run_metadata: 59880

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
59880	SRR12060554	SRX8588729	SRS6880197	SRP268145	PRJNA640816	An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution	GSE152906	Transcriptome Analysis	Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate zebrafish during the late embryonic to early larval stage a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme neural crest neural neuronal glial and pigment from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages mesenchyme subtypes and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes with distinct profiles within neuronal cells. From these analyses we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.		pubmed:33591267;pubmed:38234831;pubmed:38809858		Sox10+ 68 70hpf	GSM4629199		tissue:Derivative Sox10+ Neural Crest\|genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:68 hpf 70 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	Sox10+ 68 70hpf	Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment filtering barcode reading and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx	Derivative Sox10+ Neural Crest	none	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	Embryos were collected synchronously batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with Rice University Institutional Animal Care and Use Committee IACUC.	genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:68 hpf 70 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	GSM4629199	GSM4629199: Sox10+ 68 70hpf; Danio rerio; RNA Seq	GSM4629199		1	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	GEO Accession:GSM4629199	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP268145		loader:fastq load.py\|options: platform=Illumina readTypes=BBT read1PairFiles=GFPplus S1 L002 R1 001.fastq read2PairFiles=GFPplus S1 L002 R2 001.fastq read3PairFiles=GFPplus S1 L002 I1 001.fastq			3615497884.0	22882898.0	GSM4629199 r2	0:26 1:124 2:8	A:1062722875;C:724671651;G:825496420;T:1002262450;N:344488	26	124	8		1062722875	724671651	825496420	1002262450	344488	SRX8588729	SRS6880197	SRA1089349	GEO	The Uribe Laboratory, BioSciences, Rice University	2	0.00228	0.91709	0.00071	0.08087	0.99557	0.80984	0.37288	0.50652	26	124	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2020-06-20	Hatching	Embryo	Brain	Nervous System