{"database": "metadata", "table": "run_metadata", "rows": [[65125, "SRR14935605", "SRX11248236", "SRS9294118", "SRP325962", "PRJNA742206", "Heterogeneity and molecular programming of progenitors for motor neurons and oligodendrocytes", "GSE179096", "Other", "The pMN domain is a restricted domain in the ventral spinal cords  defined by the expression of olig2 gene. The fate determination of pMN progenitors is highly temporally and spatially regulated  with motor neurons and oligodendrocyte progenitor cells OPCs developing sequentially. Insight into the heterogeneity and molecular programs of pMN progenitors is currently lacking. With the zebrafish model  we identified multiple states of neural progenitors using single cell sequencing: proliferating progenitors  common progenitors for both motor neurons and OPCs  and restricted precursors for either motor neurons or OPCs. We found specific molecular programs for neural progenitor fate transition  and manipulations of representative genes in the motor neuron or OPC lineage confirmed their critical role in cell fate determination. Deciphering progenitor heterogeneity and molecular mechanisms for these transitions will elucidate the formation of complex neuron glia networks in the central nervous system during development  and understand the basis of neurodevelopmental disorders. Overall design: olig2+ cells were isolated from the trunks of Tgolig2:dsred by FACS and underwent scRNA seq", null, "pubmed:36063998", null, "olig2+ cells in zebrafish trunks", "GSM5406686", null, "source name:Tgolig2:dsred trunks|developmental stage:42 hpf|genotype:Tg olig2:dsred|tissue:trunk|cell type:fluorescent cells from Tgolig2:dsred trunks", "olig2+ cells in zebrafish trunks", "Alignment  filtering  barcode counting  and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Genes detectable in more than two cells were defined as \u201cexpressed\u201d. Cells with <1000 genes detected were removed. Counts were normalized to 10000 and transformed into logarithmic scales. A neighborhood graph was embedded using UMAP displaying the top 4000 highly variable genes across cells. Cells were clustered by the Louvain Algorithm. The trajectory interface of all cell clusters was done using the layout 'fa'. These analyses were performed by the Python based SCANPY package Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample", "Tgolig2:dsred trunks", null, "Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell 3\u2019 Library and Gel Bead kit V3", null, "developmental stage:42 hpf|genotype:Tg olig2:dsred|tissue:trunk|cell type:fluorescent cells from Tgolig2:dsred trunks", "GSM5406686", "GSM5406686: olig2+ cells in zebrafish trunks; Danio rerio; RNA Seq", "GSM5406686", null, "1", "Tgolig2:dsred trunks were dissected and dissociated with 0.25% trypsin. Fluorescent cells were isolated with FACS. RNA was extracted with Trizol. cDNAs were amplified and libraries were generated with the Single Cell three prime Library and Gel Bead kit V3", "GEO Accession:GSM5406686", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP325962", null, null, "191269A_Z_Olig2_2_1_R1.fq.gz 191269A_Z_Olig2_2_1_R2.fq.gz", "fastq fastq", 24958600500.0, 83195335.0, "GSM5406686 r2", "0:150 1:150", "A:5431710090;C:4568888734;G:8717963207;T:6239757593;N:280876", 150, 150, null, null, 5431710090, 4568888734, 8717963207, 6239757593, 280876, "SRX11248236", "SRS9294118", "SRA1251944", "GEO", "Nantong University", 2, 0.0, 0.89635, 0.0, 0.20299, 1.0, 0.78453, null, 0.50241, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-06-29", "Pharyngula", "Embryo", "Trunk", "Surface Structure"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["65125"], "units": {}, "query_ms": 7.574460003525019}