run_metadata: 24804
This data as json
| 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 |
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| 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 |