rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
24790,SRR25509944,SRX21240524,SRS18495447,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq,GSM7680083,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680083,GSM7680083: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680083 r1,GSM7680083,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,5DPF_WT_plus_S17_L001_R2_001.fastq.gz 5DPF_WT_plus_S17_L001_R1_001.fastq.gz 5DPF_WT_plus_S17_L001_I1_001.fastq.gz,fastq fastq fastq,5999080077.0,47236851.0,GSM7680083 r1,0:8 1:28 2:91,A:1212144705;C:959823109;G:1045323833;T:1081182723;N:79071,8,28,91,,1212144705,959823109,1045323833,1081182723,79071,SRX21240524,SRS18495447,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91673,,0.11695,,0.77481,,0.51165,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24791,SRR25509945,SRX21240524,SRS18495447,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq,GSM7680083,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680083,GSM7680083: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680083 r1,GSM7680083,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,5DPF_WT_plus_S17_L002_R2_001.fastq.gz 5DPF_WT_plus_S17_L002_R1_001.fastq.gz 5DPF_WT_plus_S17_L002_I1_001.fastq.gz,fastq fastq fastq,6012350180.0,47341340.0,GSM7680083 r2,0:8 1:28 2:91,A:1215185110;C:961739027;G:1047332997;T:1083733742;N:71064,8,28,91,,1215185110,961739027,1047332997,1083733742,71064,SRX21240524,SRS18495447,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91842,,0.11714,,0.7763,,0.51731,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24792,SRR25509946,SRX21240524,SRS18495447,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq,GSM7680083,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680083,GSM7680083: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680083 r1,GSM7680083,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,5DPF_WT_plus_S18_L001_R2_001.fastq.gz 5DPF_WT_plus_S18_L001_R1_001.fastq.gz 5DPF_WT_plus_S18_L001_I1_001.fastq.gz,fastq fastq fastq,4990947473.0,39298799.0,GSM7680083 r3,0:8 1:28 2:91,A:1007619958;C:800073636;G:871756682;T:896670984;N:69449,8,28,91,,1007619958,800073636,871756682,896670984,69449,SRX21240524,SRS18495447,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91717,,0.11737,,0.7767,,0.51879,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24793,SRR25509947,SRX21240524,SRS18495447,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq,GSM7680083,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680083,GSM7680083: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680083 r1,GSM7680083,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,5DPF_WT_plus_S18_L002_I1_001.fastq.gz 5DPF_WT_plus_S18_L002_R1_001.fastq.gz 5DPF_WT_plus_S18_L002_R2_001.fastq.gz,fastq fastq fastq,4994343707.0,39325541.0,GSM7680083 r4,0:8 1:28 2:91,A:1008545361;C:800479170;G:872044753;T:897494026;N:60921,8,28,91,,1008545361,800479170,872044753,897494026,60921,SRX21240524,SRS18495447,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.9173,,0.11671,,0.778,,0.51414,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24794,SRR25509948,SRX21240524,SRS18495447,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq,GSM7680083,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680083,GSM7680083: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680083 r1,GSM7680083,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,5DPF_WT_plus_S20_L001_R2_001.fastq.gz 5DPF_WT_plus_S20_L001_R1_001.fastq.gz 5DPF_WT_plus_S20_L001_I1_001.fastq.gz,fastq fastq fastq,4150807675.0,32683525.0,GSM7680083 r7,0:8 1:28 2:91,A:839301254;C:665476121;G:723277159;T:746089009;N:57232,8,28,91,,839301254,665476121,723277159,746089009,57232,SRX21240524,SRS18495447,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91704,,0.11665,,0.77589,,0.51231,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24795,SRR25509949,SRX21240524,SRS18495447,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq,GSM7680083,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680083,GSM7680083: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680083 r1,GSM7680083,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,5DPF_WT_plus_S20_L002_R2_001.fastq.gz 5DPF_WT_plus_S20_L002_R1_001.fastq.gz 5DPF_WT_plus_S20_L002_I1_001.fastq.gz,fastq fastq fastq,4152701499.0,32698437.0,GSM7680083 r8,0:8 1:28 2:91,A:839837413;C:665793367;G:723399518;T:746476220;N:51249,8,28,91,,839837413,665793367,723399518,746476220,51249,SRX21240524,SRS18495447,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91769,,0.11677,,0.77473,,0.5172,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24796,SRR25510006,SRX21240524,SRS18495447,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq,GSM7680083,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680083,GSM7680083: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680083 r1,GSM7680083,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,5DPF_WT_plus_S19_L001_I1_001.fastq.gz 5DPF_WT_plus_S19_L001_R1_001.fastq.gz 5DPF_WT_plus_S19_L001_R2_001.fastq.gz,fastq fastq fastq,5570139228.0,43859364.0,GSM7680083 r5,0:8 1:28 2:91,A:1124433319;C:892106407;G:974065175;T:1000519772;N:77451,8,28,91,,1124433319,892106407,974065175,1000519772,77451,SRX21240524,SRS18495447,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.9181,,0.11708,,0.77725,,0.506,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24797,SRR25510007,SRX21240524,SRS18495447,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq,GSM7680083,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680083,GSM7680083: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680083 r1,GSM7680083,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,5DPF_WT_plus_S19_L002_R2_001.fastq.gz 5DPF_WT_plus_S19_L002_R1_001.fastq.gz 5DPF_WT_plus_S19_L002_I1_001.fastq.gz,fastq fastq fastq,5568879134.0,43849442.0,GSM7680083 r6,0:8 1:28 2:91,A:1124462080;C:891765530;G:973382320;T:1000621312;N:67980,8,28,91,,1124462080,891765530,973382320,1000621312,67980,SRX21240524,SRS18495447,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91836,,0.11752,,0.77786,,0.49118,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24798,SRR25509950,SRX21240523,SRS18495446,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq,GSM7680088,,source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680088,GSM7680088: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680088 r1,GSM7680088,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,MECOM_minus_S29_L001_I1_001.fastq.gz MECOM_minus_S29_L001_R1_001.fastq.gz MECOM_minus_S29_L001_R2_001.fastq.gz,fastq fastq fastq,6472457718.0,50964234.0,GSM7680088 r1,0:8 1:28 2:91,A:1374177983;C:969847712;G:1063043909;T:1230585953;N:89737,8,28,91,,1374177983,969847712,1063043909,1230585953,89737,SRX21240523,SRS18495446,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91899,,0.23002,,0.75597,,0.50918,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24799,SRR25509951,SRX21240523,SRS18495446,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq,GSM7680088,,source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680088,GSM7680088: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680088 r1,GSM7680088,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,MECOM_minus_S29_L002_I1_001.fastq.gz MECOM_minus_S29_L002_R1_001.fastq.gz MECOM_minus_S29_L002_R2_001.fastq.gz,fastq fastq fastq,6479801747.0,51022061.0,GSM7680088 r2,0:8 1:28 2:91,A:1375879660;C:970771702;G:1064110805;T:1232166662;N:78722,8,28,91,,1375879660,970771702,1064110805,1232166662,78722,SRX21240523,SRS18495446,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91932,,0.23011,,0.75666,,0.50726,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24800,SRR25509952,SRX21240523,SRS18495446,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq,GSM7680088,,source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680088,GSM7680088: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680088 r1,GSM7680088,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,MECOM_minus_S30_L001_I1_001.fastq.gz MECOM_minus_S30_L001_R1_001.fastq.gz MECOM_minus_S30_L001_R2_001.fastq.gz,fastq fastq fastq,6055044278.0,47677514.0,GSM7680088 r3,0:8 1:28 2:91,A:1285162347;C:907248700;G:995411468;T:1150745942;N:85317,8,28,91,,1285162347,907248700,995411468,1150745942,85317,SRX21240523,SRS18495446,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91771,,0.2306,,0.75799,,0.51641,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24801,SRR25509953,SRX21240523,SRS18495446,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq,GSM7680088,,source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680088,GSM7680088: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680088 r1,GSM7680088,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,MECOM_minus_S30_L002_I1_001.fastq.gz MECOM_minus_S30_L002_R1_001.fastq.gz MECOM_minus_S30_L002_R2_001.fastq.gz,fastq fastq fastq,6065969453.0,47763539.0,GSM7680088 r4,0:8 1:28 2:91,A:1287814805;C:908939739;G:996849881;T:1152803356;N:74268,8,28,91,,1287814805,908939739,996849881,1152803356,74268,SRX21240523,SRS18495446,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91856,,0.23244,,0.75844,,0.51273,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24802,SRR25509954,SRX21240523,SRS18495446,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq,GSM7680088,,source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680088,GSM7680088: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680088 r1,GSM7680088,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,MECOM_minus_S31_L001_I1_001.fastq.gz MECOM_minus_S31_L001_R1_001.fastq.gz MECOM_minus_S31_L001_R2_001.fastq.gz,fastq fastq fastq,5279309101.0,41569363.0,GSM7680088 r5,0:8 1:28 2:91,A:1122213686;C:789300425;G:868235888;T:1002988275;N:73759,8,28,91,,1122213686,789300425,868235888,1002988275,73759,SRX21240523,SRS18495446,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91638,,0.23107,,0.75795,,0.51508,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24803,SRR25509955,SRX21240523,SRS18495446,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq,GSM7680088,,source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680088,GSM7680088: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680088 r1,GSM7680088,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,MECOM_minus_S31_L002_I1_001.fastq.gz MECOM_minus_S31_L002_R1_001.fastq.gz MECOM_minus_S31_L002_R2_001.fastq.gz,fastq fastq fastq,5282579605.0,41595115.0,GSM7680088 r6,0:8 1:28 2:91,A:1123052612;C:789776127;G:868371205;T:1003891470;N:64051,8,28,91,,1123052612,789776127,868371205,1003891470,64051,SRX21240523,SRS18495446,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91687,,0.23155,,0.75653,,0.51167,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24804,SRR25509956,SRX21240523,SRS18495446,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq,GSM7680088,,source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680088,GSM7680088: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680088 r1,GSM7680088,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,MECOM_minus_S32_L001_I1_001.fastq.gz MECOM_minus_S32_L001_R1_001.fastq.gz MECOM_minus_S32_L001_R2_001.fastq.gz,fastq fastq fastq,5155833986.0,40597118.0,GSM7680088 r7,0:8 1:28 2:91,A:1096166065;C:771837218;G:846468036;T:979794053;N:72366,8,28,91,,1096166065,771837218,846468036,979794053,72366,SRX21240523,SRS18495446,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91864,,0.23062,,0.75783,,0.5144,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24805,SRR25509957,SRX21240523,SRS18495446,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq,GSM7680088,,source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680088,GSM7680088: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP   mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680088 r1,GSM7680088,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,MECOM_minus_S32_L002_I1_001.fastq.gz MECOM_minus_S32_L002_R1_001.fastq.gz MECOM_minus_S32_L002_R2_001.fastq.gz,fastq fastq fastq,5158852395.0,40620885.0,GSM7680088 r8,0:8 1:28 2:91,A:1096925078;C:772260867;G:846795917;T:980455576;N:63097,8,28,91,,1096925078,772260867,846795917,980455576,63097,SRX21240523,SRS18495446,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91859,,0.23143,,0.75921,,0.51192,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24806,SRR25509958,SRX21240522,SRS18495445,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq,GSM7680087,,source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680087,GSM7680087: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680087 r1,GSM7680087,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,PRDM16-GFP_S1_L001_I1_001.fastq.gz PRDM16-GFP_S1_L001_R1_001.fastq.gz PRDM16-GFP_S1_L001_R2_001.fastq.gz,fastq fastq fastq,7339736654.0,57793202.0,GSM7680087 r1,0:8 1:28 2:91,A:1557377528;C:1077119414;G:1156228317;T:1468352980;N:103143,8,28,91,,1557377528,1077119414,1156228317,1468352980,103143,SRX21240522,SRS18495445,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91516,,0.25902,,0.74255,,0.49922,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24807,SRR25509959,SRX21240522,SRS18495445,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq,GSM7680087,,source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680087,GSM7680087: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680087 r1,GSM7680087,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,PRDM16-GFP_S1_L002_I1_001.fastq.gz PRDM16-GFP_S1_L002_R1_001.fastq.gz PRDM16-GFP_S1_L002_R2_001.fastq.gz,fastq fastq fastq,7410090336.0,58347168.0,GSM7680087 r2,0:8 1:28 2:91,A:1569421640;C:1090998538;G:1171253819;T:1477822651;N:95640,8,28,91,,1569421640,1090998538,1171253819,1477822651,95640,SRX21240522,SRS18495445,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91462,,0.25846,,0.74215,,0.49672,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24808,SRR25509960,SRX21240522,SRS18495445,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq,GSM7680087,,source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680087,GSM7680087: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680087 r1,GSM7680087,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,PRDM16-GFP_S2_L001_I1_001.fastq.gz PRDM16-GFP_S2_L001_R1_001.fastq.gz PRDM16-GFP_S2_L001_R2_001.fastq.gz,fastq fastq fastq,7620847217.0,60006671.0,GSM7680087 r3,0:8 1:28 2:91,A:1615026295;C:1121044318;G:1201364994;T:1523062938;N:108516,8,28,91,,1615026295,1121044318,1201364994,1523062938,108516,SRX21240522,SRS18495445,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91495,,0.26021,,0.74188,,0.49871,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24809,SRR25509961,SRX21240522,SRS18495445,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq,GSM7680087,,source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680087,GSM7680087: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680087 r1,GSM7680087,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,PRDM16-GFP_S2_L002_I1_001.fastq.gz PRDM16-GFP_S2_L002_R1_001.fastq.gz PRDM16-GFP_S2_L002_R2_001.fastq.gz,fastq fastq fastq,7658170739.0,60300557.0,GSM7680087 r4,0:8 1:28 2:91,A:1620018228;C:1130072970;G:1211145212;T:1526013817;N:100460,8,28,91,,1620018228,1130072970,1211145212,1526013817,100460,SRX21240522,SRS18495445,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.9153,,0.25733,,0.74406,,0.49822,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24810,SRR25509962,SRX21240522,SRS18495445,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq,GSM7680087,,source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680087,GSM7680087: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680087 r1,GSM7680087,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,PRDM16-GFP_S3_L001_I1_001.fastq.gz PRDM16-GFP_S3_L001_R1_001.fastq.gz PRDM16-GFP_S3_L001_R2_001.fastq.gz,fastq fastq fastq,7520150568.0,59213784.0,GSM7680087 r5,0:8 1:28 2:91,A:1592224470;C:1104917106;G:1187483622;T:1503722424;N:106722,8,28,91,,1592224470,1104917106,1187483622,1503722424,106722,SRX21240522,SRS18495445,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91528,,0.25852,,0.74168,,0.50087,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24811,SRR25509963,SRX21240522,SRS18495445,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq,GSM7680087,,source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680087,GSM7680087: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680087 r1,GSM7680087,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,PRDM16-GFP_S3_L002_I1_001.fastq.gz PRDM16-GFP_S3_L002_R1_001.fastq.gz PRDM16-GFP_S3_L002_R2_001.fastq.gz,fastq fastq fastq,7547416198.0,59428474.0,GSM7680087 r6,0:8 1:28 2:91,A:1595335949;C:1112405532;G:1195632258;T:1504519719;N:97676,8,28,91,,1595335949,1112405532,1195632258,1504519719,97676,SRX21240522,SRS18495445,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91572,,0.25684,,0.74227,,0.49429,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24812,SRR25509964,SRX21240522,SRS18495445,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq,GSM7680087,,source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680087,GSM7680087: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680087 r1,GSM7680087,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,PRDM16-GFP_S4_L001_I1_001.fastq.gz PRDM16-GFP_S4_L001_R1_001.fastq.gz PRDM16-GFP_S4_L001_R2_001.fastq.gz,fastq fastq fastq,6203887389.0,48849507.0,GSM7680087 r7,0:8 1:28 2:91,A:1315023626;C:910416020;G:979167464;T:1240610297;N:87730,8,28,91,,1315023626,910416020,979167464,1240610297,87730,SRX21240522,SRS18495445,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91294,,0.25905,,0.74426,,0.49642,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24813,SRR25509965,SRX21240522,SRS18495445,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq,GSM7680087,,source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680087,GSM7680087: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680087 r1,GSM7680087,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,PRDM16-GFP_S4_L002_I1_001.fastq.gz PRDM16-GFP_S4_L002_R1_001.fastq.gz PRDM16-GFP_S4_L002_R2_001.fastq.gz,fastq fastq fastq,6164249419.0,48537397.0,GSM7680087 r8,0:8 1:28 2:91,A:1303982345;C:907803673;G:976227040;T:1228810005;N:80064,8,28,91,,1303982345,907803673,976227040,1228810005,80064,SRX21240522,SRS18495445,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91422,,0.25666,,0.74383,,0.49596,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24814,SRR25509966,SRX21240521,SRS18495444,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq,GSM7680086,,source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680086,GSM7680086: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680086 r1,GSM7680086,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,MECOM_plus_S25_L001_I1_001.fastq.gz MECOM_plus_S25_L001_R1_001.fastq.gz MECOM_plus_S25_L001_R2_001.fastq.gz,fastq fastq fastq,2154821446.0,16967098.0,GSM7680086 r1,0:8 1:28 2:91,A:451330902;C:339756831;G:379343350;T:373544930;N:29905,8,28,91,,451330902,339756831,379343350,373544930,29905,SRX21240521,SRS18495444,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91882,,0.142,,0.78299,,0.51956,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24815,SRR25509967,SRX21240521,SRS18495444,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq,GSM7680086,,source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680086,GSM7680086: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680086 r1,GSM7680086,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,MECOM_plus_S25_L002_I1_001.fastq.gz MECOM_plus_S25_L002_R1_001.fastq.gz MECOM_plus_S25_L002_R2_001.fastq.gz,fastq fastq fastq,2158219204.0,16993852.0,GSM7680086 r2,0:8 1:28 2:91,A:452280625;C:340228509;G:379707034;T:374197697;N:26667,8,28,91,,452280625,340228509,379707034,374197697,26667,SRX21240521,SRS18495444,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91895,,0.1417,,0.78279,,0.51981,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24816,SRR25509968,SRX21240521,SRS18495444,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq,GSM7680086,,source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680086,GSM7680086: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680086 r1,GSM7680086,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,MECOM_plus_S26_L001_I1_001.fastq.gz MECOM_plus_S26_L001_R1_001.fastq.gz MECOM_plus_S26_L001_R2_001.fastq.gz,fastq fastq fastq,2361287251.0,18592813.0,GSM7680086 r3,0:8 1:28 2:91,A:492891294;C:373079069;G:416862992;T:409079819;N:32809,8,28,91,,492891294,373079069,416862992,409079819,32809,SRX21240521,SRS18495444,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.92068,,0.13997,,0.78516,,0.50532,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24817,SRR25509969,SRX21240521,SRS18495444,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq,GSM7680086,,source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680086,GSM7680086: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680086 r1,GSM7680086,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,MECOM_plus_S26_L002_I1_001.fastq.gz MECOM_plus_S26_L002_R1_001.fastq.gz MECOM_plus_S26_L002_R2_001.fastq.gz,fastq fastq fastq,2362115545.0,18599335.0,GSM7680086 r4,0:8 1:28 2:91,A:493282758;C:373220256;G:416785305;T:409222388;N:28778,8,28,91,,493282758,373220256,416785305,409222388,28778,SRX21240521,SRS18495444,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.92013,,0.14129,,0.78468,,0.52049,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24818,SRR25509970,SRX21240521,SRS18495444,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq,GSM7680086,,source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680086,GSM7680086: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680086 r1,GSM7680086,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,MECOM_plus_S27_L001_I1_001.fastq.gz MECOM_plus_S27_L001_R1_001.fastq.gz MECOM_plus_S27_L001_R2_001.fastq.gz,fastq fastq fastq,2093107066.0,16481158.0,GSM7680086 r5,0:8 1:28 2:91,A:438295698;C:330083473;G:369094473;T:362282989;N:28745,8,28,91,,438295698,330083473,369094473,362282989,28745,SRX21240521,SRS18495444,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91759,,0.13991,,0.78354,,0.51917,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24819,SRR25509971,SRX21240521,SRS18495444,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq,GSM7680086,,source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680086,GSM7680086: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680086 r1,GSM7680086,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,MECOM_plus_S27_L002_R2_001.fastq.gz MECOM_plus_S27_L002_R1_001.fastq.gz MECOM_plus_S27_L002_I1_001.fastq.gz,fastq fastq fastq,2095025401.0,16496263.0,GSM7680086 r6,0:8 1:28 2:91,A:438926470;C:330300198;G:369243520;T:362664613;N:25132,8,28,91,,438926470,330300198,369243520,362664613,25132,SRX21240521,SRS18495444,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91795,,0.14216,,0.78151,,0.5067,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24820,SRR25509972,SRX21240521,SRS18495444,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq,GSM7680086,,source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680086,GSM7680086: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680086 r1,GSM7680086,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,MECOM_plus_S28_L001_R2_001.fastq.gz MECOM_plus_S28_L001_R1_001.fastq.gz MECOM_plus_S28_L001_I1_001.fastq.gz,fastq fastq fastq,1722573390.0,13563570.0,GSM7680086 r7,0:8 1:28 2:91,A:360865837;C:272246731;G:303643951;T:297504190;N:24161,8,28,91,,360865837,272246731,303643951,297504190,24161,SRX21240521,SRS18495444,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91897,,0.13999,,0.78648,,0.49913,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24821,SRR25509973,SRX21240521,SRS18495444,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq,GSM7680086,,source name:tail|tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  mecom /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680086,GSM7680086: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP+  mecom  /   5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680086 r1,GSM7680086,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,MECOM_plus_S28_L002_I1_001.fastq.gz MECOM_plus_S28_L002_R1_001.fastq.gz MECOM_plus_S28_L002_R2_001.fastq.gz,fastq fastq fastq,1724036303.0,13575089.0,GSM7680086 r8,0:8 1:28 2:91,A:361391368;C:272402118;G:303699423;T:297819212;N:20978,8,28,91,,361391368,272402118,303699423,297819212,20978,SRX21240521,SRS18495444,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.92182,,0.14094,,0.78326,,0.50699,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24822,SRR25509974,SRX21240520,SRS18495443,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq,GSM7680085,,source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680085,GSM7680085: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680085 r1,GSM7680085,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,PRDM16plusGFP_S5_L001_R2_001.fastq.gz PRDM16plusGFP_S5_L001_R1_001.fastq.gz PRDM16plusGFP_S5_L001_I1_001.fastq.gz,fastq fastq fastq,8567717053.0,67462339.0,GSM7680085 r1,0:8 1:28 2:91,A:1758073165;C:1341216272;G:1446728174;T:1592934812;N:120426,8,28,91,,1758073165,1341216272,1446728174,1592934812,120426,SRX21240520,SRS18495443,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.90663,,0.17669,,0.75812,,0.50234,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24823,SRR25509975,SRX21240520,SRS18495443,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq,GSM7680085,,source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680085,GSM7680085: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680085 r1,GSM7680085,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,PRDM16plusGFP_S5_L002_R2_001.fastq.gz PRDM16plusGFP_S5_L002_R1_001.fastq.gz PRDM16plusGFP_S5_L002_I1_001.fastq.gz,fastq fastq fastq,8694310526.0,68459138.0,GSM7680085 r2,0:8 1:28 2:91,A:1780912602;C:1365177337;G:1472402153;T:1611176829;N:112637,8,28,91,,1780912602,1365177337,1472402153,1611176829,112637,SRX21240520,SRS18495443,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.90543,,0.17508,,0.76019,,0.51005,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24824,SRR25509976,SRX21240520,SRS18495443,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq,GSM7680085,,source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680085,GSM7680085: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680085 r1,GSM7680085,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,PRDM16plusGFP_S6_L001_R2_001.fastq.gz PRDM16plusGFP_S6_L001_R1_001.fastq.gz PRDM16plusGFP_S6_L001_I1_001.fastq.gz,fastq fastq fastq,9112215456.0,71749728.0,GSM7680085 r3,0:8 1:28 2:91,A:1868388882;C:1426817380;G:1540502920;T:1693385950;N:130116,8,28,91,,1868388882,1426817380,1540502920,1693385950,130116,SRX21240520,SRS18495443,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.90763,,0.17756,,0.76102,,0.50457,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24825,SRR25509977,SRX21240520,SRS18495443,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq,GSM7680085,,source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680085,GSM7680085: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680085 r1,GSM7680085,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,PRDM16plusGFP_S6_L002_I1_001.fastq.gz PRDM16plusGFP_S6_L002_R1_001.fastq.gz PRDM16plusGFP_S6_L002_R2_001.fastq.gz,fastq fastq fastq,9170568781.0,72209203.0,GSM7680085 r4,0:8 1:28 2:91,A:1876786596;C:1440704341;G:1555176461;T:1698251178;N:118897,8,28,91,,1876786596,1440704341,1555176461,1698251178,118897,SRX21240520,SRS18495443,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.9062,,0.17617,,0.76203,,0.49732,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24826,SRR25509978,SRX21240520,SRS18495443,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq,GSM7680085,,source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680085,GSM7680085: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680085 r1,GSM7680085,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,PRDM16plusGFP_S7_L001_R2_001.fastq.gz PRDM16plusGFP_S7_L001_R1_001.fastq.gz PRDM16plusGFP_S7_L001_I1_001.fastq.gz,fastq fastq fastq,96282510.0,758130.0,GSM7680085 r5,0:8 1:28 2:91,A:19884451;C:15070058;G:16206702;T:17827293;N:1326,8,28,91,,19884451,15070058,16206702,17827293,1326,SRX21240520,SRS18495443,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.76071,,0.14671,,0.78064,,0.49267,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24827,SRR25509979,SRX21240520,SRS18495443,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq,GSM7680085,,source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680085,GSM7680085: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680085 r1,GSM7680085,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,PRDM16plusGFP_S7_L002_I1_001.fastq.gz PRDM16plusGFP_S7_L002_R2_001.fastq.gz PRDM16plusGFP_S7_L002_R1_001.fastq.gz,fastq fastq fastq,96503236.0,759868.0,GSM7680085 r6,0:8 1:28 2:91,A:19898524;C:15152212;G:16290226;T:17805918;N:1108,8,28,91,,19898524,15152212,16290226,17805918,1108,SRX21240520,SRS18495443,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.76382,,0.1467,,0.78508,,0.48995,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24828,SRR25509980,SRX21240520,SRS18495443,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq,GSM7680085,,source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680085,GSM7680085: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680085 r1,GSM7680085,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,PRDM16plusGFP_S8_L001_I1_001.fastq.gz PRDM16plusGFP_S8_L001_R1_001.fastq.gz PRDM16plusGFP_S8_L001_R2_001.fastq.gz,fastq fastq fastq,8873313978.0,69868614.0,GSM7680085 r7,0:8 1:28 2:91,A:1820893372;C:1390912026;G:1498935631;T:1647176605;N:126240,8,28,91,,1820893372,1390912026,1498935631,1647176605,126240,SRX21240520,SRS18495443,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.90718,,0.17603,,0.76211,,0.50458,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24829,SRR25509981,SRX21240520,SRS18495443,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq,GSM7680085,,source name:tail|tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2dsRed  prdm16 /   prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680085,GSM7680085: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP +  prdm16 /  5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680085 r1,GSM7680085,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,PRDM16plusGFP_S8_L002_I1_001.fastq.gz PRDM16plusGFP_S8_L002_R1_001.fastq.gz PRDM16plusGFP_S8_L002_R2_001.fastq.gz,fastq fastq fastq,8980314526.0,70711138.0,GSM7680085 r8,0:8 1:28 2:91,A:1839681468;C:1412028536;G:1521396962;T:1661490212;N:116380,8,28,91,,1839681468,1412028536,1521396962,1661490212,116380,SRX21240520,SRS18495443,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.9078,,0.17604,,0.76037,,0.47729,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24830,SRR25509982,SRX21240519,SRS18495442,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq,GSM7680084,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680084,GSM7680084: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680084 r1,GSM7680084,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,5DPF_WT_minus_S21_L001_I1_001.fastq.gz 5DPF_WT_minus_S21_L001_R1_001.fastq.gz 5DPF_WT_minus_S21_L001_R2_001.fastq.gz,fastq fastq fastq,8634577600.0,67988800.0,GSM7680084 r1,0:8 1:28 2:91,A:1833391508;C:1279550998;G:1408086737;T:1665829499;N:122058,8,28,91,,1833391508,1279550998,1408086737,1665829499,122058,SRX21240519,SRS18495442,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.92,,0.2485,,0.75552,,0.51753,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24831,SRR25509983,SRX21240519,SRS18495442,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq,GSM7680084,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680084,GSM7680084: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680084 r1,GSM7680084,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,5DPF_WT_minus_S21_L002_I1_001.fastq.gz 5DPF_WT_minus_S21_L002_R1_001.fastq.gz 5DPF_WT_minus_S21_L002_R2_001.fastq.gz,fastq fastq fastq,8644279892.0,68065196.0,GSM7680084 r2,0:8 1:28 2:91,A:1835831383;C:1280886675;G:1409188624;T:1667919807;N:106347,8,28,91,,1835831383,1280886675,1409188624,1667919807,106347,SRX21240519,SRS18495442,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91942,,0.24867,,0.75396,,0.52058,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24832,SRR25509984,SRX21240519,SRS18495442,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq,GSM7680084,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680084,GSM7680084: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680084 r1,GSM7680084,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,5DPF_WT_minus_S22_L001_R2_001.fastq.gz 5DPF_WT_minus_S22_L001_R1_001.fastq.gz 5DPF_WT_minus_S22_L001_I1_001.fastq.gz,fastq fastq fastq,6144243998.0,48379874.0,GSM7680084 r3,0:8 1:28 2:91,A:1307018689;C:910675193;G:999334562;T:1185454346;N:85744,8,28,91,,1307018689,910675193,999334562,1185454346,85744,SRX21240519,SRS18495442,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91944,,0.2505,,0.75538,,0.5154,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24833,SRR25509985,SRX21240519,SRS18495442,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq,GSM7680084,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680084,GSM7680084: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680084 r1,GSM7680084,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,5DPF_WT_minus_S22_L002_I1_001.fastq.gz 5DPF_WT_minus_S22_L002_R1_001.fastq.gz 5DPF_WT_minus_S22_L002_R2_001.fastq.gz,fastq fastq fastq,6161162938.0,48513094.0,GSM7680084 r4,0:8 1:28 2:91,A:1310818438;C:913067206;G:1001801994;T:1188928241;N:75675,8,28,91,,1310818438,913067206,1001801994,1188928241,75675,SRX21240519,SRS18495442,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91847,,0.24895,,0.75483,,0.52092,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24834,SRR25509986,SRX21240519,SRS18495442,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq,GSM7680084,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680084,GSM7680084: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680084 r1,GSM7680084,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,5DPF_WT_minus_S23_L001_I1_001.fastq.gz 5DPF_WT_minus_S23_L001_R1_001.fastq.gz 5DPF_WT_minus_S23_L001_R2_001.fastq.gz,fastq fastq fastq,6893652075.0,54280725.0,GSM7680084 r5,0:8 1:28 2:91,A:1466387768;C:1021460104;G:1123606745;T:1327994370;N:96988,8,28,91,,1466387768,1021460104,1123606745,1327994370,96988,SRX21240519,SRS18495442,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.92042,,0.24759,,0.75663,,0.51662,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24835,SRR25509987,SRX21240519,SRS18495442,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq,GSM7680084,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680084,GSM7680084: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680084 r1,GSM7680084,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,5DPF_WT_minus_S23_L002_R1_001.fastq.gz 5DPF_WT_minus_S23_L002_R2_001.fastq.gz 5DPF_WT_minus_S23_L002_I1_001.fastq.gz,fastq fastq fastq,6907881409.0,54392767.0,GSM7680084 r6,0:8 1:28 2:91,A:1469526451;C:1023529399;G:1125771813;T:1330830542;N:83592,8,28,91,,1469526451,1023529399,1125771813,1330830542,83592,SRX21240519,SRS18495442,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91879,,0.24904,,0.75479,,0.52175,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24836,SRR25509988,SRX21240519,SRS18495442,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq,GSM7680084,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680084,GSM7680084: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680084 r1,GSM7680084,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,5DPF_WT_minus_S24_L001_R2_001.fastq.gz 5DPF_WT_minus_S24_L001_R1_001.fastq.gz 5DPF_WT_minus_S24_L001_I1_001.fastq.gz,fastq fastq fastq,6155284362.0,48466806.0,GSM7680084 r7,0:8 1:28 2:91,A:1309788155;C:909805561;G:1001863122;T:1188939208;N:83300,8,28,91,,1309788155,909805561,1001863122,1188939208,83300,SRX21240519,SRS18495442,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91932,,0.252,,0.7541,,0.52096,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
24837,SRR25509989,SRX21240519,SRS18495442,SRP453227,PRJNA1001940,Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed,GSE240026,Transcriptome Analysis,Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease  but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish  we identify novel and conserved molecular signatures for MN functional subtypes  and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants  we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors  Prdm16 and Mecom  are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT  prdm16 /   and mecom  /  zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal  then analyzed using scRNAseq.,,pubmed:37676768,,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq,GSM7680084,,source name:tail|tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing,Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files,tail,,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:tail|genotype:olig2:dsRed  prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs,GSM7680084,GSM7680084: Spinal cord MNs  olig2dsRed  prdm16:gal4UASGFP    5dpf  scRNAseq; Danio rerio; RNA Seq,GSM7680084 r1,GSM7680084,1,DsRed positive cells were isolated from 2 dpf or 5 dpf control  mecom mutant  or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade  dissociated using papain  filtered  and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP   DsRed2   and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453227,,loader:fastq load.py,5DPF_WT_minus_S24_L002_I1_001.fastq.gz 5DPF_WT_minus_S24_L002_R1_001.fastq.gz 5DPF_WT_minus_S24_L002_R2_001.fastq.gz,fastq fastq fastq,6165991605.0,48551115.0,GSM7680084 r8,0:8 1:28 2:91,A:1312424825;C:911081786;G:1003163970;T:1191408145;N:72739,8,28,91,,1312424825,911081786,1003163970,1191408145,72739,SRX21240519,SRS18495442,SRA1686067,"Dasen, Neuroscience Institute, New York University Grossman School of Medicine","Dasen, Neuroscience Institute, New York University Grossman School of Medicine",1,0.91842,,0.24989,,0.75542,,0.51918,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-03,Larval,Larval,Tail,Multi-system
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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