run_metadata: 63866

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
63866	SRR14143479	SRX10512841	SRS8636598	SRP313475	PRJNA719789	scRNA seq of tailbud development in zebrafish	GSE171482	Other	We have performed single cell RNA seq of whole tailbuds in WT zebrafish at 16 hpf. Overall design: Single cells were captured via 10X Chromium platform at 16 hpf from whole tailbuds.				Tailbud single cells at 16 hpf	GSM5226215		source name:Dissociated tailbuds from 30 hpf 16 hpf embryos\|transgenic:AB wildtypes\|age:16 hpf embryo\|tissue:dissociated tailbuds	Tailbud single cells at 16 hpf	FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: .csv file contains counts matrix for each cell that met quality thresholds	Dissociated tailbuds from 30 hpf 16 hpf embryos		Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3		transgenic:AB wildtypes\|age:16 hpf embryo\|tissue:dissociated tailbuds	GSM5226215	GSM5226215: Tailbud single cells at 16 hpf; Danio rerio; RNA Seq	GSM5226215		1	Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3	GEO Accession:GSM5226215	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP313475		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=WT tailbud S2 L003 I1 001.fastq.gz read2PairFiles=WT tailbud S2 L003 R1 001.fastq.gz read3PairFiles=WT tailbud S2 L003 R2 001.fastq.gz	WT_tailbud_S2_L003_I1_001.fastq.gz WT_tailbud_S2_L003_R1_001.fastq.gz WT_tailbud_S2_L003_R2_001.fastq.gz	fastq fastq fastq	34222167268.0	269465884.0	GSM5226215 r2	0:8 1:28 2:91	A:10380791879;C:7173180527;G:7598116520;T:9068620061;N:1458281	8	28	91		10380791879	7173180527	7598116520	9068620061	1458281	SRX10512841	SRS8636598	SRA1215249	GEO	Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine	1	0.94862		0.1236		0.79322		0.50153		91		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2021-04-05	Segmentation	Embryo	Tail	Multi-system