run_metadata: 65652

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
65652	SRR15483597	SRX11783413	SRS9786611	SRP332734	PRJNA755310	Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae	GSE182213	Transcriptome Analysis	The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.		pubmed:34525360		runx1:mCherry+ at 52 hpf #2 replicate	GSM5525118		tissue:hematopoietic cells\|developmental stage:52 hpf line:runx1+23:nls mCherry	runx1:mCherry+ at 52 hpf #2 replicate	Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities	hematopoietic cells		draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations 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 Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.		developmental stage:52 hpf line:runx1+23:nls mCherry	GSM5525118	GSM5525118: runx1:mCherry+ at 52 hpf #2 replicate; Danio rerio; RNA Seq	GSM5525118		1	draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations 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 Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.	GEO Accession:GSM5525118	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP332734		loader:fastq load.py\|options: platform=Illumina readTypes=TBT read1PairFiles=R2 2 S1 L002 R1 001.fastq.gz read2PairFiles=R2 2 S1 L002 R2 001.fastq.gz read3PairFiles=R2 2 S1 L002 I1 001.fastq.gz	R2-2_S1_L002_I1_001.fastq.gz R2-2_S1_L002_R1_001.fastq.gz R2-2_S1_L002_R2_001.fastq.gz	fastq fastq fastq	67940768588.0	220586911.0	GSM5525118 r2	0:150 1:150 2:8	A:7901205395;C:8819719149;G:8118311347;T:8243562587;N:5238172	150	150	8		7901205395	8819719149	8118311347	8243562587	5238172	SRX11783413	SRS9786611	SRA1278863	GEO	Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine	1	0.94536		0.018		0.92839		0.45489		150		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2021-08-16	Hatching	Embryo	Blood	Hematopoietic System