2158219204.0 16993852.0 GSM7680086 r2 0:8 1:28 2:91 A:452280625;C:340228509;G:379707034;T:374197697;N:26667 8 28 91   452280625 340228509 379707034 374197697 26667 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91895   0.1417   0.78279   0.51981   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24816 24816 SRR25509968 SRX21240521 SRS18495444 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_plus_S26_L001_I1_001.fastq.gz MECOM_plus_S26_L001_R1_001.fastq.gz MECOM_plus_S26_L001_R2_001.fastq.gz fastq fastq fastq 2361287251.0 18592813.0 GSM7680086 r3 0:8 1:28 2:91 A:492891294;C:373079069;G:416862992;T:409079819;N:32809 8 28 91   492891294 373079069 416862992 409079819 32809 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.92068   0.13997   0.78516   0.50532   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24817 24817 SRR25509969 SRX21240521 SRS18495444 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_plus_S26_L002_I1_001.fastq.gz MECOM_plus_S26_L002_R1_001.fastq.gz MECOM_plus_S26_L002_R2_001.fastq.gz fastq fastq fastq 2362115545.0 18599335.0 GSM7680086 r4 0:8 1:28 2:91 A:493282758;C:373220256;G:416785305;T:409222388;N:28778 8 28 91   493282758 373220256 416785305 409222388 28778 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.92013   0.14129   0.78468   0.52049   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24818 24818 SRR25509970 SRX21240521 SRS18495444 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_plus_S27_L001_I1_001.fastq.gz MECOM_plus_S27_L001_R1_001.fastq.gz MECOM_plus_S27_L001_R2_001.fastq.gz fastq fastq fastq 2093107066.0 16481158.0 GSM7680086 r5 0:8 1:28 2:91 A:438295698;C:330083473;G:369094473;T:362282989;N:28745 8 28 91   438295698 330083473 369094473 362282989 28745 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91759   0.13991   0.78354   0.51917   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24819 24819 SRR25509971 SRX21240521 SRS18495444 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_plus_S27_L002_R2_001.fastq.gz MECOM_plus_S27_L002_R1_001.fastq.gz MECOM_plus_S27_L002_I1_001.fastq.gz fastq fastq fastq 2095025401.0 16496263.0 GSM7680086 r6 0:8 1:28 2:91 A:438926470;C:330300198;G:369243520;T:362664613;N:25132 8 28 91   438926470 330300198 369243520 362664613 25132 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91795   0.14216   0.78151   0.5067   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24820 24820 SRR25509972 SRX21240521 SRS18495444 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_plus_S28_L001_R2_001.fastq.gz MECOM_plus_S28_L001_R1_001.fastq.gz MECOM_plus_S28_L001_I1_001.fastq.gz fastq fastq fastq 1722573390.0 13563570.0 GSM7680086 r7 0:8 1:28 2:91 A:360865837;C:272246731;G:303643951;T:297504190;N:24161 8 28 91   360865837 272246731 303643951 297504190 24161 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91897   0.13999   0.78648   0.49913   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24821 24821 SRR25509973 SRX21240521 SRS18495444 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq GSM7680086   source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680086 GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680086 r1 GSM7680086 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py MECOM_plus_S28_L002_I1_001.fastq.gz MECOM_plus_S28_L002_R1_001.fastq.gz MECOM_plus_S28_L002_R2_001.fastq.gz fastq fastq fastq 1724036303.0 13575089.0 GSM7680086 r8 0:8 1:28 2:91 A:361391368;C:272402118;G:303699423;T:297819212;N:20978 8 28 91   361391368 272402118 303699423 297819212 20978 SRX21240521 SRS18495444 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.92182   0.14094   0.78326   0.50699   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24822 24822 SRR25509974 SRX21240520 SRS18495443 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16plusGFP_S5_L001_R2_001.fastq.gz PRDM16plusGFP_S5_L001_R1_001.fastq.gz PRDM16plusGFP_S5_L001_I1_001.fastq.gz fastq fastq fastq 8567717053.0 67462339.0 GSM7680085 r1 0:8 1:28 2:91 A:1758073165;C:1341216272;G:1446728174;T:1592934812;N:120426 8 28 91   1758073165 1341216272 1446728174 1592934812 120426 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.90663   0.17669   0.75812   0.50234   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24823 24823 SRR25509975 SRX21240520 SRS18495443 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16plusGFP_S5_L002_R2_001.fastq.gz PRDM16plusGFP_S5_L002_R1_001.fastq.gz PRDM16plusGFP_S5_L002_I1_001.fastq.gz fastq fastq fastq 8694310526.0 68459138.0 GSM7680085 r2 0:8 1:28 2:91 A:1780912602;C:1365177337;G:1472402153;T:1611176829;N:112637 8 28 91   1780912602 1365177337 1472402153 1611176829 112637 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.90543   0.17508   0.76019   0.51005   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24824 24824 SRR25509976 SRX21240520 SRS18495443 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16plusGFP_S6_L001_R2_001.fastq.gz PRDM16plusGFP_S6_L001_R1_001.fastq.gz PRDM16plusGFP_S6_L001_I1_001.fastq.gz fastq fastq fastq 9112215456.0 71749728.0 GSM7680085 r3 0:8 1:28 2:91 A:1868388882;C:1426817380;G:1540502920;T:1693385950;N:130116 8 28 91   1868388882 1426817380 1540502920 1693385950 130116 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.90763   0.17756   0.76102   0.50457   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24825 24825 SRR25509977 SRX21240520 SRS18495443 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16plusGFP_S6_L002_I1_001.fastq.gz PRDM16plusGFP_S6_L002_R1_001.fastq.gz PRDM16plusGFP_S6_L002_R2_001.fastq.gz fastq fastq fastq 9170568781.0 72209203.0 GSM7680085 r4 0:8 1:28 2:91 A:1876786596;C:1440704341;G:1555176461;T:1698251178;N:118897 8 28 91   1876786596 1440704341 1555176461 1698251178 118897 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.9062   0.17617   0.76203   0.49732   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24826 24826 SRR25509978 SRX21240520 SRS18495443 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16plusGFP_S7_L001_R2_001.fastq.gz PRDM16plusGFP_S7_L001_R1_001.fastq.gz PRDM16plusGFP_S7_L001_I1_001.fastq.gz fastq fastq fastq 96282510.0 758130.0 GSM7680085 r5 0:8 1:28 2:91 A:19884451;C:15070058;G:16206702;T:17827293;N:1326 8 28 91   19884451 15070058 16206702 17827293 1326 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.76071   0.14671   0.78064   0.49267   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24827 24827 SRR25509979 SRX21240520 SRS18495443 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16plusGFP_S7_L002_I1_001.fastq.gz PRDM16plusGFP_S7_L002_R2_001.fastq.gz PRDM16plusGFP_S7_L002_R1_001.fastq.gz fastq fastq fastq 96503236.0 759868.0 GSM7680085 r6 0:8 1:28 2:91 A:19898524;C:15152212;G:16290226;T:17805918;N:1108 8 28 91   19898524 15152212 16290226 17805918 1108 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.76382   0.1467   0.78508   0.48995   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24828 24828 SRR25509980 SRX21240520 SRS18495443 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16plusGFP_S8_L001_I1_001.fastq.gz PRDM16plusGFP_S8_L001_R1_001.fastq.gz PRDM16plusGFP_S8_L001_R2_001.fastq.gz fastq fastq fastq 8873313978.0 69868614.0 GSM7680085 r7 0:8 1:28 2:91 A:1820893372;C:1390912026;G:1498935631;T:1647176605;N:126240 8 28 91   1820893372 1390912026 1498935631 1647176605 126240 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.90718   0.17603   0.76211   0.50458   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24829 24829 SRR25509981 SRX21240520 SRS18495443 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq GSM7680085   source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680085 GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680085 r1 GSM7680085 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py PRDM16plusGFP_S8_L002_I1_001.fastq.gz PRDM16plusGFP_S8_L002_R1_001.fastq.gz PRDM16plusGFP_S8_L002_R2_001.fastq.gz fastq fastq fastq 8980314526.0 70711138.0 GSM7680085 r8 0:8 1:28 2:91 A:1839681468;C:1412028536;G:1521396962;T:1661490212;N:116380 8 28 91   1839681468 1412028536 1521396962 1661490212 116380 SRX21240520 SRS18495443 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.9078   0.17604   0.76037   0.47729   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24830 24830 SRR25509982 SRX21240519 SRS18495442 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_minus_S21_L001_I1_001.fastq.gz 5DPF_WT_minus_S21_L001_R1_001.fastq.gz 5DPF_WT_minus_S21_L001_R2_001.fastq.gz fastq fastq fastq 8634577600.0 67988800.0 GSM7680084 r1 0:8 1:28 2:91 A:1833391508;C:1279550998;G:1408086737;T:1665829499;N:122058 8 28 91   1833391508 1279550998 1408086737 1665829499 122058 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.92   0.2485   0.75552   0.51753   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24831 24831 SRR25509983 SRX21240519 SRS18495442 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_minus_S21_L002_I1_001.fastq.gz 5DPF_WT_minus_S21_L002_R1_001.fastq.gz 5DPF_WT_minus_S21_L002_R2_001.fastq.gz fastq fastq fastq 8644279892.0 68065196.0 GSM7680084 r2 0:8 1:28 2:91 A:1835831383;C:1280886675;G:1409188624;T:1667919807;N:106347 8 28 91   1835831383 1280886675 1409188624 1667919807 106347 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91942   0.24867   0.75396   0.52058   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24832 24832 SRR25509984 SRX21240519 SRS18495442 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_minus_S22_L001_R2_001.fastq.gz 5DPF_WT_minus_S22_L001_R1_001.fastq.gz 5DPF_WT_minus_S22_L001_I1_001.fastq.gz fastq fastq fastq 6144243998.0 48379874.0 GSM7680084 r3 0:8 1:28 2:91 A:1307018689;C:910675193;G:999334562;T:1185454346;N:85744 8 28 91   1307018689 910675193 999334562 1185454346 85744 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91944   0.2505   0.75538   0.5154   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24833 24833 SRR25509985 SRX21240519 SRS18495442 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_minus_S22_L002_I1_001.fastq.gz 5DPF_WT_minus_S22_L002_R1_001.fastq.gz 5DPF_WT_minus_S22_L002_R2_001.fastq.gz fastq fastq fastq 6161162938.0 48513094.0 GSM7680084 r4 0:8 1:28 2:91 A:1310818438;C:913067206;G:1001801994;T:1188928241;N:75675 8 28 91   1310818438 913067206 1001801994 1188928241 75675 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91847   0.24895   0.75483   0.52092   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24834 24834 SRR25509986 SRX21240519 SRS18495442 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_minus_S23_L001_I1_001.fastq.gz 5DPF_WT_minus_S23_L001_R1_001.fastq.gz 5DPF_WT_minus_S23_L001_R2_001.fastq.gz fastq fastq fastq 6893652075.0 54280725.0 GSM7680084 r5 0:8 1:28 2:91 A:1466387768;C:1021460104;G:1123606745;T:1327994370;N:96988 8 28 91   1466387768 1021460104 1123606745 1327994370 96988 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.92042   0.24759   0.75663   0.51662   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24835 24835 SRR25509987 SRX21240519 SRS18495442 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_minus_S23_L002_R1_001.fastq.gz 5DPF_WT_minus_S23_L002_R2_001.fastq.gz 5DPF_WT_minus_S23_L002_I1_001.fastq.gz fastq fastq fastq 6907881409.0 54392767.0 GSM7680084 r6 0:8 1:28 2:91 A:1469526451;C:1023529399;G:1125771813;T:1330830542;N:83592 8 28 91   1469526451 1023529399 1125771813 1330830542 83592 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91879   0.24904   0.75479   0.52175   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24836 24836 SRR25509988 SRX21240519 SRS18495442 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_minus_S24_L001_R2_001.fastq.gz 5DPF_WT_minus_S24_L001_R1_001.fastq.gz 5DPF_WT_minus_S24_L001_I1_001.fastq.gz fastq fastq fastq 6155284362.0 48466806.0 GSM7680084 r7 0:8 1:28 2:91 A:1309788155;C:909805561;G:1001863122;T:1188939208;N:83300 8 28 91   1309788155 909805561 1001863122 1188939208 83300 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91932   0.252   0.7541   0.52096   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24837 24837 SRR25509989 SRX21240519 SRS18495442 SRP453227 PRJNA1001940 Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed GSE240026 Transcriptome Analysis Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.   pubmed:37676768   Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq GSM7680084   source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files tail   DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.   tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs GSM7680084 GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq GSM7680084 r1 GSM7680084 1 DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453227   loader:fastq load.py 5DPF_WT_minus_S24_L002_I1_001.fastq.gz 5DPF_WT_minus_S24_L002_R1_001.fastq.gz 5DPF_WT_minus_S24_L002_R2_001.fastq.gz fastq fastq fastq 6165991605.0 48551115.0 GSM7680084 r8 0:8 1:28 2:91 A:1312424825;C:911081786;G:1003163970;T:1191408145;N:72739 8 28 91   1312424825 911081786 1003163970 1191408145 72739 SRX21240519 SRS18495442 SRA1686067 Dasen, Neuroscience Institute, New York University Grossman School of Medicine Dasen, Neuroscience Institute, New York University Grossman School of Medicine 1 0.91842   0.24989   0.75542   0.51918   91   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2023-08-03 Larval Larval Tail Multi-system
24854 24854 SRR25519420 SRX21249697 SRS18503946 SRP453374 PRJNA1002260 Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model GSE240080 Transcriptome Analysis We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.   pubmed:37728477   zebrafish AR42 TFA 4 3dpf GSM7681266   source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing zebrafish AR42 TFA 4 3dpf Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample tail   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.   tissue:tail|treatment:AR 42 treated larvae with TFA modeling GSM7681266 GSM7681266: zebrafish AR42 TFA 4 3dpf; Danio rerio; RNA Seq GSM7681266 r1 GSM7681266 1 RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     AR42_TFA_4.R1.fq.gz AR42_TFA_4.R2.fq.gz fastq fastq 9896772900.0 32989243.0 GSM7681266 r1 0:150 1:150 A:2382403653;C:2457377213;G:2470646159;T:2586345875;N:0 150 150     2382403653 2457377213 2470646159 2586345875 0 SRX21249697 SRS18503946 SRA1687041 Chongqing medical university Chongqing medical university 2 0.70537 0.88934 0.03159 0.04209 0.78013 0.75416 0.50713 0.45138 150 150 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2023-08-04 Larval Larval Tail Multi-system
24855 24855 SRR25519421 SRX21249696 SRS18503945 SRP453374 PRJNA1002260 Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model GSE240080 Transcriptome Analysis We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.   pubmed:37728477   zebrafish AR42 TFA 3 3dpf GSM7681265   source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing zebrafish AR42 TFA 3 3dpf Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample tail   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.   tissue:tail|treatment:AR 42 treated larvae with TFA modeling GSM7681265 GSM7681265: zebrafish AR42 TFA 3 3dpf; Danio rerio; RNA Seq GSM7681265 r1 GSM7681265 1 RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     AR42_TFA_3.R1.fq.gz AR42_TFA_3.R2.fq.gz fastq fastq 10265927100.0 34219757.0 GSM7681265 r1 0:150 1:150 A:2473552302;C:2548535087;G:2562873160;T:2680966551;N:0 150 150     2473552302 2548535087 2562873160 2680966551 0 SRX21249696 SRS18503945 SRA1687041 Chongqing medical university Chongqing medical university 2 0.70516 0.88765 0.03163 0.04168 0.7782 0.75083 0.50851 0.45305 150 150 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2023-08-04 Larval Larval Tail Multi-system
24856 24856 SRR25519422 SRX21249695 SRS18503944 SRP453374 PRJNA1002260 Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model GSE240080 Transcriptome Analysis We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.   pubmed:37728477   zebrafish AR42 TFA 2 3dpf GSM7681264   source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing zebrafish AR42 TFA 2 3dpf Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample tail   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.   tissue:tail|treatment:AR 42 treated larvae with TFA modeling GSM7681264 GSM7681264: zebrafish AR42 TFA 2 3dpf; Danio rerio; RNA Seq GSM7681264 r1 GSM7681264 1 RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     AR42_TFA_2.R2.fq.gz AR42_TFA_2.R1.fq.gz fastq fastq 10003398900.0 33344663.0 GSM7681264 r1 0:150 1:150 A:2409580340;C:2483650756;G:2497057051;T:2613110753;N:0 150 150     2409580340 2483650756 2497057051 2613110753 0 SRX21249695 SRS18503944 SRA1687041 Chongqing medical university Chongqing medical university 2 0.70787 0.89158 0.03203 0.04194 0.77851 0.75108 0.5072 0.45508 150 150 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2023-08-04 Larval Larval Tail Multi-system
24857 24857 SRR25519423 SRX21249694 SRS18503943 SRP453374 PRJNA1002260 Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model GSE240080 Transcriptome Analysis We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.   pubmed:37728477   zebrafish AR42 TFA 1 3dpf GSM7681263   source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing zebrafish AR42 TFA 1 3dpf Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample tail   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.   tissue:tail|treatment:AR 42 treated larvae with TFA modeling GSM7681263 GSM7681263: zebrafish AR42 TFA 1 3dpf; Danio rerio; RNA Seq GSM7681263 r1 GSM7681263 1 RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     AR42_TFA_1.R1.fq.gz AR42_TFA_1.R2.fq.gz fastq fastq 7420308900.0 24734363.0 GSM7681263 r1 0:150 1:150 A:1791092728;C:1841012408;G:1852583633;T:1935620131;N:0 150 150     1791092728 1841012408 1852583633 1935620131 0 SRX21249694 SRS18503943 SRA1687041 Chongqing medical university Chongqing medical university 2 0.69668 0.87862 0.03153 0.04215 0.77463 0.74949 0.50657 0.45971 150 150 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2023-08-04 Larval Larval Tail Multi-system
24858 24858 SRR25519424 SRX21249693 SRS18503942 SRP453374 PRJNA1002260 Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model GSE240080 Transcriptome Analysis We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.   pubmed:37728477   zebrafish DMSO TFA 4 3dpf GSM7681262   source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing zebrafish DMSO TFA 4 3dpf Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample tail   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.   tissue:tail|treatment:DMSO treated larvae with TFA modeling GSM7681262 GSM7681262: zebrafish DMSO TFA 4 3dpf; Danio rerio; RNA Seq GSM7681262 r1 GSM7681262 1 RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     DMSO_TFA_4.R1.fq.gz DMSO_TFA_4.R2.fq.gz fastq fastq 10178474100.0 33928247.0 GSM7681262 r1 0:150 1:150 A:2452172460;C:2526571372;G:2532799116;T:2666931152;N:0 150 150     2452172460 2526571372 2532799116 2666931152 0 SRX21249693 SRS18503942 SRA1687041 Chongqing medical university Chongqing medical university 2 0.72132 0.91072 0.03161 0.04366 0.77709 0.75016 0.516 0.45312 150 150 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2023-08-04 Larval Larval Tail Multi-system
24859 24859 SRR25519425 SRX21249692 SRS18503941 SRP453374 PRJNA1002260 Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model GSE240080 Transcriptome Analysis We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.   pubmed:37728477   zebrafish DMSO TFA 3 3dpf GSM7681261   source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing zebrafish DMSO TFA 3 3dpf Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample tail   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.   tissue:tail|treatment:DMSO treated larvae with TFA modeling GSM7681261 GSM7681261: zebrafish DMSO TFA 3 3dpf; Danio rerio; RNA Seq GSM7681261 r1 GSM7681261 1 RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     DMSO_TFA_3.R1.fq.gz DMSO_TFA_3.R2.fq.gz fastq fastq 9483201300.0 31610671.0 GSM7681261 r1 0:150 1:150 A:2282797855;C:2354211318;G:2361918927;T:2484273200;N:0 150 150     2282797855 2354211318 2361918927 2484273200 0 SRX21249692 SRS18503941 SRA1687041 Chongqing medical university Chongqing medical university 2 0.71779 0.90757 0.03224 0.04329 0.77853 0.74862 0.51128 0.44891 150 150 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2023-08-04 Larval Larval Tail Multi-system
24860 24860 SRR25519426 SRX21249691 SRS18503940 SRP453374 PRJNA1002260 Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model GSE240080 Transcriptome Analysis We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.   pubmed:37728477   zebrafish DMSO TFA 2 3dpf GSM7681260   source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing zebrafish DMSO TFA 2 3dpf Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample tail   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.   tissue:tail|treatment:DMSO treated larvae with TFA modeling GSM7681260 GSM7681260: zebrafish DMSO TFA 2 3dpf; Danio rerio; RNA Seq GSM7681260 r1 GSM7681260 1 RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     DMSO_TFA_2.R1.fq.gz DMSO_TFA_2.R2.fq.gz fastq fastq 9372641700.0 31242139.0 GSM7681260 r1 0:150 1:150 A:2255045813;C:2327185536;G:2333956274;T:2456454077;N:0 150 150     2255045813 2327185536 2333956274 2456454077 0 SRX21249691 SRS18503940 SRA1687041 Chongqing medical university Chongqing medical university 2 0.71913 0.91061 0.0318 0.04251 0.7778 0.74907 0.51295 0.45006 150 150 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2023-08-04 Larval Larval Tail Multi-system
24861 24861 SRR25519427 SRX21249690 SRS18503939 SRP453374 PRJNA1002260 Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model GSE240080 Transcriptome Analysis We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.   pubmed:37728477   zebrafish DMSO TFA 1 3dpf GSM7681259   source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing zebrafish DMSO TFA 1 3dpf Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample tail   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.   tissue:tail|treatment:DMSO treated larvae with TFA modeling GSM7681259 GSM7681259: zebrafish DMSO TFA 1 3dpf; Danio rerio; RNA Seq GSM7681259 r1 GSM7681259 1 RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     DMSO_TFA_1.R1.fq.gz DMSO_TFA_1.R2.fq.gz fastq fastq 8665981200.0 28886604.0 GSM7681259 r1 0:150 1:150 A:2086560929;C:2153111953;G:2157203992;T:2269104326;N:0 150 150     2086560929 2153111953 2157203992 2269104326 0 SRX21249690 SRS18503939 SRA1687041 Chongqing medical university Chongqing medical university 2 0.71996 0.90816 0.03211 0.04297 0.77739 0.75097 0.5122 0.452 150 150 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2023-08-04 Larval Larval Tail Multi-system
24862 24862 SRR25519428 SRX21249689 SRS18503938 SRP453374 PRJNA1002260 Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model GSE240080 Transcriptome Analysis We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.   pubmed:37728477   zebrafish AR42 4 3dpf GSM7681258   source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing zebrafish AR42 4 3dpf Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample tail   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.   tissue:tail|treatment:AR 42 treated larvae without xxx modeling GSM7681258 GSM7681258: zebrafish AR42 4 3dpf; Danio rerio; RNA Seq GSM7681258 r1 GSM7681258 1 RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     AR42_4.R1.fq.gz AR42_4.R2.fq.gz fastq fastq 10199154900.0 33997183.0 GSM7681258 r1 0:150 1:150 A:2461755295;C:2524481077;G:2536143078;T:2676775450;N:0 150 150     2461755295 2524481077 2536143078 2676775450 0 SRX21249689 SRS18503938 SRA1687041 Chongqing medical university Chongqing medical university 2 0.70676 0.89456 0.031 0.04108 0.77508 0.747 0.44642 0.47521 150 150 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2023-08-04 Larval Larval Tail Multi-system
24863 24863 SRR25519429 SRX21249688 SRS18503937 SRP453374 PRJNA1002260 Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model GSE240080 Transcriptome Analysis We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.   pubmed:37728477   zebrafish AR42 3 3dpf GSM7681257   source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing zebrafish AR42 3 3dpf Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample tail   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.   tissue:tail|treatment:AR 42 treated larvae without xxx modeling GSM7681257 GSM7681257: zebrafish AR42 3 3dpf; Danio rerio; RNA Seq GSM7681257 r1 GSM7681257 1 RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     AR42_3.R1.fq.gz AR42_3.R2.fq.gz fastq fastq 9953498100.0 33178327.0 GSM7681257 r1 0:150 1:150 A:2400858967;C:2463285586;G:2477369817;T:2611983730;N:0 150 150     2400858967 2463285586 2477369817 2611983730 0 SRX21249688 SRS18503937 SRA1687041 Chongqing medical university Chongqing medical university 2 0.70865 0.89517 0.03101 0.04127 0.77325 0.74679 0.50253 0.50409 150 150 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2023-08-04 Larval Larval Tail Multi-system
24864 24864 SRR25519430 SRX21249687 SRS18503936 SRP453374 PRJNA1002260 Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model GSE240080 Transcriptome Analysis We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.   pubmed:37728477   zebrafish AR42 2 3dpf GSM7681256   source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing zebrafish AR42 2 3dpf Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample tail   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.   tissue:tail|treatment:AR 42 treated larvae without xxx modeling GSM7681256 GSM7681256: zebrafish AR42 2 3dpf; Danio rerio; RNA Seq GSM7681256 r1 GSM7681256 1 RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     AR42_2.R1.fq.gz AR42_2.R2.fq.gz fastq fastq 10005489000.0 33351630.0 GSM7681256 r1 0:150 1:150 A:2413672248;C:2477611702;G:2491304598;T:2622900452;N:0 150 150     2413672248 2477611702 2491304598 2622900452 0 SRX21249687 SRS18503936 SRA1687041 Chongqing medical university Chongqing medical university 2 0.70639 0.89204 0.03035 0.04087 0.77502 0.74955 0.50558 0.50545 150 150 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2023-08-04 Larval Larval Tail Multi-system
24865 24865 SRR25519431 SRX21249686 SRS18503935 SRP453374 PRJNA1002260 Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model GSE240080 Transcriptome Analysis We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.   pubmed:37728477   zebrafish AR42 1 3dpf GSM7681255   source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing zebrafish AR42 1 3dpf Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample tail   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.   tissue:tail|treatment:AR 42 treated larvae without xxx modeling GSM7681255 GSM7681255: zebrafish AR42 1 3dpf; Danio rerio; RNA Seq GSM7681255 r1 GSM7681255 1 RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     AR42_1.R1.fq.gz AR42_1.R2.fq.gz fastq fastq 9698587800.0 32328626.0 GSM7681255 r1 0:150 1:150 A:2337968859;C:2400315331;G:2416067610;T:2544236000;N:0 150 150     2337968859 2400315331 2416067610 2544236000 0 SRX21249686 SRS18503935 SRA1687041 Chongqing medical university Chongqing medical university 2 0.70903 0.89448 0.02976 0.04032 0.77583 0.74935 0.50747 0.5081 150 150 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2023-08-04 Larval Larval Tail Multi-system
24866 24866 SRR25519432 SRX21249685 SRS18503934 SRP453374 PRJNA1002260 Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model GSE240080 Transcriptome Analysis We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.   pubmed:37728477   zebrafish DMSO 4 3dpf GSM7681254   source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing zebrafish DMSO 4 3dpf Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample tail   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.   tissue:tail|treatment:DMSO treated larvae without xxx modeling GSM7681254 GSM7681254: zebrafish DMSO 4 3dpf; Danio rerio; RNA Seq GSM7681254 r1 GSM7681254 1 RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     DMSO_4.R1.fq.gz DMSO_4.R2.fq.gz fastq fastq 9083670000.0 30278900.0 GSM7681254 r1 0:150 1:150 A:2191941100;C:2247936730;G:2258913579;T:2384878591;N:0 150 150     2191941100 2247936730 2258913579 2384878591 0 SRX21249685 SRS18503934 SRA1687041 Chongqing medical university Chongqing medical university 2 0.71071 0.90457 0.03362 0.04688 0.77106 0.74357 0.50842 0.50975 150 150 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2023-08-04 Larval Larval Tail Multi-system
24867 24867 SRR25519433 SRX21249684 SRS18503933 SRP453374 PRJNA1002260 Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model GSE240080 Transcriptome Analysis We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.   pubmed:37728477   zebrafish DMSO 3 3dpf GSM7681253   source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing zebrafish DMSO 3 3dpf Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample tail   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.   tissue:tail|treatment:DMSO treated larvae without xxx modeling GSM7681253 GSM7681253: zebrafish DMSO 3 3dpf; Danio rerio; RNA Seq GSM7681253 r1 GSM7681253 1 RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     DMSO_3.R2.fq.gz DMSO_3.R1.fq.gz fastq fastq 9394455000.0 31314850.0 GSM7681253 r1 0:150 1:150 A:2266296733;C:2324081714;G:2335347043;T:2468729510;N:0 150 150     2266296733 2324081714 2335347043 2468729510 0 SRX21249684 SRS18503933 SRA1687041 Chongqing medical university Chongqing medical university 2 0.70975 0.90445 0.03329 0.04594 0.77005 0.7417 0.51188 0.5163 150 150 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2023-08-04 Larval Larval Tail Multi-system
24868 24868 SRR25519434 SRX21249683 SRS18503932 SRP453374 PRJNA1002260 Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model GSE240080 Transcriptome Analysis We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.   pubmed:37728477   zebrafish DMSO 2 3dpf GSM7681252   source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing zebrafish DMSO 2 3dpf Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample tail   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.   tissue:tail|treatment:DMSO treated larvae without xxx modeling GSM7681252 GSM7681252: zebrafish DMSO 2 3dpf; Danio rerio; RNA Seq GSM7681252 r1 GSM7681252 1 RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     DMSO_2.R1.fq.gz DMSO_2.R2.fq.gz fastq fastq 9157453500.0 30524845.0 GSM7681252 r1 0:150 1:150 A:2209331568;C:2266614182;G:2273923578;T:2407584172;N:0 150 150     2209331568 2266614182 2273923578 2407584172 0 SRX21249683 SRS18503932 SRA1687041 Chongqing medical university Chongqing medical university 2 0.70922 0.90538 0.03379 0.04616 0.7723 0.74213 0.50839 0.50803 150 150 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2023-08-04 Larval Larval Tail Multi-system
24869 24869 SRR25519435 SRX21249682 SRS18503931 SRP453374 PRJNA1002260 Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model GSE240080 Transcriptome Analysis We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.   pubmed:37728477   zebrafish DMSO 1 3dpf GSM7681251   source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing zebrafish DMSO 1 3dpf Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample tail   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction.   tissue:tail|treatment:DMSO treated larvae without xxx modeling GSM7681251 GSM7681251: zebrafish DMSO 1 3dpf; Danio rerio; RNA Seq GSM7681251 r1 GSM7681251 1 RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     DMSO_1.R2.fq.gz DMSO_1.R1.fq.gz fastq fastq 8769040200.0 29230134.0 GSM7681251 r1 0:150 1:150 A:2114427483;C:2170929931;G:2179906163;T:2303776623;N:0 150 150     2114427483 2170929931 2179906163 2303776623 0 SRX21249682 SRS18503931 SRA1687041 Chongqing medical university Chongqing medical university 2 0.71002 0.9037 0.0335 0.04604 0.77155 0.74308 0.51339 0.50801 150 150 B B biological fallback assumption bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   China 2023-08-04 Larval Larval Tail Multi-system
36147 36147 SRR33446914 SRX28687233 SRS24954089 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 4 GSM8970925   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970925 GSM8970925: SB 431542 treated / uncut tail replicate 4; Danio rerio; RNA Seq GSM8970925 r1 GSM8970925 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-4_S18_L001_R1_001.fastq.gz fastq 392062720.0 5158720.0 GSM8970925 r1 0:76 A:111393933;C:84178440;G:86759120;T:109728583;N:2644 76       111393933 84178440 86759120 109728583 2644 SRX28687233 SRS24954089 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36148 36148 SRR33446915 SRX28687233 SRS24954089 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 4 GSM8970925   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970925 GSM8970925: SB 431542 treated / uncut tail replicate 4; Danio rerio; RNA Seq GSM8970925 r1 GSM8970925 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-4_S18_L002_R1_001.fastq.gz fastq 382539160.0 5033410.0 GSM8970925 r2 0:76 A:108549273;C:82135694;G:84877971;T:106974218;N:2004 76       108549273 82135694 84877971 106974218 2004 SRX28687233 SRS24954089 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36149 36149 SRR33446916 SRX28687233 SRS24954089 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 4 GSM8970925   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970925 GSM8970925: SB 431542 treated / uncut tail replicate 4; Danio rerio; RNA Seq GSM8970925 r1 GSM8970925 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-4_S18_L003_R1_001.fastq.gz fastq 390689020.0 5140645.0 GSM8970925 r3 0:76 A:110921885;C:83926202;G:86538209;T:109300187;N:2537 76       110921885 83926202 86538209 109300187 2537 SRX28687233 SRS24954089 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36150 36150 SRR33446917 SRX28687233 SRS24954089 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 4 GSM8970925   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970925 GSM8970925: SB 431542 treated / uncut tail replicate 4; Danio rerio; RNA Seq GSM8970925 r1 GSM8970925 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-4_S18_L004_R1_001.fastq.gz fastq 385026032.0 5066132.0 GSM8970925 r4 0:76 A:109282089;C:82666299;G:85291625;T:107783812;N:2207 76       109282089 82666299 85291625 107783812 2207 SRX28687233 SRS24954089 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36151 36151 SRR33446918 SRX28687232 SRS24954088 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 3 GSM8970924   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 3 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970924 GSM8970924: SB 431542 treated / uncut tail replicate 3; Danio rerio; RNA Seq GSM8970924 r1 GSM8970924 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-3_S17_L001_R1_001.fastq.gz fastq 242078544.0 3185244.0 GSM8970924 r1 0:76 A:70805011;C:50935537;G:52720022;T:67616569;N:1405 76       70805011 50935537 52720022 67616569 1405 SRX28687232 SRS24954088 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36152 36152 SRR33446919 SRX28687232 SRS24954088 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 3 GSM8970924   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 3 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970924 GSM8970924: SB 431542 treated / uncut tail replicate 3; Danio rerio; RNA Seq GSM8970924 r1 GSM8970924 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-3_S17_L002_R1_001.fastq.gz fastq 236879840.0 3116840.0 GSM8970924 r2 0:76 A:69118193;C:49900432;G:51722708;T:66137243;N:1264 76       69118193 49900432 51722708 66137243 1264 SRX28687232 SRS24954088 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36153 36153 SRR33446920 SRX28687232 SRS24954088 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 3 GSM8970924   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 3 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970924 GSM8970924: SB 431542 treated / uncut tail replicate 3; Danio rerio; RNA Seq GSM8970924 r1 GSM8970924 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-3_S17_L003_R1_001.fastq.gz fastq 241246952.0 3174302.0 GSM8970924 r3 0:76 A:70493049;C:50814403;G:52594412;T:67343618;N:1470 76       70493049 50814403 52594412 67343618 1470 SRX28687232 SRS24954088 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36154 36154 SRR33446921 SRX28687232 SRS24954088 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 3 GSM8970924   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 3 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970924 GSM8970924: SB 431542 treated / uncut tail replicate 3; Danio rerio; RNA Seq GSM8970924 r1 GSM8970924 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-3_S17_L004_R1_001.fastq.gz fastq 238296936.0 3135486.0 GSM8970924 r4 0:76 A:69600911;C:50177666;G:51934697;T:66582348;N:1314 76       69600911 50177666 51934697 66582348 1314 SRX28687232 SRS24954088 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36155 36155 SRR33446922 SRX28687231 SRS24954087 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 2 GSM8970923   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970923 GSM8970923: SB 431542 treated / uncut tail replicate 2; Danio rerio; RNA Seq GSM8970923 r1 GSM8970923 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-2_S16_L001_R1_001.fastq.gz fastq 293546884.0 3862459.0 GSM8970923 r1 0:76 A:86721485;C:61000183;G:63592308;T:82231012;N:1896 76       86721485 61000183 63592308 82231012 1896 SRX28687231 SRS24954087 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36156 36156 SRR33446923 SRX28687231 SRS24954087 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 2 GSM8970923   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970923 GSM8970923: SB 431542 treated / uncut tail replicate 2; Danio rerio; RNA Seq GSM8970923 r1 GSM8970923 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-2_S16_L002_R1_001.fastq.gz fastq 287313668.0 3780443.0 GSM8970923 r2 0:76 A:84719789;C:59732524;G:62422596;T:80437282;N:1477 76       84719789 59732524 62422596 80437282 1477 SRX28687231 SRS24954087 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36157 36157 SRR33446924 SRX28687231 SRS24954087 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 2 GSM8970923   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970923 GSM8970923: SB 431542 treated / uncut tail replicate 2; Danio rerio; RNA Seq GSM8970923 r1 GSM8970923 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-2_S16_L003_R1_001.fastq.gz fastq 293081612.0 3856337.0 GSM8970923 r3 0:76 A:86491724;C:60944765;G:63551581;T:82091805;N:1737 76       86491724 60944765 63551581 82091805 1737 SRX28687231 SRS24954087 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36158 36158 SRR33446925 SRX28687231 SRS24954087 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 2 GSM8970923   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970923 GSM8970923: SB 431542 treated / uncut tail replicate 2; Danio rerio; RNA Seq GSM8970923 r1 GSM8970923 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-2_S16_L004_R1_001.fastq.gz fastq 289340284.0 3807109.0 GSM8970923 r4 0:76 A:85390241;C:60135471;G:62741618;T:81071340;N:1614 76       85390241 60135471 62741618 81071340 1614 SRX28687231 SRS24954087 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36159 36159 SRR33446926 SRX28687230 SRS24954086 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 4 GSM8970922   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970922 GSM8970922: SB 431542 treated / cut tail replicate 4; Danio rerio; RNA Seq GSM8970922 r1 GSM8970922 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-4_S15_L001_R1_001.fastq.gz fastq 293676616.0 3864166.0 GSM8970922 r1 0:76 A:85055525;C:61514402;G:62951777;T:84153135;N:1777 76       85055525 61514402 62951777 84153135 1777 SRX28687230 SRS24954086 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36160 36160 SRR33446927 SRX28687230 SRS24954086 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 4 GSM8970922   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970922 GSM8970922: SB 431542 treated / cut tail replicate 4; Danio rerio; RNA Seq GSM8970922 r1 GSM8970922 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-4_S15_L002_R1_001.fastq.gz fastq 287550712.0 3783562.0 GSM8970922 r2 0:76 A:83130155;C:60249305;G:61817163;T:82352632;N:1457 76       83130155 60249305 61817163 82352632 1457 SRX28687230 SRS24954086 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36161 36161 SRR33446928 SRX28687230 SRS24954086 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 4 GSM8970922   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970922 GSM8970922: SB 431542 treated / cut tail replicate 4; Danio rerio; RNA Seq GSM8970922 r1 GSM8970922 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-4_S15_L003_R1_001.fastq.gz fastq 293005460.0 3855335.0 GSM8970922 r3 0:76 A:84798214;C:61435286;G:62865004;T:83905146;N:1810 76       84798214 61435286 62865004 83905146 1810 SRX28687230 SRS24954086 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36162 36162 SRR33446929 SRX28687230 SRS24954086 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 4 GSM8970922   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970922 GSM8970922: SB 431542 treated / cut tail replicate 4; Danio rerio; RNA Seq GSM8970922 r1 GSM8970922 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-4_S15_L004_R1_001.fastq.gz fastq 289004668.0 3802693.0 GSM8970922 r4 0:76 A:83595831;C:60570265;G:62006632;T:82830364;N:1576 76       83595831 60570265 62006632 82830364 1576 SRX28687230 SRS24954086 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36163 36163 SRR33446930 SRX28687229 SRS24954085 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 3 GSM8970921   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 3 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970921 GSM8970921: SB 431542 treated / cut tail replicate 3; Danio rerio; RNA Seq GSM8970921 r1 GSM8970921 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-3_S14_L001_R1_001.fastq.gz fastq 300231768.0 3950418.0 GSM8970921 r1 0:76 A:88106516;C:61818857;G:65466450;T:84838096;N:1849 76       88106516 61818857 65466450 84838096 1849 SRX28687229 SRS24954085 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36164 36164 SRR33446931 SRX28687229 SRS24954085 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 3 GSM8970921   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 3 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970921 GSM8970921: SB 431542 treated / cut tail replicate 3; Danio rerio; RNA Seq GSM8970921 r1 GSM8970921 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-3_S14_L002_R1_001.fastq.gz fastq 293677452.0 3864177.0 GSM8970921 r2 0:76 A:86015379;C:60508410;G:64229226;T:82922956;N:1481 76       86015379 60508410 64229226 82922956 1481 SRX28687229 SRS24954085 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36165 36165 SRR33446932 SRX28687229 SRS24954085 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 3 GSM8970921   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 3 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970921 GSM8970921: SB 431542 treated / cut tail replicate 3; Danio rerio; RNA Seq GSM8970921 r1 GSM8970921 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-3_S14_L003_R1_001.fastq.gz fastq 299518280.0 3941030.0 GSM8970921 r3 0:76 A:87800455;C:61713738;G:65389216;T:84612972;N:1899 76       87800455 61713738 65389216 84612972 1899 SRX28687229 SRS24954085 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36166 36166 SRR33446933 SRX28687229 SRS24954085 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 3 GSM8970921   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 3 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970921 GSM8970921: SB 431542 treated / cut tail replicate 3; Danio rerio; RNA Seq GSM8970921 r1 GSM8970921 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-3_S14_L004_R1_001.fastq.gz fastq 295680204.0 3890529.0 GSM8970921 r4 0:76 A:86636984;C:60930934;G:64539123;T:83571354;N:1809 76       86636984 60930934 64539123 83571354 1809 SRX28687229 SRS24954085 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36167 36167 SRR33446934 SRX28687228 SRS24954084 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 2 GSM8970920   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970920 GSM8970920: SB 431542 treated / cut tail replicate 2; Danio rerio; RNA Seq GSM8970920 r1 GSM8970920 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-2_S13_L001_R1_001.fastq.gz fastq 266233396.0 3503071.0 GSM8970920 r1 0:76 A:78387833;C:55246603;G:58347116;T:74250158;N:1686 76       78387833 55246603 58347116 74250158 1686 SRX28687228 SRS24954084 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36168 36168 SRR33446935 SRX28687228 SRS24954084 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 2 GSM8970920   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970920 GSM8970920: SB 431542 treated / cut tail replicate 2; Danio rerio; RNA Seq GSM8970920 r1 GSM8970920 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-2_S13_L002_R1_001.fastq.gz fastq 260317404.0 3425229.0 GSM8970920 r2 0:76 A:76487964;C:54052872;G:57202492;T:72572684;N:1392 76       76487964 54052872 57202492 72572684 1392 SRX28687228 SRS24954084 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36169 36169 SRR33446936 SRX28687228 SRS24954084 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 2 GSM8970920   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970920 GSM8970920: SB 431542 treated / cut tail replicate 2; Danio rerio; RNA Seq GSM8970920 r1 GSM8970920 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-2_S13_L003_R1_001.fastq.gz fastq 265513676.0 3493601.0 GSM8970920 r3 0:76 A:78116084;C:55123773;G:58227738;T:74044386;N:1695 76       78116084 55123773 58227738 74044386 1695 SRX28687228 SRS24954084 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36170 36170 SRR33446937 SRX28687228 SRS24954084 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 2 GSM8970920   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970920 GSM8970920: SB 431542 treated / cut tail replicate 2; Danio rerio; RNA Seq GSM8970920 r1 GSM8970920 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-2_S13_L004_R1_001.fastq.gz fastq 262010532.0 3447507.0 GSM8970920 r4 0:76 A:77058783;C:54402656;G:57452833;T:73094822;N:1438 76       77058783 54402656 57452833 73094822 1438 SRX28687228 SRS24954084 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36171 36171 SRR33446938 SRX28687227 SRS24954083 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 4 GSM8970919   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970919 GSM8970919: DMSO treated / uncut tail replicate 4; Danio rerio; RNA Seq GSM8970919 r1 GSM8970919 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-4_S24_L001_R1_001.fastq.gz fastq 334535736.0 4401786.0 GSM8970919 r1 0:76 A:104303278;C:67025244;G:65441286;T:97763807;N:2121 76       104303278 67025244 65441286 97763807 2121 SRX28687227 SRS24954083 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36172 36172 SRR33446939 SRX28687227 SRS24954083 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 4 GSM8970919   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970919 GSM8970919: DMSO treated / uncut tail replicate 4; Danio rerio; RNA Seq GSM8970919 r1 GSM8970919 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-4_S24_L002_R1_001.fastq.gz fastq 325405780.0 4281655.0 GSM8970919 r2 0:76 A:101185453;C:65289632;G:63869692;T:95059316;N:1687 76       101185453 65289632 63869692 95059316 1687 SRX28687227 SRS24954083 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36173 36173 SRR33446940 SRX28687227 SRS24954083 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 4 GSM8970919   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970919 GSM8970919: DMSO treated / uncut tail replicate 4; Danio rerio; RNA Seq GSM8970919 r1 GSM8970919 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-4_S24_L003_R1_001.fastq.gz fastq 333272540.0 4385165.0 GSM8970919 r3 0:76 A:103781471;C:66831319;G:65274288;T:97383334;N:2128 76       103781471 66831319 65274288 97383334 2128 SRX28687227 SRS24954083 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36174 36174 SRR33446941 SRX28687227 SRS24954083 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 4 GSM8970919   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970919 GSM8970919: DMSO treated / uncut tail replicate 4; Danio rerio; RNA Seq GSM8970919 r1 GSM8970919 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-4_S24_L004_R1_001.fastq.gz fastq 328778432.0 4326032.0 GSM8970919 r4 0:76 A:102340372;C:65917125;G:64384673;T:96134375;N:1887 76       102340372 65917125 64384673 96134375 1887 SRX28687227 SRS24954083 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36175 36175 SRR33446942 SRX28687226 SRS24954082 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 2 GSM8970918   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970918 GSM8970918: DMSO treated / uncut tail replicate 2; Danio rerio; RNA Seq GSM8970918 r1 GSM8970918 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-2_S23_L001_R1_001.fastq.gz fastq 254273428.0 3345703.0 GSM8970918 r1 0:76 A:73868437;C:53712396;G:55649268;T:71041836;N:1491 76       73868437 53712396 55649268 71041836 1491 SRX28687226 SRS24954082 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36176 36176 SRR33446943 SRX28687226 SRS24954082 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 2 GSM8970918   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970918 GSM8970918: DMSO treated / uncut tail replicate 2; Danio rerio; RNA Seq GSM8970918 r1 GSM8970918 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-2_S23_L002_R1_001.fastq.gz fastq 247479256.0 3256306.0 GSM8970918 r2 0:76 A:71749772;C:52269437;G:54304263;T:69154447;N:1337 76       71749772 52269437 54304263 69154447 1337 SRX28687226 SRS24954082 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36177 36177 SRR33446944 SRX28687226 SRS24954082 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 2 GSM8970918   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970918 GSM8970918: DMSO treated / uncut tail replicate 2; Danio rerio; RNA Seq GSM8970918 r1 GSM8970918 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-2_S23_L003_R1_001.fastq.gz fastq 252975424.0 3328624.0 GSM8970918 r3 0:76 A:73431938;C:53451559;G:55422676;T:70667726;N:1525 76       73431938 53451559 55422676 70667726 1525 SRX28687226 SRS24954082 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36178 36178 SRR33446945 SRX28687226 SRS24954082 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 2 GSM8970918   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970918 GSM8970918: DMSO treated / uncut tail replicate 2; Danio rerio; RNA Seq GSM8970918 r1 GSM8970918 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-2_S23_L004_R1_001.fastq.gz fastq 249310400.0 3280400.0 GSM8970918 r4 0:76 A:72326303;C:52679056;G:54605938;T:69697722;N:1381 76       72326303 52679056 54605938 69697722 1381 SRX28687226 SRS24954082 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36179 36179 SRR33446946 SRX28687225 SRS24954081 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 1 GSM8970917   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 1 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970917 GSM8970917: DMSO treated / uncut tail replicate 1; Danio rerio; RNA Seq GSM8970917 r1 GSM8970917 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-1_S22_L001_R1_001.fastq.gz fastq 270570108.0 3560133.0 GSM8970917 r1 0:76 A:78499185;C:56484520;G:59318322;T:76266342;N:1739 76       78499185 56484520 59318322 76266342 1739 SRX28687225 SRS24954081 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36180 36180 SRR33446947 SRX28687225 SRS24954081 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 1 GSM8970917   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 1 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970917 GSM8970917: DMSO treated / uncut tail replicate 1; Danio rerio; RNA Seq GSM8970917 r1 GSM8970917 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-1_S22_L002_R1_001.fastq.gz fastq 263995348.0 3473623.0 GSM8970917 r2 0:76 A:76492301;C:55131794;G:58036716;T:74333178;N:1359 76       76492301 55131794 58036716 74333178 1359 SRX28687225 SRS24954081 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36181 36181 SRR33446948 SRX28687225 SRS24954081 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 1 GSM8970917   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 1 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970917 GSM8970917: DMSO treated / uncut tail replicate 1; Danio rerio; RNA Seq GSM8970917 r1 GSM8970917 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-1_S22_L003_R1_001.fastq.gz fastq 269322036.0 3543711.0 GSM8970917 r3 0:76 A:78091756;C:56257589;G:59094882;T:75876132;N:1677 76       78091756 56257589 59094882 75876132 1677 SRX28687225 SRS24954081 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36182 36182 SRR33446949 SRX28687225 SRS24954081 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 1 GSM8970917   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 1 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970917 GSM8970917: DMSO treated / uncut tail replicate 1; Danio rerio; RNA Seq GSM8970917 r1 GSM8970917 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-1_S22_L004_R1_001.fastq.gz fastq 265691820.0 3495945.0 GSM8970917 r4 0:76 A:77002713;C:55467944;G:58293660;T:74926013;N:1490 76       77002713 55467944 58293660 74926013 1490 SRX28687225 SRS24954081 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system

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