run_metadata: 54729

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
54729	SRR10150438	SRX6875871	SRS5411730	SRP222654	PRJNA571187	single cell RNA Seq of juvenile zebrafish	PRJNA571187	Other	single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit				whole organism single cell RNA seq of juvenile zebrafish	SC2S3		strain:AB\|age:30 dpf\|sex:not collected\|tissue:whole organism\|genotype:WT\|BioSampleModel:Model organism or animal									single cell RNA Seq of zebrafish: whole organism of juvenile	I3S2	I3S2	A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	HiSeq X Ten		SRP222654			S3-I3-Hiseq_S2_L001_R1_001.fastq.gz S3-I3-Hiseq_S2_L001_R2_001.fastq.gz	fastq fastq	4273728900.0	14245763.0	S3 I3 Hiseq S2 L001 R1 001.fastq.gz	0:150 1:150	A:1093044190;C:680068409;G:740119940;T:1760292389;N:203972	150	150			1093044190	680068409	740119940	1760292389	203972	SRX6875871	SRS5411730	SRA965192	Sun Yat- sen University\|Life Sicence School	Sun Yat- sen University	2	0.20465	0.90036	0.05289	0.14865	0.98553	0.7877	0.49162	0.55234	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x		China	2019-09-20	Juvenile	Juvenile	Whole Organism	All anatomical structures