run_metadata: 49405

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
49405	SRR7904989	SRX4741349	SRS3822681	SRP162658	PRJNA493234	Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x]	GSE120503	Other	To investigate the peculiarity of CHT HSPCs as well as the interaction of CHT niche and HSPCs at higher resolution we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics.	parent bioproject:PRJNA493631	pubmed:31042481;pubmed:33785593		52 hpf CHT cells	GSM3402061		tissue:zebrafish embryos\|region:CHT\|cells:endothelial cells+hematopoietic cells+ double negative niche cells\|Stage:52 hpf	52 hpf CHT cells	UMI tools was used to analysis our single cell data. Firstly in “whitelist” step we set 5000 as cell number and check quality plots. The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by UMI counts	zebrafish embryos		The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture’s introduction.		region:CHT\|cells:endothelial cells+hematopoietic cells+ double negative niche cells\|Stage:52 hpf	GSM3402061	GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq	GSM3402061		1	The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture's introduction.	GEO Accession:GSM3402061	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten		SRP162658			171353A_zebrafish_HSC_mixture-1_S9_L001_R1_001.fastq.gz 171353A_zebrafish_HSC_mixture-1_S9_L001_R2_001.fastq.gz	fastq fastq	20612658541.0	68497783.0	GSM3402061 r1	0:150.50 1:150.43	A:5839137036;C:3293726779;G:3429783599;T:8049467865;N:543262	150	150			5839137036	3293726779	3429783599	8049467865	543262	SRX4741349	SRS3822681	SRA784241	GEO	Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB)	2	0.04293	0.91361	0.0057	0.0679	0.97494	0.8187	0.48327	0.49296	150	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		China	2018-09-26	Hatching	Embryo	Embryo Imprecise	All anatomical structures