run_metadata: 65127

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
65127	SRR14935607	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		pubmed:36063998		olig2+ cells in zebrafish trunks	GSM5406686		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 “expressed”. 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		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’ Library and Gel Bead kit V3		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		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		SRP325962			191269A_Z_Olig2_4_1_R1.fq.gz 191269A_Z_Olig2_4_1_R2.fq.gz	fastq fastq	22347557700.0	74491859.0	GSM5406686 r4	0:150 1:150	A:4874539429;C:4084280591;G:7793747016;T:5594741104;N:249560	150	150			4874539429	4084280591	7793747016	5594741104	249560	SRX11248236	SRS9294118	SRA1251944	GEO	Nantong University	2	0.0	0.89737	0.0	0.20476	1.0	0.78675		0.5017	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		China	2021-06-29	Pharyngula	Embryo	Trunk	Surface Structure