run_metadata: 63329

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
63329	SRR13724920	SRX10112994	SRS8268890	SRP306756	PRJNA702191	Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells	GSE166900	Transcriptome Analysis	Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.		pubmed:33714985		SBF 3	GSM5087773		tissue:Aorta Gonad Mes1phros\|developmental stage:36hpf	SBF 3	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Aorta Gonad Mesonephros		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:36hpf\|sort day see plate layout:3\|genotype or treatment see plate layout:wildtype and LY294002 treated	GSM5087773	GSM5087773: SBF 3; Danio rerio; RNA Seq	GSM5087773		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5087773	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP306756			SBF-3_AH5WKHBGX3_S4_L002_R1_001.fastq.gz SBF-3_AH5WKHBGX3_S4_L002_R2_001.fastq.gz	fastq fastq	3222130047.0	21338414.0	GSM5087773 r2	0:75.53 1:75.47	A:911955596;C:450527126;G:564151778;T:1295111718;N:383829	75	75			911955596	450527126	564151778	1295111718	383829	SRX10112994	SRS8268890	SRA1196923	GEO	Hubrecht Institute	2	0.31155	0.73818	0.23573	0.27589	0.96968	0.83114	0.46101	0.52203	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq		Netherlands	2021-02-16	Pharyngula	Embryo	Multi-tissue	Multi-system