run_metadata
804 rows where tissue_curation = "Tail" and tissue_curation_coarse = "Multi-system"
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| Link | rowid ▼ | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 24790 | 24790 | SRR25509944 | SRX21240524 | SRS18495447 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq | GSM7680083 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680083 | GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680083 r1 | GSM7680083 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | 5DPF_WT_plus_S17_L001_R2_001.fastq.gz 5DPF_WT_plus_S17_L001_R1_001.fastq.gz 5DPF_WT_plus_S17_L001_I1_001.fastq.gz | fastq fastq fastq | 5999080077.0 | 47236851.0 | GSM7680083 r1 | 0:8 1:28 2:91 | A:1212144705;C:959823109;G:1045323833;T:1081182723;N:79071 | 8 | 28 | 91 | 1212144705 | 959823109 | 1045323833 | 1081182723 | 79071 | SRX21240524 | SRS18495447 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91673 | 0.11695 | 0.77481 | 0.51165 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24791 | 24791 | SRR25509945 | SRX21240524 | SRS18495447 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq | GSM7680083 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680083 | GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680083 r1 | GSM7680083 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | 5DPF_WT_plus_S17_L002_R2_001.fastq.gz 5DPF_WT_plus_S17_L002_R1_001.fastq.gz 5DPF_WT_plus_S17_L002_I1_001.fastq.gz | fastq fastq fastq | 6012350180.0 | 47341340.0 | GSM7680083 r2 | 0:8 1:28 2:91 | A:1215185110;C:961739027;G:1047332997;T:1083733742;N:71064 | 8 | 28 | 91 | 1215185110 | 961739027 | 1047332997 | 1083733742 | 71064 | SRX21240524 | SRS18495447 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91842 | 0.11714 | 0.7763 | 0.51731 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24792 | 24792 | SRR25509946 | SRX21240524 | SRS18495447 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq | GSM7680083 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680083 | GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680083 r1 | GSM7680083 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | 5DPF_WT_plus_S18_L001_R2_001.fastq.gz 5DPF_WT_plus_S18_L001_R1_001.fastq.gz 5DPF_WT_plus_S18_L001_I1_001.fastq.gz | fastq fastq fastq | 4990947473.0 | 39298799.0 | GSM7680083 r3 | 0:8 1:28 2:91 | A:1007619958;C:800073636;G:871756682;T:896670984;N:69449 | 8 | 28 | 91 | 1007619958 | 800073636 | 871756682 | 896670984 | 69449 | SRX21240524 | SRS18495447 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91717 | 0.11737 | 0.7767 | 0.51879 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24793 | 24793 | SRR25509947 | SRX21240524 | SRS18495447 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq | GSM7680083 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680083 | GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680083 r1 | GSM7680083 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | 5DPF_WT_plus_S18_L002_I1_001.fastq.gz 5DPF_WT_plus_S18_L002_R1_001.fastq.gz 5DPF_WT_plus_S18_L002_R2_001.fastq.gz | fastq fastq fastq | 4994343707.0 | 39325541.0 | GSM7680083 r4 | 0:8 1:28 2:91 | A:1008545361;C:800479170;G:872044753;T:897494026;N:60921 | 8 | 28 | 91 | 1008545361 | 800479170 | 872044753 | 897494026 | 60921 | SRX21240524 | SRS18495447 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.9173 | 0.11671 | 0.778 | 0.51414 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24794 | 24794 | SRR25509948 | SRX21240524 | SRS18495447 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq | GSM7680083 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680083 | GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680083 r1 | GSM7680083 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | 5DPF_WT_plus_S20_L001_R2_001.fastq.gz 5DPF_WT_plus_S20_L001_R1_001.fastq.gz 5DPF_WT_plus_S20_L001_I1_001.fastq.gz | fastq fastq fastq | 4150807675.0 | 32683525.0 | GSM7680083 r7 | 0:8 1:28 2:91 | A:839301254;C:665476121;G:723277159;T:746089009;N:57232 | 8 | 28 | 91 | 839301254 | 665476121 | 723277159 | 746089009 | 57232 | SRX21240524 | SRS18495447 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91704 | 0.11665 | 0.77589 | 0.51231 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24795 | 24795 | SRR25509949 | SRX21240524 | SRS18495447 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq | GSM7680083 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680083 | GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680083 r1 | GSM7680083 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | 5DPF_WT_plus_S20_L002_R2_001.fastq.gz 5DPF_WT_plus_S20_L002_R1_001.fastq.gz 5DPF_WT_plus_S20_L002_I1_001.fastq.gz | fastq fastq fastq | 4152701499.0 | 32698437.0 | GSM7680083 r8 | 0:8 1:28 2:91 | A:839837413;C:665793367;G:723399518;T:746476220;N:51249 | 8 | 28 | 91 | 839837413 | 665793367 | 723399518 | 746476220 | 51249 | SRX21240524 | SRS18495447 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91769 | 0.11677 | 0.77473 | 0.5172 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24796 | 24796 | SRR25510006 | SRX21240524 | SRS18495447 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq | GSM7680083 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680083 | GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680083 r1 | GSM7680083 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | 5DPF_WT_plus_S19_L001_I1_001.fastq.gz 5DPF_WT_plus_S19_L001_R1_001.fastq.gz 5DPF_WT_plus_S19_L001_R2_001.fastq.gz | fastq fastq fastq | 5570139228.0 | 43859364.0 | GSM7680083 r5 | 0:8 1:28 2:91 | A:1124433319;C:892106407;G:974065175;T:1000519772;N:77451 | 8 | 28 | 91 | 1124433319 | 892106407 | 974065175 | 1000519772 | 77451 | SRX21240524 | SRS18495447 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.9181 | 0.11708 | 0.77725 | 0.506 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24797 | 24797 | SRR25510007 | SRX21240524 | SRS18495447 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq | GSM7680083 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680083 | GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680083 r1 | GSM7680083 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | 5DPF_WT_plus_S19_L002_R2_001.fastq.gz 5DPF_WT_plus_S19_L002_R1_001.fastq.gz 5DPF_WT_plus_S19_L002_I1_001.fastq.gz | fastq fastq fastq | 5568879134.0 | 43849442.0 | GSM7680083 r6 | 0:8 1:28 2:91 | A:1124462080;C:891765530;G:973382320;T:1000621312;N:67980 | 8 | 28 | 91 | 1124462080 | 891765530 | 973382320 | 1000621312 | 67980 | SRX21240524 | SRS18495447 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91836 | 0.11752 | 0.77786 | 0.49118 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24798 | 24798 | SRR25509950 | SRX21240523 | SRS18495446 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq | GSM7680088 | source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680088 | GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680088 r1 | GSM7680088 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | MECOM_minus_S29_L001_I1_001.fastq.gz MECOM_minus_S29_L001_R1_001.fastq.gz MECOM_minus_S29_L001_R2_001.fastq.gz | fastq fastq fastq | 6472457718.0 | 50964234.0 | GSM7680088 r1 | 0:8 1:28 2:91 | A:1374177983;C:969847712;G:1063043909;T:1230585953;N:89737 | 8 | 28 | 91 | 1374177983 | 969847712 | 1063043909 | 1230585953 | 89737 | SRX21240523 | SRS18495446 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91899 | 0.23002 | 0.75597 | 0.50918 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24799 | 24799 | SRR25509951 | SRX21240523 | SRS18495446 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq | GSM7680088 | source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680088 | GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680088 r1 | GSM7680088 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | MECOM_minus_S29_L002_I1_001.fastq.gz MECOM_minus_S29_L002_R1_001.fastq.gz MECOM_minus_S29_L002_R2_001.fastq.gz | fastq fastq fastq | 6479801747.0 | 51022061.0 | GSM7680088 r2 | 0:8 1:28 2:91 | A:1375879660;C:970771702;G:1064110805;T:1232166662;N:78722 | 8 | 28 | 91 | 1375879660 | 970771702 | 1064110805 | 1232166662 | 78722 | SRX21240523 | SRS18495446 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91932 | 0.23011 | 0.75666 | 0.50726 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24800 | 24800 | SRR25509952 | SRX21240523 | SRS18495446 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq | GSM7680088 | source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680088 | GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680088 r1 | GSM7680088 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | MECOM_minus_S30_L001_I1_001.fastq.gz MECOM_minus_S30_L001_R1_001.fastq.gz MECOM_minus_S30_L001_R2_001.fastq.gz | fastq fastq fastq | 6055044278.0 | 47677514.0 | GSM7680088 r3 | 0:8 1:28 2:91 | A:1285162347;C:907248700;G:995411468;T:1150745942;N:85317 | 8 | 28 | 91 | 1285162347 | 907248700 | 995411468 | 1150745942 | 85317 | SRX21240523 | SRS18495446 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91771 | 0.2306 | 0.75799 | 0.51641 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24801 | 24801 | SRR25509953 | SRX21240523 | SRS18495446 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq | GSM7680088 | source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680088 | GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680088 r1 | GSM7680088 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | MECOM_minus_S30_L002_I1_001.fastq.gz MECOM_minus_S30_L002_R1_001.fastq.gz MECOM_minus_S30_L002_R2_001.fastq.gz | fastq fastq fastq | 6065969453.0 | 47763539.0 | GSM7680088 r4 | 0:8 1:28 2:91 | A:1287814805;C:908939739;G:996849881;T:1152803356;N:74268 | 8 | 28 | 91 | 1287814805 | 908939739 | 996849881 | 1152803356 | 74268 | SRX21240523 | SRS18495446 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91856 | 0.23244 | 0.75844 | 0.51273 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24802 | 24802 | SRR25509954 | SRX21240523 | SRS18495446 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq | GSM7680088 | source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680088 | GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680088 r1 | GSM7680088 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | MECOM_minus_S31_L001_I1_001.fastq.gz MECOM_minus_S31_L001_R1_001.fastq.gz MECOM_minus_S31_L001_R2_001.fastq.gz | fastq fastq fastq | 5279309101.0 | 41569363.0 | GSM7680088 r5 | 0:8 1:28 2:91 | A:1122213686;C:789300425;G:868235888;T:1002988275;N:73759 | 8 | 28 | 91 | 1122213686 | 789300425 | 868235888 | 1002988275 | 73759 | SRX21240523 | SRS18495446 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91638 | 0.23107 | 0.75795 | 0.51508 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24803 | 24803 | SRR25509955 | SRX21240523 | SRS18495446 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq | GSM7680088 | source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680088 | GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680088 r1 | GSM7680088 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | MECOM_minus_S31_L002_I1_001.fastq.gz MECOM_minus_S31_L002_R1_001.fastq.gz MECOM_minus_S31_L002_R2_001.fastq.gz | fastq fastq fastq | 5282579605.0 | 41595115.0 | GSM7680088 r6 | 0:8 1:28 2:91 | A:1123052612;C:789776127;G:868371205;T:1003891470;N:64051 | 8 | 28 | 91 | 1123052612 | 789776127 | 868371205 | 1003891470 | 64051 | SRX21240523 | SRS18495446 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91687 | 0.23155 | 0.75653 | 0.51167 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24804 | 24804 | SRR25509956 | SRX21240523 | SRS18495446 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq | GSM7680088 | source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680088 | GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680088 r1 | GSM7680088 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | MECOM_minus_S32_L001_I1_001.fastq.gz MECOM_minus_S32_L001_R1_001.fastq.gz MECOM_minus_S32_L001_R2_001.fastq.gz | fastq fastq fastq | 5155833986.0 | 40597118.0 | GSM7680088 r7 | 0:8 1:28 2:91 | A:1096166065;C:771837218;G:846468036;T:979794053;N:72366 | 8 | 28 | 91 | 1096166065 | 771837218 | 846468036 | 979794053 | 72366 | SRX21240523 | SRS18495446 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91864 | 0.23062 | 0.75783 | 0.5144 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24805 | 24805 | SRR25509957 | SRX21240523 | SRS18495446 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq | GSM7680088 | source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680088 | GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680088 r1 | GSM7680088 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | MECOM_minus_S32_L002_I1_001.fastq.gz MECOM_minus_S32_L002_R1_001.fastq.gz MECOM_minus_S32_L002_R2_001.fastq.gz | fastq fastq fastq | 5158852395.0 | 40620885.0 | GSM7680088 r8 | 0:8 1:28 2:91 | A:1096925078;C:772260867;G:846795917;T:980455576;N:63097 | 8 | 28 | 91 | 1096925078 | 772260867 | 846795917 | 980455576 | 63097 | SRX21240523 | SRS18495446 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91859 | 0.23143 | 0.75921 | 0.51192 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24806 | 24806 | SRR25509958 | SRX21240522 | SRS18495445 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq | GSM7680087 | source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680087 | GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680087 r1 | GSM7680087 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | PRDM16-GFP_S1_L001_I1_001.fastq.gz PRDM16-GFP_S1_L001_R1_001.fastq.gz PRDM16-GFP_S1_L001_R2_001.fastq.gz | fastq fastq fastq | 7339736654.0 | 57793202.0 | GSM7680087 r1 | 0:8 1:28 2:91 | A:1557377528;C:1077119414;G:1156228317;T:1468352980;N:103143 | 8 | 28 | 91 | 1557377528 | 1077119414 | 1156228317 | 1468352980 | 103143 | SRX21240522 | SRS18495445 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91516 | 0.25902 | 0.74255 | 0.49922 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24807 | 24807 | SRR25509959 | SRX21240522 | SRS18495445 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq | GSM7680087 | source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680087 | GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680087 r1 | GSM7680087 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | PRDM16-GFP_S1_L002_I1_001.fastq.gz PRDM16-GFP_S1_L002_R1_001.fastq.gz PRDM16-GFP_S1_L002_R2_001.fastq.gz | fastq fastq fastq | 7410090336.0 | 58347168.0 | GSM7680087 r2 | 0:8 1:28 2:91 | A:1569421640;C:1090998538;G:1171253819;T:1477822651;N:95640 | 8 | 28 | 91 | 1569421640 | 1090998538 | 1171253819 | 1477822651 | 95640 | SRX21240522 | SRS18495445 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91462 | 0.25846 | 0.74215 | 0.49672 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24808 | 24808 | SRR25509960 | SRX21240522 | SRS18495445 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq | GSM7680087 | source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680087 | GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680087 r1 | GSM7680087 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | PRDM16-GFP_S2_L001_I1_001.fastq.gz PRDM16-GFP_S2_L001_R1_001.fastq.gz PRDM16-GFP_S2_L001_R2_001.fastq.gz | fastq fastq fastq | 7620847217.0 | 60006671.0 | GSM7680087 r3 | 0:8 1:28 2:91 | A:1615026295;C:1121044318;G:1201364994;T:1523062938;N:108516 | 8 | 28 | 91 | 1615026295 | 1121044318 | 1201364994 | 1523062938 | 108516 | SRX21240522 | SRS18495445 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91495 | 0.26021 | 0.74188 | 0.49871 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24809 | 24809 | SRR25509961 | SRX21240522 | SRS18495445 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq | GSM7680087 | source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680087 | GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680087 r1 | GSM7680087 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | PRDM16-GFP_S2_L002_I1_001.fastq.gz PRDM16-GFP_S2_L002_R1_001.fastq.gz PRDM16-GFP_S2_L002_R2_001.fastq.gz | fastq fastq fastq | 7658170739.0 | 60300557.0 | GSM7680087 r4 | 0:8 1:28 2:91 | A:1620018228;C:1130072970;G:1211145212;T:1526013817;N:100460 | 8 | 28 | 91 | 1620018228 | 1130072970 | 1211145212 | 1526013817 | 100460 | SRX21240522 | SRS18495445 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.9153 | 0.25733 | 0.74406 | 0.49822 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24810 | 24810 | SRR25509962 | SRX21240522 | SRS18495445 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq | GSM7680087 | source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680087 | GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680087 r1 | GSM7680087 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | PRDM16-GFP_S3_L001_I1_001.fastq.gz PRDM16-GFP_S3_L001_R1_001.fastq.gz PRDM16-GFP_S3_L001_R2_001.fastq.gz | fastq fastq fastq | 7520150568.0 | 59213784.0 | GSM7680087 r5 | 0:8 1:28 2:91 | A:1592224470;C:1104917106;G:1187483622;T:1503722424;N:106722 | 8 | 28 | 91 | 1592224470 | 1104917106 | 1187483622 | 1503722424 | 106722 | SRX21240522 | SRS18495445 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91528 | 0.25852 | 0.74168 | 0.50087 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24811 | 24811 | SRR25509963 | SRX21240522 | SRS18495445 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq | GSM7680087 | source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680087 | GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680087 r1 | GSM7680087 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | PRDM16-GFP_S3_L002_I1_001.fastq.gz PRDM16-GFP_S3_L002_R1_001.fastq.gz PRDM16-GFP_S3_L002_R2_001.fastq.gz | fastq fastq fastq | 7547416198.0 | 59428474.0 | GSM7680087 r6 | 0:8 1:28 2:91 | A:1595335949;C:1112405532;G:1195632258;T:1504519719;N:97676 | 8 | 28 | 91 | 1595335949 | 1112405532 | 1195632258 | 1504519719 | 97676 | SRX21240522 | SRS18495445 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91572 | 0.25684 | 0.74227 | 0.49429 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24812 | 24812 | SRR25509964 | SRX21240522 | SRS18495445 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq | GSM7680087 | source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680087 | GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680087 r1 | GSM7680087 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | PRDM16-GFP_S4_L001_I1_001.fastq.gz PRDM16-GFP_S4_L001_R1_001.fastq.gz PRDM16-GFP_S4_L001_R2_001.fastq.gz | fastq fastq fastq | 6203887389.0 | 48849507.0 | GSM7680087 r7 | 0:8 1:28 2:91 | A:1315023626;C:910416020;G:979167464;T:1240610297;N:87730 | 8 | 28 | 91 | 1315023626 | 910416020 | 979167464 | 1240610297 | 87730 | SRX21240522 | SRS18495445 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91294 | 0.25905 | 0.74426 | 0.49642 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24813 | 24813 | SRR25509965 | SRX21240522 | SRS18495445 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq | GSM7680087 | source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680087 | GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680087 r1 | GSM7680087 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | PRDM16-GFP_S4_L002_I1_001.fastq.gz PRDM16-GFP_S4_L002_R1_001.fastq.gz PRDM16-GFP_S4_L002_R2_001.fastq.gz | fastq fastq fastq | 6164249419.0 | 48537397.0 | GSM7680087 r8 | 0:8 1:28 2:91 | A:1303982345;C:907803673;G:976227040;T:1228810005;N:80064 | 8 | 28 | 91 | 1303982345 | 907803673 | 976227040 | 1228810005 | 80064 | SRX21240522 | SRS18495445 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91422 | 0.25666 | 0.74383 | 0.49596 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24814 | 24814 | SRR25509966 | SRX21240521 | SRS18495444 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq | GSM7680086 | source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680086 | GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680086 r1 | GSM7680086 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | MECOM_plus_S25_L001_I1_001.fastq.gz MECOM_plus_S25_L001_R1_001.fastq.gz MECOM_plus_S25_L001_R2_001.fastq.gz | fastq fastq fastq | 2154821446.0 | 16967098.0 | GSM7680086 r1 | 0:8 1:28 2:91 | A:451330902;C:339756831;G:379343350;T:373544930;N:29905 | 8 | 28 | 91 | 451330902 | 339756831 | 379343350 | 373544930 | 29905 | SRX21240521 | SRS18495444 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91882 | 0.142 | 0.78299 | 0.51956 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24815 | 24815 | SRR25509967 | SRX21240521 | SRS18495444 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq | GSM7680086 | source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680086 | GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680086 r1 | GSM7680086 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | MECOM_plus_S25_L002_I1_001.fastq.gz MECOM_plus_S25_L002_R1_001.fastq.gz MECOM_plus_S25_L002_R2_001.fastq.gz | fastq fastq fastq | 2158219204.0 | 16993852.0 | GSM7680086 r2 | 0:8 1:28 2:91 | A:452280625;C:340228509;G:379707034;T:374197697;N:26667 | 8 | 28 | 91 | 452280625 | 340228509 | 379707034 | 374197697 | 26667 | SRX21240521 | SRS18495444 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91895 | 0.1417 | 0.78279 | 0.51981 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24816 | 24816 | SRR25509968 | SRX21240521 | SRS18495444 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq | GSM7680086 | source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680086 | GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680086 r1 | GSM7680086 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | MECOM_plus_S26_L001_I1_001.fastq.gz MECOM_plus_S26_L001_R1_001.fastq.gz MECOM_plus_S26_L001_R2_001.fastq.gz | fastq fastq fastq | 2361287251.0 | 18592813.0 | GSM7680086 r3 | 0:8 1:28 2:91 | A:492891294;C:373079069;G:416862992;T:409079819;N:32809 | 8 | 28 | 91 | 492891294 | 373079069 | 416862992 | 409079819 | 32809 | SRX21240521 | SRS18495444 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.92068 | 0.13997 | 0.78516 | 0.50532 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24817 | 24817 | SRR25509969 | SRX21240521 | SRS18495444 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq | GSM7680086 | source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680086 | GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680086 r1 | GSM7680086 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | MECOM_plus_S26_L002_I1_001.fastq.gz MECOM_plus_S26_L002_R1_001.fastq.gz MECOM_plus_S26_L002_R2_001.fastq.gz | fastq fastq fastq | 2362115545.0 | 18599335.0 | GSM7680086 r4 | 0:8 1:28 2:91 | A:493282758;C:373220256;G:416785305;T:409222388;N:28778 | 8 | 28 | 91 | 493282758 | 373220256 | 416785305 | 409222388 | 28778 | SRX21240521 | SRS18495444 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.92013 | 0.14129 | 0.78468 | 0.52049 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24818 | 24818 | SRR25509970 | SRX21240521 | SRS18495444 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq | GSM7680086 | source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680086 | GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680086 r1 | GSM7680086 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | MECOM_plus_S27_L001_I1_001.fastq.gz MECOM_plus_S27_L001_R1_001.fastq.gz MECOM_plus_S27_L001_R2_001.fastq.gz | fastq fastq fastq | 2093107066.0 | 16481158.0 | GSM7680086 r5 | 0:8 1:28 2:91 | A:438295698;C:330083473;G:369094473;T:362282989;N:28745 | 8 | 28 | 91 | 438295698 | 330083473 | 369094473 | 362282989 | 28745 | SRX21240521 | SRS18495444 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91759 | 0.13991 | 0.78354 | 0.51917 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24819 | 24819 | SRR25509971 | SRX21240521 | SRS18495444 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq | GSM7680086 | source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680086 | GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680086 r1 | GSM7680086 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | MECOM_plus_S27_L002_R2_001.fastq.gz MECOM_plus_S27_L002_R1_001.fastq.gz MECOM_plus_S27_L002_I1_001.fastq.gz | fastq fastq fastq | 2095025401.0 | 16496263.0 | GSM7680086 r6 | 0:8 1:28 2:91 | A:438926470;C:330300198;G:369243520;T:362664613;N:25132 | 8 | 28 | 91 | 438926470 | 330300198 | 369243520 | 362664613 | 25132 | SRX21240521 | SRS18495444 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91795 | 0.14216 | 0.78151 | 0.5067 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24820 | 24820 | SRR25509972 | SRX21240521 | SRS18495444 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq | GSM7680086 | source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680086 | GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680086 r1 | GSM7680086 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | MECOM_plus_S28_L001_R2_001.fastq.gz MECOM_plus_S28_L001_R1_001.fastq.gz MECOM_plus_S28_L001_I1_001.fastq.gz | fastq fastq fastq | 1722573390.0 | 13563570.0 | GSM7680086 r7 | 0:8 1:28 2:91 | A:360865837;C:272246731;G:303643951;T:297504190;N:24161 | 8 | 28 | 91 | 360865837 | 272246731 | 303643951 | 297504190 | 24161 | SRX21240521 | SRS18495444 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91897 | 0.13999 | 0.78648 | 0.49913 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24821 | 24821 | SRR25509973 | SRX21240521 | SRS18495444 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq | GSM7680086 | source name:tail|tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed mecom / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680086 | GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680086 r1 | GSM7680086 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | MECOM_plus_S28_L002_I1_001.fastq.gz MECOM_plus_S28_L002_R1_001.fastq.gz MECOM_plus_S28_L002_R2_001.fastq.gz | fastq fastq fastq | 1724036303.0 | 13575089.0 | GSM7680086 r8 | 0:8 1:28 2:91 | A:361391368;C:272402118;G:303699423;T:297819212;N:20978 | 8 | 28 | 91 | 361391368 | 272402118 | 303699423 | 297819212 | 20978 | SRX21240521 | SRS18495444 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.92182 | 0.14094 | 0.78326 | 0.50699 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24822 | 24822 | SRR25509974 | SRX21240520 | SRS18495443 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq | GSM7680085 | source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680085 | GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680085 r1 | GSM7680085 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | PRDM16plusGFP_S5_L001_R2_001.fastq.gz PRDM16plusGFP_S5_L001_R1_001.fastq.gz PRDM16plusGFP_S5_L001_I1_001.fastq.gz | fastq fastq fastq | 8567717053.0 | 67462339.0 | GSM7680085 r1 | 0:8 1:28 2:91 | A:1758073165;C:1341216272;G:1446728174;T:1592934812;N:120426 | 8 | 28 | 91 | 1758073165 | 1341216272 | 1446728174 | 1592934812 | 120426 | SRX21240520 | SRS18495443 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.90663 | 0.17669 | 0.75812 | 0.50234 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24823 | 24823 | SRR25509975 | SRX21240520 | SRS18495443 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq | GSM7680085 | source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680085 | GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680085 r1 | GSM7680085 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | PRDM16plusGFP_S5_L002_R2_001.fastq.gz PRDM16plusGFP_S5_L002_R1_001.fastq.gz PRDM16plusGFP_S5_L002_I1_001.fastq.gz | fastq fastq fastq | 8694310526.0 | 68459138.0 | GSM7680085 r2 | 0:8 1:28 2:91 | A:1780912602;C:1365177337;G:1472402153;T:1611176829;N:112637 | 8 | 28 | 91 | 1780912602 | 1365177337 | 1472402153 | 1611176829 | 112637 | SRX21240520 | SRS18495443 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.90543 | 0.17508 | 0.76019 | 0.51005 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24824 | 24824 | SRR25509976 | SRX21240520 | SRS18495443 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq | GSM7680085 | source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680085 | GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680085 r1 | GSM7680085 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | PRDM16plusGFP_S6_L001_R2_001.fastq.gz PRDM16plusGFP_S6_L001_R1_001.fastq.gz PRDM16plusGFP_S6_L001_I1_001.fastq.gz | fastq fastq fastq | 9112215456.0 | 71749728.0 | GSM7680085 r3 | 0:8 1:28 2:91 | A:1868388882;C:1426817380;G:1540502920;T:1693385950;N:130116 | 8 | 28 | 91 | 1868388882 | 1426817380 | 1540502920 | 1693385950 | 130116 | SRX21240520 | SRS18495443 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.90763 | 0.17756 | 0.76102 | 0.50457 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24825 | 24825 | SRR25509977 | SRX21240520 | SRS18495443 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq | GSM7680085 | source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680085 | GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680085 r1 | GSM7680085 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | PRDM16plusGFP_S6_L002_I1_001.fastq.gz PRDM16plusGFP_S6_L002_R1_001.fastq.gz PRDM16plusGFP_S6_L002_R2_001.fastq.gz | fastq fastq fastq | 9170568781.0 | 72209203.0 | GSM7680085 r4 | 0:8 1:28 2:91 | A:1876786596;C:1440704341;G:1555176461;T:1698251178;N:118897 | 8 | 28 | 91 | 1876786596 | 1440704341 | 1555176461 | 1698251178 | 118897 | SRX21240520 | SRS18495443 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.9062 | 0.17617 | 0.76203 | 0.49732 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24826 | 24826 | SRR25509978 | SRX21240520 | SRS18495443 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq | GSM7680085 | source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680085 | GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680085 r1 | GSM7680085 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | PRDM16plusGFP_S7_L001_R2_001.fastq.gz PRDM16plusGFP_S7_L001_R1_001.fastq.gz PRDM16plusGFP_S7_L001_I1_001.fastq.gz | fastq fastq fastq | 96282510.0 | 758130.0 | GSM7680085 r5 | 0:8 1:28 2:91 | A:19884451;C:15070058;G:16206702;T:17827293;N:1326 | 8 | 28 | 91 | 19884451 | 15070058 | 16206702 | 17827293 | 1326 | SRX21240520 | SRS18495443 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.76071 | 0.14671 | 0.78064 | 0.49267 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24827 | 24827 | SRR25509979 | SRX21240520 | SRS18495443 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq | GSM7680085 | source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680085 | GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680085 r1 | GSM7680085 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | PRDM16plusGFP_S7_L002_I1_001.fastq.gz PRDM16plusGFP_S7_L002_R2_001.fastq.gz PRDM16plusGFP_S7_L002_R1_001.fastq.gz | fastq fastq fastq | 96503236.0 | 759868.0 | GSM7680085 r6 | 0:8 1:28 2:91 | A:19898524;C:15152212;G:16290226;T:17805918;N:1108 | 8 | 28 | 91 | 19898524 | 15152212 | 16290226 | 17805918 | 1108 | SRX21240520 | SRS18495443 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.76382 | 0.1467 | 0.78508 | 0.48995 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24828 | 24828 | SRR25509980 | SRX21240520 | SRS18495443 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq | GSM7680085 | source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680085 | GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680085 r1 | GSM7680085 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | PRDM16plusGFP_S8_L001_I1_001.fastq.gz PRDM16plusGFP_S8_L001_R1_001.fastq.gz PRDM16plusGFP_S8_L001_R2_001.fastq.gz | fastq fastq fastq | 8873313978.0 | 69868614.0 | GSM7680085 r7 | 0:8 1:28 2:91 | A:1820893372;C:1390912026;G:1498935631;T:1647176605;N:126240 | 8 | 28 | 91 | 1820893372 | 1390912026 | 1498935631 | 1647176605 | 126240 | SRX21240520 | SRS18495443 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.90718 | 0.17603 | 0.76211 | 0.50458 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24829 | 24829 | SRR25509981 | SRX21240520 | SRS18495443 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq | GSM7680085 | source name:tail|tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680085 | GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680085 r1 | GSM7680085 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | PRDM16plusGFP_S8_L002_I1_001.fastq.gz PRDM16plusGFP_S8_L002_R1_001.fastq.gz PRDM16plusGFP_S8_L002_R2_001.fastq.gz | fastq fastq fastq | 8980314526.0 | 70711138.0 | GSM7680085 r8 | 0:8 1:28 2:91 | A:1839681468;C:1412028536;G:1521396962;T:1661490212;N:116380 | 8 | 28 | 91 | 1839681468 | 1412028536 | 1521396962 | 1661490212 | 116380 | SRX21240520 | SRS18495443 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.9078 | 0.17604 | 0.76037 | 0.47729 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24830 | 24830 | SRR25509982 | SRX21240519 | SRS18495442 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq | GSM7680084 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680084 | GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680084 r1 | GSM7680084 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | 5DPF_WT_minus_S21_L001_I1_001.fastq.gz 5DPF_WT_minus_S21_L001_R1_001.fastq.gz 5DPF_WT_minus_S21_L001_R2_001.fastq.gz | fastq fastq fastq | 8634577600.0 | 67988800.0 | GSM7680084 r1 | 0:8 1:28 2:91 | A:1833391508;C:1279550998;G:1408086737;T:1665829499;N:122058 | 8 | 28 | 91 | 1833391508 | 1279550998 | 1408086737 | 1665829499 | 122058 | SRX21240519 | SRS18495442 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.92 | 0.2485 | 0.75552 | 0.51753 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24831 | 24831 | SRR25509983 | SRX21240519 | SRS18495442 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq | GSM7680084 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680084 | GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680084 r1 | GSM7680084 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | 5DPF_WT_minus_S21_L002_I1_001.fastq.gz 5DPF_WT_minus_S21_L002_R1_001.fastq.gz 5DPF_WT_minus_S21_L002_R2_001.fastq.gz | fastq fastq fastq | 8644279892.0 | 68065196.0 | GSM7680084 r2 | 0:8 1:28 2:91 | A:1835831383;C:1280886675;G:1409188624;T:1667919807;N:106347 | 8 | 28 | 91 | 1835831383 | 1280886675 | 1409188624 | 1667919807 | 106347 | SRX21240519 | SRS18495442 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91942 | 0.24867 | 0.75396 | 0.52058 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24832 | 24832 | SRR25509984 | SRX21240519 | SRS18495442 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq | GSM7680084 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680084 | GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680084 r1 | GSM7680084 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | 5DPF_WT_minus_S22_L001_R2_001.fastq.gz 5DPF_WT_minus_S22_L001_R1_001.fastq.gz 5DPF_WT_minus_S22_L001_I1_001.fastq.gz | fastq fastq fastq | 6144243998.0 | 48379874.0 | GSM7680084 r3 | 0:8 1:28 2:91 | A:1307018689;C:910675193;G:999334562;T:1185454346;N:85744 | 8 | 28 | 91 | 1307018689 | 910675193 | 999334562 | 1185454346 | 85744 | SRX21240519 | SRS18495442 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91944 | 0.2505 | 0.75538 | 0.5154 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24833 | 24833 | SRR25509985 | SRX21240519 | SRS18495442 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq | GSM7680084 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680084 | GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680084 r1 | GSM7680084 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | 5DPF_WT_minus_S22_L002_I1_001.fastq.gz 5DPF_WT_minus_S22_L002_R1_001.fastq.gz 5DPF_WT_minus_S22_L002_R2_001.fastq.gz | fastq fastq fastq | 6161162938.0 | 48513094.0 | GSM7680084 r4 | 0:8 1:28 2:91 | A:1310818438;C:913067206;G:1001801994;T:1188928241;N:75675 | 8 | 28 | 91 | 1310818438 | 913067206 | 1001801994 | 1188928241 | 75675 | SRX21240519 | SRS18495442 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91847 | 0.24895 | 0.75483 | 0.52092 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24834 | 24834 | SRR25509986 | SRX21240519 | SRS18495442 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq | GSM7680084 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680084 | GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680084 r1 | GSM7680084 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | 5DPF_WT_minus_S23_L001_I1_001.fastq.gz 5DPF_WT_minus_S23_L001_R1_001.fastq.gz 5DPF_WT_minus_S23_L001_R2_001.fastq.gz | fastq fastq fastq | 6893652075.0 | 54280725.0 | GSM7680084 r5 | 0:8 1:28 2:91 | A:1466387768;C:1021460104;G:1123606745;T:1327994370;N:96988 | 8 | 28 | 91 | 1466387768 | 1021460104 | 1123606745 | 1327994370 | 96988 | SRX21240519 | SRS18495442 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.92042 | 0.24759 | 0.75663 | 0.51662 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24835 | 24835 | SRR25509987 | SRX21240519 | SRS18495442 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq | GSM7680084 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680084 | GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680084 r1 | GSM7680084 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | 5DPF_WT_minus_S23_L002_R1_001.fastq.gz 5DPF_WT_minus_S23_L002_R2_001.fastq.gz 5DPF_WT_minus_S23_L002_I1_001.fastq.gz | fastq fastq fastq | 6907881409.0 | 54392767.0 | GSM7680084 r6 | 0:8 1:28 2:91 | A:1469526451;C:1023529399;G:1125771813;T:1330830542;N:83592 | 8 | 28 | 91 | 1469526451 | 1023529399 | 1125771813 | 1330830542 | 83592 | SRX21240519 | SRS18495442 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91879 | 0.24904 | 0.75479 | 0.52175 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24836 | 24836 | SRR25509988 | SRX21240519 | SRS18495442 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq | GSM7680084 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680084 | GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680084 r1 | GSM7680084 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | 5DPF_WT_minus_S24_L001_R2_001.fastq.gz 5DPF_WT_minus_S24_L001_R1_001.fastq.gz 5DPF_WT_minus_S24_L001_I1_001.fastq.gz | fastq fastq fastq | 6155284362.0 | 48466806.0 | GSM7680084 r7 | 0:8 1:28 2:91 | A:1309788155;C:909805561;G:1001863122;T:1188939208;N:83300 | 8 | 28 | 91 | 1309788155 | 909805561 | 1001863122 | 1188939208 | 83300 | SRX21240519 | SRS18495442 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91932 | 0.252 | 0.7541 | 0.52096 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24837 | 24837 | SRR25509989 | SRX21240519 | SRS18495442 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq | GSM7680084 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:5dpf|cell type:Spinal cord MNs | GSM7680084 | GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq | GSM7680084 r1 | GSM7680084 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | 5DPF_WT_minus_S24_L002_I1_001.fastq.gz 5DPF_WT_minus_S24_L002_R1_001.fastq.gz 5DPF_WT_minus_S24_L002_R2_001.fastq.gz | fastq fastq fastq | 6165991605.0 | 48551115.0 | GSM7680084 r8 | 0:8 1:28 2:91 | A:1312424825;C:911081786;G:1003163970;T:1191408145;N:72739 | 8 | 28 | 91 | 1312424825 | 911081786 | 1003163970 | 1191408145 | 72739 | SRX21240519 | SRS18495442 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91842 | 0.24989 | 0.75542 | 0.51918 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Larval | Larval | Tail | Multi-system | ||||||||||||||||
| 24838 | 24838 | SRR25509990 | SRX21240518 | SRS18495441 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed 2dpf scRNAseq | GSM7680082 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed 2dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs | GSM7680082 | GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq | GSM7680082 r1 | GSM7680082 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | Kristen_10X_101620_S65_L001_I1_001.fastq.gz Kristen_10X_101620_S65_L001_R1_001.fastq.gz Kristen_10X_101620_S65_L001_R2_001.fastq.gz | fastq fastq fastq | 3327423622.0 | 26200186.0 | GSM7680082 r1 | 0:8 1:28 2:91 | A:693698335;C:494975421;G:540414923;T:654926705;N:201542 | 8 | 28 | 91 | 693698335 | 494975421 | 540414923 | 654926705 | 201542 | SRX21240518 | SRS18495441 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91351 | 0.22865 | 0.77723 | 0.49805 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Hatching | Embryo | Tail | Multi-system | ||||||||||||||||
| 24839 | 24839 | SRR25509991 | SRX21240518 | SRS18495441 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed 2dpf scRNAseq | GSM7680082 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed 2dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs | GSM7680082 | GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq | GSM7680082 r1 | GSM7680082 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | Kristen_10X_101620_S67_L002_I1_001.fastq.gz Kristen_10X_101620_S67_L002_R1_001.fastq.gz Kristen_10X_101620_S67_L002_R2_001.fastq.gz | fastq fastq fastq | 4430975390.0 | 34889570.0 | GSM7680082 r10 | 0:8 1:28 2:91 | A:923557751;C:658731986;G:718325003;T:874072049;N:264081 | 8 | 28 | 91 | 923557751 | 658731986 | 718325003 | 874072049 | 264081 | SRX21240518 | SRS18495441 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91797 | 0.22868 | 0.77863 | 0.50737 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Hatching | Embryo | Tail | Multi-system | ||||||||||||||||
| 24840 | 24840 | SRR25509992 | SRX21240518 | SRS18495441 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed 2dpf scRNAseq | GSM7680082 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed 2dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs | GSM7680082 | GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq | GSM7680082 r1 | GSM7680082 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | Kristen_10X_101620_S67_L003_I1_001.fastq.gz Kristen_10X_101620_S67_L003_R1_001.fastq.gz Kristen_10X_101620_S67_L003_R2_001.fastq.gz | fastq fastq fastq | 4429223552.0 | 34875776.0 | GSM7680082 r11 | 0:8 1:28 2:91 | A:923277621;C:658440918;G:718036099;T:873676803;N:264175 | 8 | 28 | 91 | 923277621 | 658440918 | 718036099 | 873676803 | 264175 | SRX21240518 | SRS18495441 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91753 | 0.22978 | 0.77942 | 0.50977 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Hatching | Embryo | Tail | Multi-system | ||||||||||||||||
| 24841 | 24841 | SRR25509993 | SRX21240518 | SRS18495441 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed 2dpf scRNAseq | GSM7680082 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed 2dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs | GSM7680082 | GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq | GSM7680082 r1 | GSM7680082 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | Kristen_10X_101620_S67_L004_I1_001.fastq.gz Kristen_10X_101620_S67_L004_R1_001.fastq.gz Kristen_10X_101620_S67_L004_R2_001.fastq.gz | fastq fastq fastq | 4549656890.0 | 35824070.0 | GSM7680082 r12 | 0:8 1:28 2:91 | A:950423951;C:673969790;G:734760168;T:900554096;N:282365 | 8 | 28 | 91 | 950423951 | 673969790 | 734760168 | 900554096 | 282365 | SRX21240518 | SRS18495441 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91687 | 0.23323 | 0.77932 | 0.50984 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Hatching | Embryo | Tail | Multi-system | ||||||||||||||||
| 24842 | 24842 | SRR25509994 | SRX21240518 | SRS18495441 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed 2dpf scRNAseq | GSM7680082 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed 2dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs | GSM7680082 | GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq | GSM7680082 r1 | GSM7680082 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | Kristen_10X_101620_S68_L001_I1_001.fastq.gz Kristen_10X_101620_S68_L001_R1_001.fastq.gz Kristen_10X_101620_S68_L001_R2_001.fastq.gz | fastq fastq fastq | 2696456634.0 | 21231942.0 | GSM7680082 r13 | 0:8 1:28 2:91 | A:562209710;C:401113540;G:437836456;T:530785441;N:161575 | 8 | 28 | 91 | 562209710 | 401113540 | 437836456 | 530785441 | 161575 | SRX21240518 | SRS18495441 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91384 | 0.22885 | 0.77912 | 0.50672 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Hatching | Embryo | Tail | Multi-system | ||||||||||||||||
| 24843 | 24843 | SRR25509995 | SRX21240518 | SRS18495441 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed 2dpf scRNAseq | GSM7680082 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed 2dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs | GSM7680082 | GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq | GSM7680082 r1 | GSM7680082 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | Kristen_10X_101620_S68_L002_I1_001.fastq.gz Kristen_10X_101620_S68_L002_R1_001.fastq.gz Kristen_10X_101620_S68_L002_R2_001.fastq.gz | fastq fastq fastq | 2735162932.0 | 21536716.0 | GSM7680082 r14 | 0:8 1:28 2:91 | A:570169460;C:406846839;G:443964376;T:538696359;N:164122 | 8 | 28 | 91 | 570169460 | 406846839 | 443964376 | 538696359 | 164122 | SRX21240518 | SRS18495441 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91691 | 0.22998 | 0.77942 | 0.51035 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Hatching | Embryo | Tail | Multi-system | ||||||||||||||||
| 24844 | 24844 | SRR25509996 | SRX21240518 | SRS18495441 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed 2dpf scRNAseq | GSM7680082 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed 2dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs | GSM7680082 | GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq | GSM7680082 r1 | GSM7680082 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | Kristen_10X_101620_S68_L003_I1_001.fastq.gz Kristen_10X_101620_S68_L003_R1_001.fastq.gz Kristen_10X_101620_S68_L003_R2_001.fastq.gz | fastq fastq fastq | 2739703563.0 | 21572469.0 | GSM7680082 r15 | 0:8 1:28 2:91 | A:571283074;C:407511119;G:444574049;T:539563747;N:162690 | 8 | 28 | 91 | 571283074 | 407511119 | 444574049 | 539563747 | 162690 | SRX21240518 | SRS18495441 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91526 | 0.22747 | 0.7793 | 0.51387 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Hatching | Embryo | Tail | Multi-system | ||||||||||||||||
| 24845 | 24845 | SRR25509997 | SRX21240518 | SRS18495441 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed 2dpf scRNAseq | GSM7680082 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed 2dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs | GSM7680082 | GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq | GSM7680082 r1 | GSM7680082 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | Kristen_10X_101620_S68_L004_I1_001.fastq.gz Kristen_10X_101620_S68_L004_R1_001.fastq.gz Kristen_10X_101620_S68_L004_R2_001.fastq.gz | fastq fastq fastq | 2828960433.0 | 22275279.0 | GSM7680082 r16 | 0:8 1:28 2:91 | A:591166850;C:419193897;G:457332081;T:559181603;N:175958 | 8 | 28 | 91 | 591166850 | 419193897 | 457332081 | 559181603 | 175958 | SRX21240518 | SRS18495441 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91651 | 0.23126 | 0.77613 | 0.50223 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Hatching | Embryo | Tail | Multi-system | ||||||||||||||||
| 24846 | 24846 | SRR25509998 | SRX21240518 | SRS18495441 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed 2dpf scRNAseq | GSM7680082 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed 2dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs | GSM7680082 | GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq | GSM7680082 r1 | GSM7680082 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | Kristen_10X_101620_S65_L002_I1_001.fastq.gz Kristen_10X_101620_S65_L002_R1_001.fastq.gz Kristen_10X_101620_S65_L002_R2_001.fastq.gz | fastq fastq fastq | 3374189340.0 | 26568420.0 | GSM7680082 r2 | 0:8 1:28 2:91 | A:703424426;C:501911907;G:547786373;T:664402117;N:201397 | 8 | 28 | 91 | 703424426 | 501911907 | 547786373 | 664402117 | 201397 | SRX21240518 | SRS18495441 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91522 | 0.22812 | 0.77753 | 0.50208 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Hatching | Embryo | Tail | Multi-system | ||||||||||||||||
| 24847 | 24847 | SRR25509999 | SRX21240518 | SRS18495441 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed 2dpf scRNAseq | GSM7680082 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed 2dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs | GSM7680082 | GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq | GSM7680082 r1 | GSM7680082 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | Kristen_10X_101620_S65_L003_I1_001.fastq.gz Kristen_10X_101620_S65_L003_R1_001.fastq.gz Kristen_10X_101620_S65_L003_R2_001.fastq.gz | fastq fastq fastq | 3383217516.0 | 26639508.0 | GSM7680082 r3 | 0:8 1:28 2:91 | A:705514047;C:503189161;G:549089218;T:666200894;N:201908 | 8 | 28 | 91 | 705514047 | 503189161 | 549089218 | 666200894 | 201908 | SRX21240518 | SRS18495441 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91535 | 0.23036 | 0.78078 | 0.50202 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Hatching | Embryo | Tail | Multi-system | ||||||||||||||||
| 24848 | 24848 | SRR25510000 | SRX21240518 | SRS18495441 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed 2dpf scRNAseq | GSM7680082 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed 2dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs | GSM7680082 | GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq | GSM7680082 r1 | GSM7680082 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | Kristen_10X_101620_S65_L004_I1_001.fastq.gz Kristen_10X_101620_S65_L004_R1_001.fastq.gz Kristen_10X_101620_S65_L004_R2_001.fastq.gz | fastq fastq fastq | 3493154050.0 | 27505150.0 | GSM7680082 r4 | 0:8 1:28 2:91 | A:729910298;C:517582902;G:564926384;T:690333365;N:215701 | 8 | 28 | 91 | 729910298 | 517582902 | 564926384 | 690333365 | 215701 | SRX21240518 | SRS18495441 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91569 | 0.22913 | 0.77873 | 0.50186 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Hatching | Embryo | Tail | Multi-system | ||||||||||||||||
| 24849 | 24849 | SRR25510001 | SRX21240518 | SRS18495441 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed 2dpf scRNAseq | GSM7680082 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed 2dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs | GSM7680082 | GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq | GSM7680082 r1 | GSM7680082 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | Kristen_10X_101620_S66_L001_I1_001.fastq.gz Kristen_10X_101620_S66_L001_R1_001.fastq.gz Kristen_10X_101620_S66_L001_R2_001.fastq.gz | fastq fastq fastq | 3237456187.0 | 25491781.0 | GSM7680082 r5 | 0:8 1:28 2:91 | A:674885196;C:481871349;G:525642933;T:637154812;N:197781 | 8 | 28 | 91 | 674885196 | 481871349 | 525642933 | 637154812 | 197781 | SRX21240518 | SRS18495441 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91378 | 0.22852 | 0.77843 | 0.50985 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Hatching | Embryo | Tail | Multi-system | ||||||||||||||||
| 24850 | 24850 | SRR25510002 | SRX21240518 | SRS18495441 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed 2dpf scRNAseq | GSM7680082 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed 2dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs | GSM7680082 | GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq | GSM7680082 r1 | GSM7680082 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | Kristen_10X_101620_S66_L002_I1_001.fastq.gz Kristen_10X_101620_S66_L002_R1_001.fastq.gz Kristen_10X_101620_S66_L002_R2_001.fastq.gz | fastq fastq fastq | 3287789081.0 | 25888103.0 | GSM7680082 r6 | 0:8 1:28 2:91 | A:685408765;C:489232060;G:533550966;T:647427897;N:197685 | 8 | 28 | 91 | 685408765 | 489232060 | 533550966 | 647427897 | 197685 | SRX21240518 | SRS18495441 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91484 | 0.22872 | 0.78001 | 0.49909 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Hatching | Embryo | Tail | Multi-system | ||||||||||||||||
| 24851 | 24851 | SRR25510003 | SRX21240518 | SRS18495441 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed 2dpf scRNAseq | GSM7680082 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed 2dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs | GSM7680082 | GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq | GSM7680082 r1 | GSM7680082 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | Kristen_10X_101620_S66_L003_I1_001.fastq.gz Kristen_10X_101620_S66_L003_R1_001.fastq.gz Kristen_10X_101620_S66_L003_R2_001.fastq.gz | fastq fastq fastq | 3298207145.0 | 25970135.0 | GSM7680082 r7 | 0:8 1:28 2:91 | A:687621787;C:490851045;G:535230137;T:649382247;N:197069 | 8 | 28 | 91 | 687621787 | 490851045 | 535230137 | 649382247 | 197069 | SRX21240518 | SRS18495441 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91559 | 0.2268 | 0.77766 | 0.50935 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Hatching | Embryo | Tail | Multi-system | ||||||||||||||||
| 24852 | 24852 | SRR25510004 | SRX21240518 | SRS18495441 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed 2dpf scRNAseq | GSM7680082 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed 2dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs | GSM7680082 | GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq | GSM7680082 r1 | GSM7680082 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | Kristen_10X_101620_S66_L004_I1_001.fastq.gz Kristen_10X_101620_S66_L004_R1_001.fastq.gz Kristen_10X_101620_S66_L004_R2_001.fastq.gz | fastq fastq fastq | 3377888088.0 | 26597544.0 | GSM7680082 r8 | 0:8 1:28 2:91 | A:705624374;C:500985504;G:546306692;T:667248332;N:211602 | 8 | 28 | 91 | 705624374 | 500985504 | 546306692 | 667248332 | 211602 | SRX21240518 | SRS18495441 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91679 | 0.22965 | 0.77837 | 0.51495 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Hatching | Embryo | Tail | Multi-system | ||||||||||||||||
| 24853 | 24853 | SRR25510005 | SRX21240518 | SRS18495441 | SRP453227 | PRJNA1001940 | Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed | GSE240026 | Transcriptome Analysis | Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq. | pubmed:37676768 | Spinal cord MNs olig2dsRed 2dpf scRNAseq | GSM7680082 | source name:tail|tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs|geo loc name:missing|collection date:missing | Spinal cord MNs olig2dsRed 2dpf scRNAseq | The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files | tail | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. | tissue:tail|genotype:olig2:dsRed prdm16gal4:UASGFP|age:2dpf|cell type:Spinal cord MNs | GSM7680082 | GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq | GSM7680082 r1 | GSM7680082 | 1 | DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP453227 | loader:fastq load.py | Kristen_10X_101620_S67_L001_I1_001.fastq.gz Kristen_10X_101620_S67_L001_R1_001.fastq.gz Kristen_10X_101620_S67_L001_R2_001.fastq.gz | fastq fastq fastq | 4346114117.0 | 34221371.0 | GSM7680082 r9 | 0:8 1:28 2:91 | A:905838814;C:646261347;G:704993570;T:856789016;N:262014 | 8 | 28 | 91 | 905838814 | 646261347 | 704993570 | 856789016 | 262014 | SRX21240518 | SRS18495441 | SRA1686067 | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | Dasen, Neuroscience Institute, New York University Grossman School of Medicine | 1 | 0.91558 | 0.22834 | 0.7783 | 0.49972 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2023-08-03 | Hatching | Embryo | Tail | Multi-system | ||||||||||||||||
| 24854 | 24854 | SRR25519420 | SRX21249697 | SRS18503946 | SRP453374 | PRJNA1002260 | Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model | GSE240080 | Transcriptome Analysis | We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation. | pubmed:37728477 | zebrafish AR42 TFA 4 3dpf | GSM7681266 | source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing | zebrafish AR42 TFA 4 3dpf | Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | tail | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:tail|treatment:AR 42 treated larvae with TFA modeling | GSM7681266 | GSM7681266: zebrafish AR42 TFA 4 3dpf; Danio rerio; RNA Seq | GSM7681266 r1 | GSM7681266 | 1 | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP453374 | AR42_TFA_4.R1.fq.gz AR42_TFA_4.R2.fq.gz | fastq fastq | 9896772900.0 | 32989243.0 | GSM7681266 r1 | 0:150 1:150 | A:2382403653;C:2457377213;G:2470646159;T:2586345875;N:0 | 150 | 150 | 2382403653 | 2457377213 | 2470646159 | 2586345875 | 0 | SRX21249697 | SRS18503946 | SRA1687041 | Chongqing medical university | Chongqing medical university | 2 | 0.70537 | 0.88934 | 0.03159 | 0.04209 | 0.78013 | 0.75416 | 0.50713 | 0.45138 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2023-08-04 | Larval | Larval | Tail | Multi-system | ||||||||||||
| 24855 | 24855 | SRR25519421 | SRX21249696 | SRS18503945 | SRP453374 | PRJNA1002260 | Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model | GSE240080 | Transcriptome Analysis | We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation. | pubmed:37728477 | zebrafish AR42 TFA 3 3dpf | GSM7681265 | source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing | zebrafish AR42 TFA 3 3dpf | Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | tail | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:tail|treatment:AR 42 treated larvae with TFA modeling | GSM7681265 | GSM7681265: zebrafish AR42 TFA 3 3dpf; Danio rerio; RNA Seq | GSM7681265 r1 | GSM7681265 | 1 | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP453374 | AR42_TFA_3.R1.fq.gz AR42_TFA_3.R2.fq.gz | fastq fastq | 10265927100.0 | 34219757.0 | GSM7681265 r1 | 0:150 1:150 | A:2473552302;C:2548535087;G:2562873160;T:2680966551;N:0 | 150 | 150 | 2473552302 | 2548535087 | 2562873160 | 2680966551 | 0 | SRX21249696 | SRS18503945 | SRA1687041 | Chongqing medical university | Chongqing medical university | 2 | 0.70516 | 0.88765 | 0.03163 | 0.04168 | 0.7782 | 0.75083 | 0.50851 | 0.45305 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2023-08-04 | Larval | Larval | Tail | Multi-system | ||||||||||||
| 24856 | 24856 | SRR25519422 | SRX21249695 | SRS18503944 | SRP453374 | PRJNA1002260 | Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model | GSE240080 | Transcriptome Analysis | We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation. | pubmed:37728477 | zebrafish AR42 TFA 2 3dpf | GSM7681264 | source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing | zebrafish AR42 TFA 2 3dpf | Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | tail | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:tail|treatment:AR 42 treated larvae with TFA modeling | GSM7681264 | GSM7681264: zebrafish AR42 TFA 2 3dpf; Danio rerio; RNA Seq | GSM7681264 r1 | GSM7681264 | 1 | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP453374 | AR42_TFA_2.R2.fq.gz AR42_TFA_2.R1.fq.gz | fastq fastq | 10003398900.0 | 33344663.0 | GSM7681264 r1 | 0:150 1:150 | A:2409580340;C:2483650756;G:2497057051;T:2613110753;N:0 | 150 | 150 | 2409580340 | 2483650756 | 2497057051 | 2613110753 | 0 | SRX21249695 | SRS18503944 | SRA1687041 | Chongqing medical university | Chongqing medical university | 2 | 0.70787 | 0.89158 | 0.03203 | 0.04194 | 0.77851 | 0.75108 | 0.5072 | 0.45508 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2023-08-04 | Larval | Larval | Tail | Multi-system | ||||||||||||
| 24857 | 24857 | SRR25519423 | SRX21249694 | SRS18503943 | SRP453374 | PRJNA1002260 | Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model | GSE240080 | Transcriptome Analysis | We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation. | pubmed:37728477 | zebrafish AR42 TFA 1 3dpf | GSM7681263 | source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing | zebrafish AR42 TFA 1 3dpf | Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | tail | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:tail|treatment:AR 42 treated larvae with TFA modeling | GSM7681263 | GSM7681263: zebrafish AR42 TFA 1 3dpf; Danio rerio; RNA Seq | GSM7681263 r1 | GSM7681263 | 1 | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP453374 | AR42_TFA_1.R1.fq.gz AR42_TFA_1.R2.fq.gz | fastq fastq | 7420308900.0 | 24734363.0 | GSM7681263 r1 | 0:150 1:150 | A:1791092728;C:1841012408;G:1852583633;T:1935620131;N:0 | 150 | 150 | 1791092728 | 1841012408 | 1852583633 | 1935620131 | 0 | SRX21249694 | SRS18503943 | SRA1687041 | Chongqing medical university | Chongqing medical university | 2 | 0.69668 | 0.87862 | 0.03153 | 0.04215 | 0.77463 | 0.74949 | 0.50657 | 0.45971 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2023-08-04 | Larval | Larval | Tail | Multi-system | ||||||||||||
| 24858 | 24858 | SRR25519424 | SRX21249693 | SRS18503942 | SRP453374 | PRJNA1002260 | Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model | GSE240080 | Transcriptome Analysis | We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation. | pubmed:37728477 | zebrafish DMSO TFA 4 3dpf | GSM7681262 | source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing | zebrafish DMSO TFA 4 3dpf | Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | tail | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:tail|treatment:DMSO treated larvae with TFA modeling | GSM7681262 | GSM7681262: zebrafish DMSO TFA 4 3dpf; Danio rerio; RNA Seq | GSM7681262 r1 | GSM7681262 | 1 | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP453374 | DMSO_TFA_4.R1.fq.gz DMSO_TFA_4.R2.fq.gz | fastq fastq | 10178474100.0 | 33928247.0 | GSM7681262 r1 | 0:150 1:150 | A:2452172460;C:2526571372;G:2532799116;T:2666931152;N:0 | 150 | 150 | 2452172460 | 2526571372 | 2532799116 | 2666931152 | 0 | SRX21249693 | SRS18503942 | SRA1687041 | Chongqing medical university | Chongqing medical university | 2 | 0.72132 | 0.91072 | 0.03161 | 0.04366 | 0.77709 | 0.75016 | 0.516 | 0.45312 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2023-08-04 | Larval | Larval | Tail | Multi-system | ||||||||||||
| 24859 | 24859 | SRR25519425 | SRX21249692 | SRS18503941 | SRP453374 | PRJNA1002260 | Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model | GSE240080 | Transcriptome Analysis | We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation. | pubmed:37728477 | zebrafish DMSO TFA 3 3dpf | GSM7681261 | source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing | zebrafish DMSO TFA 3 3dpf | Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | tail | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:tail|treatment:DMSO treated larvae with TFA modeling | GSM7681261 | GSM7681261: zebrafish DMSO TFA 3 3dpf; Danio rerio; RNA Seq | GSM7681261 r1 | GSM7681261 | 1 | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP453374 | DMSO_TFA_3.R1.fq.gz DMSO_TFA_3.R2.fq.gz | fastq fastq | 9483201300.0 | 31610671.0 | GSM7681261 r1 | 0:150 1:150 | A:2282797855;C:2354211318;G:2361918927;T:2484273200;N:0 | 150 | 150 | 2282797855 | 2354211318 | 2361918927 | 2484273200 | 0 | SRX21249692 | SRS18503941 | SRA1687041 | Chongqing medical university | Chongqing medical university | 2 | 0.71779 | 0.90757 | 0.03224 | 0.04329 | 0.77853 | 0.74862 | 0.51128 | 0.44891 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2023-08-04 | Larval | Larval | Tail | Multi-system | ||||||||||||
| 24860 | 24860 | SRR25519426 | SRX21249691 | SRS18503940 | SRP453374 | PRJNA1002260 | Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model | GSE240080 | Transcriptome Analysis | We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation. | pubmed:37728477 | zebrafish DMSO TFA 2 3dpf | GSM7681260 | source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing | zebrafish DMSO TFA 2 3dpf | Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | tail | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:tail|treatment:DMSO treated larvae with TFA modeling | GSM7681260 | GSM7681260: zebrafish DMSO TFA 2 3dpf; Danio rerio; RNA Seq | GSM7681260 r1 | GSM7681260 | 1 | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP453374 | DMSO_TFA_2.R1.fq.gz DMSO_TFA_2.R2.fq.gz | fastq fastq | 9372641700.0 | 31242139.0 | GSM7681260 r1 | 0:150 1:150 | A:2255045813;C:2327185536;G:2333956274;T:2456454077;N:0 | 150 | 150 | 2255045813 | 2327185536 | 2333956274 | 2456454077 | 0 | SRX21249691 | SRS18503940 | SRA1687041 | Chongqing medical university | Chongqing medical university | 2 | 0.71913 | 0.91061 | 0.0318 | 0.04251 | 0.7778 | 0.74907 | 0.51295 | 0.45006 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2023-08-04 | Larval | Larval | Tail | Multi-system | ||||||||||||
| 24861 | 24861 | SRR25519427 | SRX21249690 | SRS18503939 | SRP453374 | PRJNA1002260 | Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model | GSE240080 | Transcriptome Analysis | We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation. | pubmed:37728477 | zebrafish DMSO TFA 1 3dpf | GSM7681259 | source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing | zebrafish DMSO TFA 1 3dpf | Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | tail | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:tail|treatment:DMSO treated larvae with TFA modeling | GSM7681259 | GSM7681259: zebrafish DMSO TFA 1 3dpf; Danio rerio; RNA Seq | GSM7681259 r1 | GSM7681259 | 1 | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP453374 | DMSO_TFA_1.R1.fq.gz DMSO_TFA_1.R2.fq.gz | fastq fastq | 8665981200.0 | 28886604.0 | GSM7681259 r1 | 0:150 1:150 | A:2086560929;C:2153111953;G:2157203992;T:2269104326;N:0 | 150 | 150 | 2086560929 | 2153111953 | 2157203992 | 2269104326 | 0 | SRX21249690 | SRS18503939 | SRA1687041 | Chongqing medical university | Chongqing medical university | 2 | 0.71996 | 0.90816 | 0.03211 | 0.04297 | 0.77739 | 0.75097 | 0.5122 | 0.452 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2023-08-04 | Larval | Larval | Tail | Multi-system | ||||||||||||
| 24862 | 24862 | SRR25519428 | SRX21249689 | SRS18503938 | SRP453374 | PRJNA1002260 | Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model | GSE240080 | Transcriptome Analysis | We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation. | pubmed:37728477 | zebrafish AR42 4 3dpf | GSM7681258 | source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing | zebrafish AR42 4 3dpf | Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | tail | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:tail|treatment:AR 42 treated larvae without xxx modeling | GSM7681258 | GSM7681258: zebrafish AR42 4 3dpf; Danio rerio; RNA Seq | GSM7681258 r1 | GSM7681258 | 1 | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP453374 | AR42_4.R1.fq.gz AR42_4.R2.fq.gz | fastq fastq | 10199154900.0 | 33997183.0 | GSM7681258 r1 | 0:150 1:150 | A:2461755295;C:2524481077;G:2536143078;T:2676775450;N:0 | 150 | 150 | 2461755295 | 2524481077 | 2536143078 | 2676775450 | 0 | SRX21249689 | SRS18503938 | SRA1687041 | Chongqing medical university | Chongqing medical university | 2 | 0.70676 | 0.89456 | 0.031 | 0.04108 | 0.77508 | 0.747 | 0.44642 | 0.47521 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2023-08-04 | Larval | Larval | Tail | Multi-system | ||||||||||||
| 24863 | 24863 | SRR25519429 | SRX21249688 | SRS18503937 | SRP453374 | PRJNA1002260 | Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model | GSE240080 | Transcriptome Analysis | We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation. | pubmed:37728477 | zebrafish AR42 3 3dpf | GSM7681257 | source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing | zebrafish AR42 3 3dpf | Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | tail | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:tail|treatment:AR 42 treated larvae without xxx modeling | GSM7681257 | GSM7681257: zebrafish AR42 3 3dpf; Danio rerio; RNA Seq | GSM7681257 r1 | GSM7681257 | 1 | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP453374 | AR42_3.R1.fq.gz AR42_3.R2.fq.gz | fastq fastq | 9953498100.0 | 33178327.0 | GSM7681257 r1 | 0:150 1:150 | A:2400858967;C:2463285586;G:2477369817;T:2611983730;N:0 | 150 | 150 | 2400858967 | 2463285586 | 2477369817 | 2611983730 | 0 | SRX21249688 | SRS18503937 | SRA1687041 | Chongqing medical university | Chongqing medical university | 2 | 0.70865 | 0.89517 | 0.03101 | 0.04127 | 0.77325 | 0.74679 | 0.50253 | 0.50409 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2023-08-04 | Larval | Larval | Tail | Multi-system | ||||||||||||
| 24864 | 24864 | SRR25519430 | SRX21249687 | SRS18503936 | SRP453374 | PRJNA1002260 | Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model | GSE240080 | Transcriptome Analysis | We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation. | pubmed:37728477 | zebrafish AR42 2 3dpf | GSM7681256 | source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing | zebrafish AR42 2 3dpf | Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | tail | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:tail|treatment:AR 42 treated larvae without xxx modeling | GSM7681256 | GSM7681256: zebrafish AR42 2 3dpf; Danio rerio; RNA Seq | GSM7681256 r1 | GSM7681256 | 1 | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP453374 | AR42_2.R1.fq.gz AR42_2.R2.fq.gz | fastq fastq | 10005489000.0 | 33351630.0 | GSM7681256 r1 | 0:150 1:150 | A:2413672248;C:2477611702;G:2491304598;T:2622900452;N:0 | 150 | 150 | 2413672248 | 2477611702 | 2491304598 | 2622900452 | 0 | SRX21249687 | SRS18503936 | SRA1687041 | Chongqing medical university | Chongqing medical university | 2 | 0.70639 | 0.89204 | 0.03035 | 0.04087 | 0.77502 | 0.74955 | 0.50558 | 0.50545 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2023-08-04 | Larval | Larval | Tail | Multi-system | ||||||||||||
| 24865 | 24865 | SRR25519431 | SRX21249686 | SRS18503935 | SRP453374 | PRJNA1002260 | Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model | GSE240080 | Transcriptome Analysis | We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation. | pubmed:37728477 | zebrafish AR42 1 3dpf | GSM7681255 | source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing | zebrafish AR42 1 3dpf | Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | tail | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:tail|treatment:AR 42 treated larvae without xxx modeling | GSM7681255 | GSM7681255: zebrafish AR42 1 3dpf; Danio rerio; RNA Seq | GSM7681255 r1 | GSM7681255 | 1 | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP453374 | AR42_1.R1.fq.gz AR42_1.R2.fq.gz | fastq fastq | 9698587800.0 | 32328626.0 | GSM7681255 r1 | 0:150 1:150 | A:2337968859;C:2400315331;G:2416067610;T:2544236000;N:0 | 150 | 150 | 2337968859 | 2400315331 | 2416067610 | 2544236000 | 0 | SRX21249686 | SRS18503935 | SRA1687041 | Chongqing medical university | Chongqing medical university | 2 | 0.70903 | 0.89448 | 0.02976 | 0.04032 | 0.77583 | 0.74935 | 0.50747 | 0.5081 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2023-08-04 | Larval | Larval | Tail | Multi-system | ||||||||||||
| 24866 | 24866 | SRR25519432 | SRX21249685 | SRS18503934 | SRP453374 | PRJNA1002260 | Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model | GSE240080 | Transcriptome Analysis | We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation. | pubmed:37728477 | zebrafish DMSO 4 3dpf | GSM7681254 | source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing | zebrafish DMSO 4 3dpf | Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | tail | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:tail|treatment:DMSO treated larvae without xxx modeling | GSM7681254 | GSM7681254: zebrafish DMSO 4 3dpf; Danio rerio; RNA Seq | GSM7681254 r1 | GSM7681254 | 1 | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP453374 | DMSO_4.R1.fq.gz DMSO_4.R2.fq.gz | fastq fastq | 9083670000.0 | 30278900.0 | GSM7681254 r1 | 0:150 1:150 | A:2191941100;C:2247936730;G:2258913579;T:2384878591;N:0 | 150 | 150 | 2191941100 | 2247936730 | 2258913579 | 2384878591 | 0 | SRX21249685 | SRS18503934 | SRA1687041 | Chongqing medical university | Chongqing medical university | 2 | 0.71071 | 0.90457 | 0.03362 | 0.04688 | 0.77106 | 0.74357 | 0.50842 | 0.50975 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2023-08-04 | Larval | Larval | Tail | Multi-system | ||||||||||||
| 24867 | 24867 | SRR25519433 | SRX21249684 | SRS18503933 | SRP453374 | PRJNA1002260 | Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model | GSE240080 | Transcriptome Analysis | We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation. | pubmed:37728477 | zebrafish DMSO 3 3dpf | GSM7681253 | source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing | zebrafish DMSO 3 3dpf | Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | tail | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:tail|treatment:DMSO treated larvae without xxx modeling | GSM7681253 | GSM7681253: zebrafish DMSO 3 3dpf; Danio rerio; RNA Seq | GSM7681253 r1 | GSM7681253 | 1 | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP453374 | DMSO_3.R2.fq.gz DMSO_3.R1.fq.gz | fastq fastq | 9394455000.0 | 31314850.0 | GSM7681253 r1 | 0:150 1:150 | A:2266296733;C:2324081714;G:2335347043;T:2468729510;N:0 | 150 | 150 | 2266296733 | 2324081714 | 2335347043 | 2468729510 | 0 | SRX21249684 | SRS18503933 | SRA1687041 | Chongqing medical university | Chongqing medical university | 2 | 0.70975 | 0.90445 | 0.03329 | 0.04594 | 0.77005 | 0.7417 | 0.51188 | 0.5163 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2023-08-04 | Larval | Larval | Tail | Multi-system | ||||||||||||
| 24868 | 24868 | SRR25519434 | SRX21249683 | SRS18503932 | SRP453374 | PRJNA1002260 | Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model | GSE240080 | Transcriptome Analysis | We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation. | pubmed:37728477 | zebrafish DMSO 2 3dpf | GSM7681252 | source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing | zebrafish DMSO 2 3dpf | Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | tail | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:tail|treatment:DMSO treated larvae without xxx modeling | GSM7681252 | GSM7681252: zebrafish DMSO 2 3dpf; Danio rerio; RNA Seq | GSM7681252 r1 | GSM7681252 | 1 | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP453374 | DMSO_2.R1.fq.gz DMSO_2.R2.fq.gz | fastq fastq | 9157453500.0 | 30524845.0 | GSM7681252 r1 | 0:150 1:150 | A:2209331568;C:2266614182;G:2273923578;T:2407584172;N:0 | 150 | 150 | 2209331568 | 2266614182 | 2273923578 | 2407584172 | 0 | SRX21249683 | SRS18503932 | SRA1687041 | Chongqing medical university | Chongqing medical university | 2 | 0.70922 | 0.90538 | 0.03379 | 0.04616 | 0.7723 | 0.74213 | 0.50839 | 0.50803 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2023-08-04 | Larval | Larval | Tail | Multi-system | ||||||||||||
| 24869 | 24869 | SRR25519435 | SRX21249682 | SRS18503931 | SRP453374 | PRJNA1002260 | Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model | GSE240080 | Transcriptome Analysis | We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis the 3 dpf WT zebrafish larvae receiving DMSO or 10 µM AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO ? AR 42 treated larvae without xxx modeling AR 42 ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation larvae were immediately treated with DMSO or 10 µM AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation. | pubmed:37728477 | zebrafish DMSO 1 3dpf | GSM7681251 | source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing | zebrafish DMSO 1 3dpf | Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample | tail | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. | tissue:tail|treatment:DMSO treated larvae without xxx modeling | GSM7681251 | GSM7681251: zebrafish DMSO 1 3dpf; Danio rerio; RNA Seq | GSM7681251 r1 | GSM7681251 | 1 | RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-T7 | SRP453374 | DMSO_1.R2.fq.gz DMSO_1.R1.fq.gz | fastq fastq | 8769040200.0 | 29230134.0 | GSM7681251 r1 | 0:150 1:150 | A:2114427483;C:2170929931;G:2179906163;T:2303776623;N:0 | 150 | 150 | 2114427483 | 2170929931 | 2179906163 | 2303776623 | 0 | SRX21249682 | SRS18503931 | SRA1687041 | Chongqing medical university | Chongqing medical university | 2 | 0.71002 | 0.9037 | 0.0335 | 0.04604 | 0.77155 | 0.74308 | 0.51339 | 0.50801 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2023-08-04 | Larval | Larval | Tail | Multi-system | ||||||||||||
| 28818 | 28818 | SRR26711836 | SRX22410952 | SRS19443730 | SRP470622 | PRJNA1036688 | Cohesin composition and dosage independently affect early development in zebrafish | GSE247246 | Transcriptome Analysis | Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime. | pubmed:38975838 | rad21 heterozugous tailbud Wnt stimulation replicate 4 | GSM7885889 | source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing | rad21 heterozugous tailbud Wnt stimulation replicate 4 | Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups | tailbud | 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | E3 media 28 C | tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation | GSM7885889 | GSM7885889: rad21 heterozugous tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq | GSM7885889 r1 | GSM7885889 | 1 | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP470622 | loader:fastq load.py | Rad21-BIO-8-HET_S32_L001_R2_001.fastq.gz Rad21-BIO-8-HET_S32_L001_R1_001.fastq.gz | fastq fastq | 3261739218.0 | 21610373.0 | GSM7885889 r1 | 0:75.52 1:75.42 | A:816426262;C:810367718;G:804831968;T:829974289;N:138981 | 75 | 75 | 816426262 | 810367718 | 804831968 | 829974289 | 138981 | SRX22410952 | SRS19443730 | SRA1747076 | Chromosome Structure and Development, Pathology, Otago University | Chromosome Structure and Development, Pathology, Otago University | 2 | 0.96738 | 0.97053 | 0.05473 | 0.05415 | 0.72283 | 0.72338 | 0.46691 | 0.46731 | 76 | 76 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | New Zealand | 2023-11-07 | Multi-stage | Embryo | Tail | Multi-system | |||||||||
| 28819 | 28819 | SRR26711837 | SRX22410952 | SRS19443730 | SRP470622 | PRJNA1036688 | Cohesin composition and dosage independently affect early development in zebrafish | GSE247246 | Transcriptome Analysis | Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime. | pubmed:38975838 | rad21 heterozugous tailbud Wnt stimulation replicate 4 | GSM7885889 | source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing | rad21 heterozugous tailbud Wnt stimulation replicate 4 | Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups | tailbud | 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | E3 media 28 C | tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation | GSM7885889 | GSM7885889: rad21 heterozugous tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq | GSM7885889 r1 | GSM7885889 | 1 | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP470622 | loader:fastq load.py | Rad21-BIO-8-HET_S32_L002_R2_001.fastq.gz Rad21-BIO-8-HET_S32_L002_R1_001.fastq.gz | fastq fastq | 3279254436.0 | 21726495.0 | GSM7885889 r2 | 0:75.52 1:75.42 | A:821154343;C:814711347;G:809025779;T:834224252;N:138715 | 75 | 75 | 821154343 | 814711347 | 809025779 | 834224252 | 138715 | SRX22410952 | SRS19443730 | SRA1747076 | Chromosome Structure and Development, Pathology, Otago University | Chromosome Structure and Development, Pathology, Otago University | 2 | 0.96764 | 0.97012 | 0.05449 | 0.05364 | 0.72362 | 0.72478 | 0.46065 | 0.44816 | 75 | 76 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | New Zealand | 2023-11-07 | Multi-stage | Embryo | Tail | Multi-system | |||||||||
| 28820 | 28820 | SRR26711838 | SRX22410951 | SRS19443729 | SRP470622 | PRJNA1036688 | Cohesin composition and dosage independently affect early development in zebrafish | GSE247246 | Transcriptome Analysis | Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime. | pubmed:38975838 | rad21 homozygous tailbud Wnt stimulation replicate 4 | GSM7885888 | source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing | rad21 homozygous tailbud Wnt stimulation replicate 4 | Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups | tailbud | 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | E3 media 28 C | tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation | GSM7885888 | GSM7885888: rad21 homozygous tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq | GSM7885888 r1 | GSM7885888 | 1 | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP470622 | loader:fastq load.py | Rad21-BIO-4-MUT_S31_L001_R1_001.fastq.gz Rad21-BIO-4-MUT_S31_L001_R2_001.fastq.gz | fastq fastq | 3815700579.0 | 25275353.0 | GSM7885888 r1 | 0:75.53 1:75.43 | A:962537652;C:941667596;G:934433379;T:976947974;N:113978 | 75 | 75 | 962537652 | 941667596 | 934433379 | 976947974 | 113978 | SRX22410951 | SRS19443729 | SRA1747076 | Chromosome Structure and Development, Pathology, Otago University | Chromosome Structure and Development, Pathology, Otago University | 2 | 0.96535 | 0.96731 | 0.06446 | 0.06372 | 0.71928 | 0.71956 | 0.47233 | 0.47166 | 76 | 75 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | New Zealand | 2023-11-07 | Multi-stage | Embryo | Tail | Multi-system | |||||||||
| 28821 | 28821 | SRR26711839 | SRX22410951 | SRS19443729 | SRP470622 | PRJNA1036688 | Cohesin composition and dosage independently affect early development in zebrafish | GSE247246 | Transcriptome Analysis | Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime. | pubmed:38975838 | rad21 homozygous tailbud Wnt stimulation replicate 4 | GSM7885888 | source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing | rad21 homozygous tailbud Wnt stimulation replicate 4 | Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups | tailbud | 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | E3 media 28 C | tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation | GSM7885888 | GSM7885888: rad21 homozygous tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq | GSM7885888 r1 | GSM7885888 | 1 | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP470622 | loader:fastq load.py | Rad21-BIO-4-MUT_S31_L002_R1_001.fastq.gz Rad21-BIO-4-MUT_S31_L002_R2_001.fastq.gz | fastq fastq | 3837906036.0 | 25422663.0 | GSM7885888 r2 | 0:75.53 1:75.43 | A:968455256;C:947191550;G:939808490;T:982330983;N:119757 | 75 | 75 | 968455256 | 947191550 | 939808490 | 982330983 | 119757 | SRX22410951 | SRS19443729 | SRA1747076 | Chromosome Structure and Development, Pathology, Otago University | Chromosome Structure and Development, Pathology, Otago University | 2 | 0.96615 | 0.96781 | 0.0624 | 0.06196 | 0.71725 | 0.71827 | 0.47042 | 0.46294 | 76 | 75 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | New Zealand | 2023-11-07 | Multi-stage | Embryo | Tail | Multi-system | |||||||||
| 28822 | 28822 | SRR26711840 | SRX22410950 | SRS19443727 | SRP470622 | PRJNA1036688 | Cohesin composition and dosage independently affect early development in zebrafish | GSE247246 | Transcriptome Analysis | Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime. | pubmed:38975838 | rad21 heterozugous tailbud no treatment replicate 4 | GSM7885887 | source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing | rad21 heterozugous tailbud no treatment replicate 4 | Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups | tailbud | 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | E3 media 28 C | tissue:tailbud|genotype:heterozygous rad21 mutant | GSM7885887 | GSM7885887: rad21 heterozugous tailbud no treatment replicate 4; Danio rerio; RNA Seq | GSM7885887 r1 | GSM7885887 | 1 | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP470622 | loader:fastq load.py | Rad21-8-HET_S30_L001_R2_001.fastq.gz Rad21-8-HET_S30_L001_R1_001.fastq.gz | fastq fastq | 4150580457.0 | 27506773.0 | GSM7885887 r1 | 0:75.51 1:75.39 | A:1061191322;C:1016515755;G:1039117012;T:1033588629;N:167739 | 75 | 75 | 1061191322 | 1016515755 | 1039117012 | 1033588629 | 167739 | SRX22410950 | SRS19443727 | SRA1747076 | Chromosome Structure and Development, Pathology, Otago University | Chromosome Structure and Development, Pathology, Otago University | 2 | 0.96699 | 0.96687 | 0.0501 | 0.04959 | 0.71642 | 0.72017 | 0.44914 | 0.44833 | 76 | 76 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | New Zealand | 2023-11-07 | Multi-stage | Embryo | Tail | Multi-system | |||||||||
| 28823 | 28823 | SRR26711841 | SRX22410950 | SRS19443727 | SRP470622 | PRJNA1036688 | Cohesin composition and dosage independently affect early development in zebrafish | GSE247246 | Transcriptome Analysis | Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime. | pubmed:38975838 | rad21 heterozugous tailbud no treatment replicate 4 | GSM7885887 | source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing | rad21 heterozugous tailbud no treatment replicate 4 | Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups | tailbud | 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | E3 media 28 C | tissue:tailbud|genotype:heterozygous rad21 mutant | GSM7885887 | GSM7885887: rad21 heterozugous tailbud no treatment replicate 4; Danio rerio; RNA Seq | GSM7885887 r1 | GSM7885887 | 1 | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP470622 | loader:fastq load.py | Rad21-8-HET_S30_L002_R2_001.fastq.gz Rad21-8-HET_S30_L002_R1_001.fastq.gz | fastq fastq | 4170430033.0 | 27638560.0 | GSM7885887 r2 | 0:75.50 1:75.39 | A:1067297262;C:1021226653;G:1043544460;T:1038184807;N:176851 | 75 | 75 | 1067297262 | 1021226653 | 1043544460 | 1038184807 | 176851 | SRX22410950 | SRS19443727 | SRA1747076 | Chromosome Structure and Development, Pathology, Otago University | Chromosome Structure and Development, Pathology, Otago University | 2 | 0.96619 | 0.96635 | 0.05062 | 0.05015 | 0.7139 | 0.71918 | 0.44965 | 0.45175 | 76 | 75 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | New Zealand | 2023-11-07 | Multi-stage | Embryo | Tail | Multi-system | |||||||||
| 28824 | 28824 | SRR26711842 | SRX22410949 | SRS19443728 | SRP470622 | PRJNA1036688 | Cohesin composition and dosage independently affect early development in zebrafish | GSE247246 | Transcriptome Analysis | Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime. | pubmed:38975838 | rad21 homozygous tailbud no treatment replicate 4 | GSM7885886 | source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing | rad21 homozygous tailbud no treatment replicate 4 | Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups | tailbud | 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | E3 media 28 C | tissue:tailbud|genotype:homozygous rad21 mutant | GSM7885886 | GSM7885886: rad21 homozygous tailbud no treatment replicate 4; Danio rerio; RNA Seq | GSM7885886 r1 | GSM7885886 | 1 | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP470622 | loader:fastq load.py | Rad21-4-MUT_S29_L001_R1_001.fastq.gz Rad21-4-MUT_S29_L001_R2_001.fastq.gz | fastq fastq | 3860758586.0 | 25585267.0 | GSM7885886 r1 | 0:75.50 1:75.40 | A:962978350;C:961963514;G:957530709;T:978120083;N:165930 | 75 | 75 | 962978350 | 961963514 | 957530709 | 978120083 | 165930 | SRX22410949 | SRS19443728 | SRA1747076 | Chromosome Structure and Development, Pathology, Otago University | Chromosome Structure and Development, Pathology, Otago University | 2 | 0.96679 | 0.96899 | 0.05708 | 0.05592 | 0.71991 | 0.72021 | 0.44331 | 0.44736 | 76 | 76 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | New Zealand | 2023-11-07 | Multi-stage | Embryo | Tail | Multi-system | |||||||||
| 28825 | 28825 | SRR26711843 | SRX22410949 | SRS19443728 | SRP470622 | PRJNA1036688 | Cohesin composition and dosage independently affect early development in zebrafish | GSE247246 | Transcriptome Analysis | Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime. | pubmed:38975838 | rad21 homozygous tailbud no treatment replicate 4 | GSM7885886 | source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing | rad21 homozygous tailbud no treatment replicate 4 | Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups | tailbud | 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | E3 media 28 C | tissue:tailbud|genotype:homozygous rad21 mutant | GSM7885886 | GSM7885886: rad21 homozygous tailbud no treatment replicate 4; Danio rerio; RNA Seq | GSM7885886 r1 | GSM7885886 | 1 | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP470622 | loader:fastq load.py | Rad21-4-MUT_S29_L002_R1_001.fastq.gz Rad21-4-MUT_S29_L002_R2_001.fastq.gz | fastq fastq | 3886411017.0 | 25755387.0 | GSM7885886 r2 | 0:75.50 1:75.40 | A:969709828;C:968345638;G:963787543;T:984390915;N:177093 | 75 | 75 | 969709828 | 968345638 | 963787543 | 984390915 | 177093 | SRX22410949 | SRS19443728 | SRA1747076 | Chromosome Structure and Development, Pathology, Otago University | Chromosome Structure and Development, Pathology, Otago University | 2 | 0.96682 | 0.96836 | 0.05697 | 0.05624 | 0.71812 | 0.71819 | 0.4505 | 0.44685 | 76 | 76 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | New Zealand | 2023-11-07 | Multi-stage | Embryo | Tail | Multi-system | |||||||||
| 28826 | 28826 | SRR26711844 | SRX22410948 | SRS19443726 | SRP470622 | PRJNA1036688 | Cohesin composition and dosage independently affect early development in zebrafish | GSE247246 | Transcriptome Analysis | Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime. | pubmed:38975838 | stag2b tailbud Wnt stimulation replicate 4 | GSM7885885 | source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing | stag2b tailbud Wnt stimulation replicate 4 | Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups | tailbud | 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | E3 media 28 C | tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation | GSM7885885 | GSM7885885: stag2b tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq | GSM7885885 r1 | GSM7885885 | 1 | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP470622 | loader:fastq load.py | S2B-BIO-4_S28_L001_R1_001.fastq.gz S2B-BIO-4_S28_L001_R2_001.fastq.gz | fastq fastq | 3727162917.0 | 24693169.0 | GSM7885885 r1 | 0:75.53 1:75.41 | A:922580573;C:935922329;G:933433047;T:935120514;N:106454 | 75 | 75 | 922580573 | 935922329 | 933433047 | 935120514 | 106454 | SRX22410948 | SRS19443726 | SRA1747076 | Chromosome Structure and Development, Pathology, Otago University | Chromosome Structure and Development, Pathology, Otago University | 2 | 0.96731 | 0.96936 | 0.04393 | 0.04403 | 0.72234 | 0.72397 | 0.46015 | 0.45955 | 76 | 74 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | New Zealand | 2023-11-07 | Multi-stage | Embryo | Tail | Multi-system | |||||||||
| 28827 | 28827 | SRR26711845 | SRX22410948 | SRS19443726 | SRP470622 | PRJNA1036688 | Cohesin composition and dosage independently affect early development in zebrafish | GSE247246 | Transcriptome Analysis | Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime. | pubmed:38975838 | stag2b tailbud Wnt stimulation replicate 4 | GSM7885885 | source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing | stag2b tailbud Wnt stimulation replicate 4 | Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups | tailbud | 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | E3 media 28 C | tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation | GSM7885885 | GSM7885885: stag2b tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq | GSM7885885 r1 | GSM7885885 | 1 | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP470622 | loader:fastq load.py | S2B-BIO-4_S28_L002_R1_001.fastq.gz S2B-BIO-4_S28_L002_R2_001.fastq.gz | fastq fastq | 3749916462.0 | 24844024.0 | GSM7885885 r2 | 0:75.53 1:75.41 | A:928588967;C:941571510;G:939049263;T:940598432;N:108290 | 75 | 75 | 928588967 | 941571510 | 939049263 | 940598432 | 108290 | SRX22410948 | SRS19443726 | SRA1747076 | Chromosome Structure and Development, Pathology, Otago University | Chromosome Structure and Development, Pathology, Otago University | 2 | 0.96668 | 0.96881 | 0.04401 | 0.04387 | 0.72387 | 0.72519 | 0.45814 | 0.457 | 76 | 76 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | New Zealand | 2023-11-07 | Multi-stage | Embryo | Tail | Multi-system | |||||||||
| 28828 | 28828 | SRR26711846 | SRX22410947 | SRS19443724 | SRP470622 | PRJNA1036688 | Cohesin composition and dosage independently affect early development in zebrafish | GSE247246 | Transcriptome Analysis | Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime. | pubmed:38975838 | stag2b tailbud no treatment replicate 4 | GSM7885884 | source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing | stag2b tailbud no treatment replicate 4 | Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups | tailbud | 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | E3 media 28 C | tissue:tailbud|genotype:homozygous stag2b mutant | GSM7885884 | GSM7885884: stag2b tailbud no treatment replicate 4; Danio rerio; RNA Seq | GSM7885884 r1 | GSM7885884 | 1 | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP470622 | loader:fastq load.py | S2B-4_S27_L001_R1_001.fastq.gz S2B-4_S27_L001_R2_001.fastq.gz | fastq fastq | 4559287327.0 | 30217717.0 | GSM7885884 r1 | 0:75.49 1:75.39 | A:1129871064;C:1144626195;G:1141080047;T:1143531432;N:178589 | 75 | 75 | 1129871064 | 1144626195 | 1141080047 | 1143531432 | 178589 | SRX22410947 | SRS19443724 | SRA1747076 | Chromosome Structure and Development, Pathology, Otago University | Chromosome Structure and Development, Pathology, Otago University | 2 | 0.96507 | 0.96728 | 0.04397 | 0.04385 | 0.72338 | 0.72456 | 0.44876 | 0.45623 | 76 | 75 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | New Zealand | 2023-11-07 | Multi-stage | Embryo | Tail | Multi-system | |||||||||
| 28829 | 28829 | SRR26711847 | SRX22410947 | SRS19443724 | SRP470622 | PRJNA1036688 | Cohesin composition and dosage independently affect early development in zebrafish | GSE247246 | Transcriptome Analysis | Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime. | pubmed:38975838 | stag2b tailbud no treatment replicate 4 | GSM7885884 | source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing | stag2b tailbud no treatment replicate 4 | Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups | tailbud | 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | E3 media 28 C | tissue:tailbud|genotype:homozygous stag2b mutant | GSM7885884 | GSM7885884: stag2b tailbud no treatment replicate 4; Danio rerio; RNA Seq | GSM7885884 r1 | GSM7885884 | 1 | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP470622 | loader:fastq load.py | S2B-4_S27_L002_R1_001.fastq.gz S2B-4_S27_L002_R2_001.fastq.gz | fastq fastq | 4586674313.0 | 30399355.0 | GSM7885884 r2 | 0:75.49 1:75.39 | A:1137101056;C:1151500029;G:1147768493;T:1150129054;N:175681 | 75 | 75 | 1137101056 | 1151500029 | 1147768493 | 1150129054 | 175681 | SRX22410947 | SRS19443724 | SRA1747076 | Chromosome Structure and Development, Pathology, Otago University | Chromosome Structure and Development, Pathology, Otago University | 2 | 0.96454 | 0.96735 | 0.04449 | 0.04408 | 0.72435 | 0.72583 | 0.45339 | 0.45434 | 76 | 76 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | New Zealand | 2023-11-07 | Multi-stage | Embryo | Tail | Multi-system | |||||||||
| 28830 | 28830 | SRR26711848 | SRX22410946 | SRS19443725 | SRP470622 | PRJNA1036688 | Cohesin composition and dosage independently affect early development in zebrafish | GSE247246 | Transcriptome Analysis | Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime. | pubmed:38975838 | Wild type tailbud Wnt stimulation replicate 4 | GSM7885883 | source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing | Wild type tailbud Wnt stimulation replicate 4 | Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups | tailbud | 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | E3 media 28 C | tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation | GSM7885883 | GSM7885883: Wild type tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq | GSM7885883 r1 | GSM7885883 | 1 | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP470622 | loader:fastq load.py | WT-BIO-4_S26_L001_R2_001.fastq.gz WT-BIO-4_S26_L001_R1_001.fastq.gz | fastq fastq | 5251141754.0 | 34808166.0 | GSM7885883 r1 | 0:75.48 1:75.38 | A:1316653671;C:1303617399;G:1296205519;T:1334442750;N:222415 | 75 | 75 | 1316653671 | 1303617399 | 1296205519 | 1334442750 | 222415 | SRX22410946 | SRS19443725 | SRA1747076 | Chromosome Structure and Development, Pathology, Otago University | Chromosome Structure and Development, Pathology, Otago University | 2 | 0.96497 | 0.96673 | 0.04868 | 0.04837 | 0.72332 | 0.72324 | 0.47006 | 0.45832 | 75 | 76 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | New Zealand | 2023-11-07 | Multi-stage | Embryo | Tail | Multi-system | |||||||||
| 28831 | 28831 | SRR26711849 | SRX22410946 | SRS19443725 | SRP470622 | PRJNA1036688 | Cohesin composition and dosage independently affect early development in zebrafish | GSE247246 | Transcriptome Analysis | Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime. | pubmed:38975838 | Wild type tailbud Wnt stimulation replicate 4 | GSM7885883 | source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing | Wild type tailbud Wnt stimulation replicate 4 | Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups | tailbud | 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | E3 media 28 C | tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation | GSM7885883 | GSM7885883: Wild type tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq | GSM7885883 r1 | GSM7885883 | 1 | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP470622 | loader:fastq load.py | WT-BIO-4_S26_L002_R2_001.fastq.gz WT-BIO-4_S26_L002_R1_001.fastq.gz | fastq fastq | 5280302307.0 | 35001391.0 | GSM7885883 r2 | 0:75.48 1:75.38 | A:1324401398;C:1310930748;G:1303177704;T:1341576726;N:215731 | 75 | 75 | 1324401398 | 1310930748 | 1303177704 | 1341576726 | 215731 | SRX22410946 | SRS19443725 | SRA1747076 | Chromosome Structure and Development, Pathology, Otago University | Chromosome Structure and Development, Pathology, Otago University | 2 | 0.96424 | 0.96713 | 0.04917 | 0.04864 | 0.72241 | 0.72271 | 0.46443 | 0.45274 | 76 | 75 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | New Zealand | 2023-11-07 | Multi-stage | Embryo | Tail | Multi-system | |||||||||
| 28832 | 28832 | SRR26711850 | SRX22410945 | SRS19443723 | SRP470622 | PRJNA1036688 | Cohesin composition and dosage independently affect early development in zebrafish | GSE247246 | Transcriptome Analysis | Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime. | pubmed:38975838 | Wild type tailbud no treatment replicate 4 | GSM7885882 | source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing | Wild type tailbud no treatment replicate 4 | Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups | tailbud | 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | E3 media 28 C | tissue:tailbud|genotype:wild type | GSM7885882 | GSM7885882: Wild type tailbud no treatment replicate 4; Danio rerio; RNA Seq | GSM7885882 r1 | GSM7885882 | 1 | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP470622 | loader:fastq load.py | WT4_S25_L001_R1_001.fastq.gz WT4_S25_L001_R2_001.fastq.gz | fastq fastq | 7405469360.0 | 49089434.0 | GSM7885882 r1 | 0:75.49 1:75.37 | A:1847973647;C:1841169648;G:1840295933;T:1875743550;N:286582 | 75 | 75 | 1847973647 | 1841169648 | 1840295933 | 1875743550 | 286582 | SRX22410945 | SRS19443723 | SRA1747076 | Chromosome Structure and Development, Pathology, Otago University | Chromosome Structure and Development, Pathology, Otago University | 2 | 0.96338 | 0.96738 | 0.04317 | 0.04296 | 0.71737 | 0.71851 | 0.45679 | 0.45543 | 76 | 76 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | New Zealand | 2023-11-07 | Multi-stage | Embryo | Tail | Multi-system | |||||||||
| 28833 | 28833 | SRR26711851 | SRX22410945 | SRS19443723 | SRP470622 | PRJNA1036688 | Cohesin composition and dosage independently affect early development in zebrafish | GSE247246 | Transcriptome Analysis | Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime. | pubmed:38975838 | Wild type tailbud no treatment replicate 4 | GSM7885882 | source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing | Wild type tailbud no treatment replicate 4 | Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups | tailbud | 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | E3 media 28 C | tissue:tailbud|genotype:wild type | GSM7885882 | GSM7885882: Wild type tailbud no treatment replicate 4; Danio rerio; RNA Seq | GSM7885882 r1 | GSM7885882 | 1 | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP470622 | loader:fastq load.py | WT4_S25_L002_R1_001.fastq.gz WT4_S25_L002_R2_001.fastq.gz | fastq fastq | 7449020435.0 | 49378676.0 | GSM7885882 r2 | 0:75.48 1:75.37 | A:1859225781;C:1852173354;G:1850890621;T:1886441454;N:289225 | 75 | 75 | 1859225781 | 1852173354 | 1850890621 | 1886441454 | 289225 | SRX22410945 | SRS19443723 | SRA1747076 | Chromosome Structure and Development, Pathology, Otago University | Chromosome Structure and Development, Pathology, Otago University | 2 | 0.96307 | 0.9662 | 0.04334 | 0.04269 | 0.7167 | 0.71679 | 0.45909 | 0.45956 | 75 | 75 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | New Zealand | 2023-11-07 | Multi-stage | Embryo | Tail | Multi-system | |||||||||
| 28834 | 28834 | SRR26711852 | SRX22410944 | SRS19443721 | SRP470622 | PRJNA1036688 | Cohesin composition and dosage independently affect early development in zebrafish | GSE247246 | Transcriptome Analysis | Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime. | pubmed:38975838 | rad21 heterozugous tailbud Wnt stimulation replicate 3 | GSM7885881 | source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing | rad21 heterozugous tailbud Wnt stimulation replicate 3 | Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups | tailbud | 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | E3 media 28 C | tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation | GSM7885881 | GSM7885881: rad21 heterozugous tailbud Wnt stimulation replicate 3; Danio rerio; RNA Seq | GSM7885881 r1 | GSM7885881 | 1 | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP470622 | loader:fastq load.py | Rad21-BIO-7-HET_S24_L001_R1_001.fastq.gz Rad21-BIO-7-HET_S24_L001_R2_001.fastq.gz | fastq fastq | 3984218790.0 | 26397905.0 | GSM7885881 r1 | 0:75.51 1:75.42 | A:1024724878;C:960806363;G:958470013;T:1040115284;N:102252 | 75 | 75 | 1024724878 | 960806363 | 958470013 | 1040115284 | 102252 | SRX22410944 | SRS19443721 | SRA1747076 | Chromosome Structure and Development, Pathology, Otago University | Chromosome Structure and Development, Pathology, Otago University | 2 | 0.95932 | 0.96163 | 0.06729 | 0.06702 | 0.71979 | 0.71981 | 0.4528 | 0.4607 | 76 | 74 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | New Zealand | 2023-11-07 | Multi-stage | Embryo | Tail | Multi-system | |||||||||
| 28835 | 28835 | SRR26711853 | SRX22410944 | SRS19443721 | SRP470622 | PRJNA1036688 | Cohesin composition and dosage independently affect early development in zebrafish | GSE247246 | Transcriptome Analysis | Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime. | pubmed:38975838 | rad21 heterozugous tailbud Wnt stimulation replicate 3 | GSM7885881 | source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing | rad21 heterozugous tailbud Wnt stimulation replicate 3 | Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups | tailbud | 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | E3 media 28 C | tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation | GSM7885881 | GSM7885881: rad21 heterozugous tailbud Wnt stimulation replicate 3; Danio rerio; RNA Seq | GSM7885881 r1 | GSM7885881 | 1 | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP470622 | loader:fastq load.py | Rad21-BIO-7-HET_S24_L002_R1_001.fastq.gz Rad21-BIO-7-HET_S24_L002_R2_001.fastq.gz | fastq fastq | 4008829445.0 | 26560912.0 | GSM7885881 r2 | 0:75.51 1:75.42 | A:1031275075;C:966838521;G:964312635;T:1046301501;N:101713 | 75 | 75 | 1031275075 | 966838521 | 964312635 | 1046301501 | 101713 | SRX22410944 | SRS19443721 | SRA1747076 | Chromosome Structure and Development, Pathology, Otago University | Chromosome Structure and Development, Pathology, Otago University | 2 | 0.9587 | 0.96152 | 0.06791 | 0.06665 | 0.71989 | 0.72157 | 0.45962 | 0.46712 | 76 | 76 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | New Zealand | 2023-11-07 | Multi-stage | Embryo | Tail | Multi-system | |||||||||
| 28836 | 28836 | SRR26711854 | SRX22410943 | SRS19443722 | SRP470622 | PRJNA1036688 | Cohesin composition and dosage independently affect early development in zebrafish | GSE247246 | Transcriptome Analysis | Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime. | pubmed:38975838 | rad21 homozygous tailbud Wnt stimulation replicate 3 | GSM7885880 | source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing | rad21 homozygous tailbud Wnt stimulation replicate 3 | Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups | tailbud | 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | E3 media 28 C | tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation | GSM7885880 | GSM7885880: rad21 homozygous tailbud Wnt stimulation replicate 3; Danio rerio; RNA Seq | GSM7885880 r1 | GSM7885880 | 1 | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP470622 | loader:fastq load.py | Rad21-BIO-3-MUT_S23_L001_R1_001.fastq.gz Rad21-BIO-3-MUT_S23_L001_R2_001.fastq.gz | fastq fastq | 5599192259.0 | 37097144.0 | GSM7885880 r1 | 0:75.51 1:75.43 | A:1432393511;C:1358888032;G:1349825352;T:1457936919;N:148445 | 75 | 75 | 1432393511 | 1358888032 | 1349825352 | 1457936919 | 148445 | SRX22410943 | SRS19443722 | SRA1747076 | Chromosome Structure and Development, Pathology, Otago University | Chromosome Structure and Development, Pathology, Otago University | 2 | 0.96008 | 0.96296 | 0.0752 | 0.07458 | 0.71518 | 0.71595 | 0.45869 | 0.45262 | 76 | 74 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | New Zealand | 2023-11-07 | Multi-stage | Embryo | Tail | Multi-system | |||||||||
| 28837 | 28837 | SRR26711855 | SRX22410943 | SRS19443722 | SRP470622 | PRJNA1036688 | Cohesin composition and dosage independently affect early development in zebrafish | GSE247246 | Transcriptome Analysis | Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime. | pubmed:38975838 | rad21 homozygous tailbud Wnt stimulation replicate 3 | GSM7885880 | source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing | rad21 homozygous tailbud Wnt stimulation replicate 3 | Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups | tailbud | 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | E3 media 28 C | tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation | GSM7885880 | GSM7885880: rad21 homozygous tailbud Wnt stimulation replicate 3; Danio rerio; RNA Seq | GSM7885880 r1 | GSM7885880 | 1 | RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP470622 | loader:fastq load.py | Rad21-BIO-3-MUT_S23_L002_R1_001.fastq.gz Rad21-BIO-3-MUT_S23_L002_R2_001.fastq.gz | fastq fastq | 5635998309.0 | 37340801.0 | GSM7885880 r2 | 0:75.51 1:75.43 | A:1442157325;C:1367898781;G:1358570964;T:1467225614;N:145625 | 75 | 75 | 1442157325 | 1367898781 | 1358570964 | 1467225614 | 145625 | SRX22410943 | SRS19443722 | SRA1747076 | Chromosome Structure and Development, Pathology, Otago University | Chromosome Structure and Development, Pathology, Otago University | 2 | 0.95976 | 0.96205 | 0.07516 | 0.07494 | 0.71415 | 0.71498 | 0.4588 | 0.45974 | 75 | 74 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | trueseq | sc_generic | single_cell_generic | generic-scrnaseq-only | New Zealand | 2023-11-07 | Multi-stage | Embryo | Tail | Multi-system |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;