{"database": "metadata", "table": "run_metadata", "rows": [[35499, "SRR32834045", "SRX28117232", "SRS24473013", "SRP572644", "PRJNA1241156", "Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish", "GSE292726", "Transcriptome Analysis", "Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.", null, null, null, "mCherry cells  early HSPCs 6 dpf", "GSM8864260", null, "tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing", "mCherry cells  early HSPCs 6 dpf", "For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix", "Hematopoietic & Immune Cells", "The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf", "Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.", "Larvae were maintained in standard conditions  at 28C", "cell type:Hematopoietic & Immune Cells", "GSM8864260", "GSM8864260: mCherry cells  early HSPCs 6 dpf; Danio rerio; RNA Seq", "GSM8864260 r1", "GSM8864260", "1", "Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP572644", null, "loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=earlyHSPC 6dpf S1 L001 R1 001.fastq.gz   read2PairFiles=earlyHSPC 6dpf S1 L001 R2 001.fastq.gz   read3PairFiles=earlyHSPC 6dpf S1 L001 I1 001.fastq.gz   read4PairFiles=earlyHSPC 6dpf S1 L001 I2 001.fastq.gz", "earlyHSPC_6dpf_S1_L001_I1_001.fastq.gz earlyHSPC_6dpf_S1_L001_I2_001.fastq.gz earlyHSPC_6dpf_S1_L001_R1_001.fastq.gz earlyHSPC_6dpf_S1_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 234759123200.0, 733622260.0, "GSM8864260 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX28117232", "SRS24473013", "SRA2098862", "Albert Einstein College of Medicine", "Albert Einstein College of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2025-03-24", "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": ["35499"], "units": {}, "query_ms": 8.72026800061576}