run_metadata: 68541

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
68541	SRR17982194	SRX14137997	SRS11964030	SRP359373	PRJNA805357	Quality assurance of hematopoietic stem cells by macrophages determines stem cell clonality [macrophages]	GSE196551	Transcriptome Analysis	Tissue specific stem cells persist for a lifetime and can differentiate to maintain homeostasis or transform to initiate cancer. Despite their importance there are no described quality assurance mechanisms for newly formed stem cells. We observed intimate and specific interactions between macrophages and blood stem cells in zebrafish embryos. Stressed stem cells were marked by surface Calreticulin which stimulates macrophage interaction as an “eat me” signal. Macrophage stem cell interactions either lead to removal of cytoplasmic material and stem cell proliferation or resulted in complete stem cell engulfment. Using cellular barcoding we found that calreticulin knock down or embryonic macrophage depletion substantially reduced the number of stem cell clones into maturity. Our work supports a model in which embryonic macrophages determine hematopoietic clonality by monitoring stem cell quality. Overall design: Single cell RNA seq of FACS purified embryonic mpeg1:EGFP macrophages on the basis of uptake of fluorescence from runx1+23:mCherry HSPCs.	parent bioproject:PRJNA805354	pubmed:36137040		SW002 Plate 2	GSM5889062		tissue:embryonic macrophages\|transgenic line:mpeg1:EGFP; runx1+23:mCherry\|developmental stage:3 dpf embryo\|cell type:macrophages\|facs profile:EGFP+Cherry+ cells 1 192 EGFP+mCherry cells 193 384	SW002 Plate 2	During sequencing  Read 1 was assigned 26 base pairs and was used to identify the Illumina library barcode cell barcode and UMI. Read 2 was assigned 60 base pairs and used to map to the zebrafish GRCz11 with BWA MEM4. Data was demultiplexed as described in Grün et al. Mapping and generation of count tables were automated using the MapAndGo script. Unsupervised clustering and differential gene expression analysis was performed with the Seurat R toolkit. Grün D Kester L van Oudenaarden A. Validation of noise models for single cell transcriptomics. Nat Methods. 2014 Jun;116:637 40. doi: 10.1038/nmeth.2930. MapAndGo: https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Genome build: GRCz11 Supplementary files format and content: *.tsv	embryonic macrophages		Tails were amputated at the tip of yolk extension in ice cold PBS dissociated using liberase buffered to 0.1% FBS and filtered for flow cytometry. Single live EGFP+mCherry+ or EGFP+mCherry cells were sorted into individual wells of 384 well plates with both sample types represented on each plate to account for potential batch effects. Each well contained 50 nl droplets of barcoded RT primers in 10uL of mineral oil. RNA libraries were prepared for sequencing using the SORT seq protocol see Muraro et al. 2016 Cell Syst.		transgenic line:mpeg1:EGFP; runx1+23:mCherry\|developmental stage:3 dpf embryo\|cell type:macrophages\|facs profile:EGFP+Cherry+ cells 1 192 EGFP+mCherry cells 193 384	GSM5889062	GSM5889062: SW002 Plate 2; Danio rerio; RNA Seq	GSM5889062 r1	GSM5889062	1	Tails were amputated at the tip of yolk extension in ice cold PBS dissociated using liberase buffered to 0.1% FBS and filtered for flow cytometry. Single live EGFP+mCherry+ or EGFP+mCherry cells were sorted into individual wells of 384 well plates with both sample types represented on each plate to account for potential batch effects. Each well contained 50 nl droplets of barcoded RT primers in 10uL of mineral oil. RNA libraries were prepared for sequencing using the SORT seq protocol see Muraro et al. 2016 Cell Syst.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP359373			HAR-SW-002_HNMNYBGXC_S6_R1.fastq.gz HAR-SW-002_HNMNYBGXC_S6_R2.fastq.gz	fastq fastq	2627835952.0	30556232.0	GSM5889062 r1	0:26 1:60	A:617144731;C:503769922;G:471619208;T:1035178927;N:123164	26	60			617144731	503769922	471619208	1035178927	123164	SRX14137997	SRS11964030			Oncology/Hematology, Boston Children's Hospital	2	0.10029	0.88263	0.09465	0.20635	0.99255	0.80789	0.62005	0.55152	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq		United States	2022-02-10	Larval	Larval	Blood	Hematopoietic System