{"database": "metadata", "table": "run_metadata", "rows": [[68540, "SRR17982193", "SRX14137998", "SRS11964031", "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 \u201ceat me\u201d 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", null, "SW001 Plate 1", "GSM5889061", null, "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", "SW001 Plate 1", "During\u202fsequencing \u202fRead\u202f1 was assigned 26 base pairs and was used to identify\u202fthe Illumina library barcode  cell barcode  and UMI. Read 2 was\u202fassigned 60 base pairs and used to map to the zebrafish GRCz11\u202fwith BWA MEM4. Data was demultiplexed as described in\u202fGr\u00fcn\u202fet al.\u202fMapping and generation of count tables were automated\u202fusing the\u202fMapAndGo\u202fscript.\u202fUnsupervised clustering and differential gene expression analysis was performed with the Seurat R toolkit. Gr\u00fcn 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", null, "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.", null, "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", "GSM5889061", "GSM5889061: SW001 Plate 1; Danio rerio; RNA Seq", "GSM5889061 r1", "GSM5889061", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP359373", null, null, "HAR-SW-001_HNMNYBGXC_S5_R1.fastq.gz HAR-SW-001_HNMNYBGXC_S5_R2.fastq.gz", "fastq fastq", 2952248592.0, 34328472.0, "GSM5889061 r1", "0:26 1:60", "A:705524530;C:558984210;G:536965097;T:1150640179;N:134576", 26, 60, null, null, 705524530, 558984210, 536965097, 1150640179, 134576, "SRX14137998", "SRS11964031", null, null, "Oncology/Hematology, Boston Children's Hospital", 2, 0.11246, 0.87351, 0.10506, 0.26554, 0.99086, 0.78561, 0.58974, 0.53787, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "United States", "2022-02-10", "Larval", "Larval", "Blood", "Hematopoietic System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["68540"], "units": {}, "query_ms": 11.69486399157904}