run_metadata: 57179

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
57179	SRR11243179	SRX7854785	SRS6264267	SRP251673	PRJNA610520	A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish	GSE146404	Transcriptome Analysis	To profile the developmental landscape of fetal HSPCs and their local niche here by using single cell RNA sequencing we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10× Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study.		pubmed:33785593		3.5 dpf CHT cells	GSM4384817		source name:zebrafish embryos\|genotype/variation:Tg kdrl:mCherry/CD41:GFP\|age:3.5 dpf\|tissue:caudal hematopoietic tissue CHT region\|cell type:endothelial cells+hematopoietic cells+ double negative niche cells	3.5 dpf 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 three samples measured by UMI counts	zebrafish embryos		Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics 120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen 37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics 120237 following the manufacture’s introduction.		genotype/variation:Tg kdrl:mCherry/CD41:GFP\|age:3.5 dpf\|tissue:caudal hematopoietic tissue CHT region\|cell type:endothelial cells+hematopoietic cells+ double negative niche cells	GSM4384817	GSM4384817: 3.5 dpf CHT cells; Danio rerio; RNA Seq	GSM4384817		1	Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics 120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen 37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics 120237 following the manufacture's introduction.	GEO Accession:GSM4384817	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten		SRP251673			171353F_CHT-3dpf_2_R1.fq.gz 171353F_CHT-3dpf_2_R2.fq.gz	fastq fastq	71620433400.0	238734778.0	GSM4384817 r4	0:150 1:150	A:16843285494;C:13823957864;G:21855431757;T:19095628638;N:2129647	150	150			16843285494	13823957864	21855431757	19095628638	2129647	SRX7854785	SRS6264267	SRA1051251	GEO	Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES	2	0.0	0.90995	0.0	0.06019	1.0	0.82767		0.49515	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		China	2020-03-05	Larval	Larval	Blood	Hematopoietic System