{"database": "metadata", "table": "run_metadata", "rows": [[24711, "SRR25492014", "SRX21223187", "SRS18479990", "SRP452960", "PRJNA1001330", "Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish", "GSE239880", "Transcriptome Analysis", "The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.", null, null, null, "KBTGR  normal  replicate S5", "GSM7676112", null, "source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing", "KBTGR  normal  replicate S5", "Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files", "whole embryo", null, "For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 \u00b5m nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3\u2019 Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.", null, "tissue:whole embryo|cell type:neutrophils", "GSM7676112", "GSM7676112: KBTGR  normal  replicate S5; Danio rerio; RNA Seq", "GSM7676112 r1", "GSM7676112", "1", "For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 \u00b5m nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "loader:fastq load.py", "HYWGVBCXY_KBTGRnormal_S5_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S5_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S5_L002_R2_001.fastq.gz", "fastq fastq fastq", 1254798732.0, 9506051.0, "GSM7676112 r8", "0:8 1:26 2:98", "A:268758608;C:193670297;G:213835768;T:255268464;N:59861", 8, 26, 98, null, 268758608, 193670297, 213835768, 255268464, 59861, "SRX21223187", "SRS18479990", "SRA1685258", "Facultad de Ciencias de la vida, Universidad Andres Bello", "Facultad de Ciencias de la vida, Universidad Andres Bello", 1, 0.9283, null, 0.09341, null, 0.82211, null, 0.49121, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "Chile", "2023-08-02", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"]], "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": ["24711"], "units": {}, "query_ms": 10.417176999908406}