{"database": "metadata", "table": "run_metadata", "rows": [[61615, "SRR12888601", "SRX9353789", "SRS7576887", "SRP288474", "PRJNA671679", "Using a Zebrafish Model to Identify Cellular Responses to Uropathogenic E. coli Bacteremia", "GSE160038", "Transcriptome Analysis", "Urinary tract infections UTIs are the second most common infections encountered in the pediatric population  second only to respiratory tract infections. UTIs are also a major cause of morbidity and mortality. UTIs can often ascend causing infection in the upper urinary tract or even progress to bacteremia or urosepsis. Urosepsis accounts for 10 30% of septic shock cases and Uropathogenic E.coli UPEC is responsible for almost 75% of cases. Therefore  increased understanding of the effects of urosepsis at the cellular and organ specific level will provide the foundation for improvements in clinical care. Overall design: Two zebrafish cohorts were injected with either sterile saline or UPEC and subjected to scRNA seq. Cell clusters were identified and subjected to RNA velocity analysis. Selected clusters relevant to the innate immune system and bactericidal activity underwent canonical pathway analysis. RNA velocity analysis revealed several key changes in the transcriptional state of UPEC infected cells and pathway analysis provided key information regarding changes in innate immune pathways within the cell clusters.", null, null, null, "UPEC injected 5 dpf embryo cells", "GSM4855812", null, "source name:5 dpf embryo|tissue preparation:Single cell suspension|tissue:embryo|age:5 days|treatment:UPEC", "UPEC injected 5 dpf embryo cells", "CellRanger version 3.1 was utilized to process the raw sequence data generated by the sequencer. CellRanger uses bcl2fastq to demultiplex raw base sequence calls generated from the sequencer into sample specific FASTQ files The FASTQ files were then aligned to the zebrafish reference genome Danio rerio.GRCz11 with RNAseq aligner STAR The aligned reads were traced back to individual cells and the gene expression level of individual genes were quantified based on the number of UMIs unique molecular indices detected in each cell.The filtered feature cell barcode matrices generated by CellRanger were used for further analysis. Genome build: GRCz11 3.1.0 Supplementary files format and content: Tab delimited text file containing count matrix for each gene and cell", "5 dpf embryo", "Zebrafish were injected with red fluorescent protein RFP expressing UPEC. post 24 hours  the zebrafish were dissociated and then homogenate was placed on a glass slide and evaluated for RFP expression on Keyence BZII microscope. Allowed embryos to mature for 4 dpf dpf in a 28.5\u00b0C incubator in egg water filled petri dishes. Embryos were collected via visualization through dissecting microscope and separated into control and experimental groups each containing about 30 embryos. The embryos were anesthetized with tricaine and immobilized in methylcellulose. A mixture of the bacterial solution described above  phenol red  and PBS was made.The mixture was loaded into microneedle and about 1nl of the mixture was injected into the pericardial cavity of each embryo in the experimental group. The control group was injected with 1nl of phenol red and PBS. The embryos were then incubated for 24 hours at 28.5\u00b0C.", "The embryos were euthanized with tricaine and ice added to egg water. The embryos were then added to methylcellulose and the heads of the embryos were removed using a straight blade sterile scalpel. The remaining portion of the embryos were collected and washed 2x with cold PBS at 700g for 5 min then dissociated with Liberase TL Sigma containing DNAse I Sigma in DMEM using gentleMACS Miltenyi Biotec in C tubes then cells were incubated at 370C for 10 minutes with continuous monitoring. When cell homogenate started to disappear  DMEM containing 10% FBS was added to stop the dissociation reaction. Cells were then filtered on 70\u00b5m filter and centrifuged at 1500 rpm for 10 min. Cells were counted on hemocytometer then dead cells were removed using dead cell removal microbead Miltenyi Biotec with MS column. Live cells were then centrifuged and resuspended in DPBS without xxx+ or Mg2+ and processed for single cell RNA sequencing on 10x genomics platform. Library preparation was performed usingChromium\u2122 Next GEM Single Cell 3\u02b9 GEM  Library & Gel Bead Kit v3.1.", null, "tissue preparation:Single cell suspension|tissue:embryo|age:5 days|treatment:UPEC", "GSM4855812", "GSM4855812: UPEC injected 5 dpf embryo cells; Danio rerio; RNA Seq", "GSM4855812", null, "1", "The embryos were euthanized with tricaine and ice added to egg water. The embryos were then added to methylcellulose and the heads of the embryos were removed using a straight blade sterile scalpel. The remaining portion of the embryos were collected and washed 2x with cold PBS at 700g for 5 min then dissociated with Liberase TL Sigma containing DNAse I Sigma in DMEM using gentleMACS Miltenyi Biotec in C tubes then cells were incubated at 370C for 10 minutes with continuous monitoring. When cell homogenate started to disappear  DMEM containing 10% FBS was added to stop the dissociation reaction. Cells were then filtered on 70\u00b5m filter and centrifuged at 1500 rpm for 10 min. Cells were counted on hemocytometer then dead cells were removed using dead cell removal microbead Miltenyi Biotec with MS column. Live cells were then centrifuged and resuspended in DPBS without xxx+ or Mg2+ and processed for single cell RNA sequencing on 10x genomics platform. Library preparation was performed usingChromium\u2122 Next GEM Single Cell 3\u02b9 GEM  Library & Gel Bead Kit v3.1.", "GEO Accession:GSM4855812", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP288474", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=Upec S4 L001 I1 001.fastq.gz   read2PairFiles=Upec S4 L001 R1 001.fastq.gz   read3PairFiles=Upec S4 L001 R2 001.fastq.gz", "Upec_S4_L001_I1_001.fastq.gz Upec_S4_L001_R1_001.fastq.gz Upec_S4_L001_R2_001.fastq.gz", "fastq fastq fastq", 30696246075.0, 241702725.0, "GSM4855812 r1", "0:8 1:28 2:91", "A:8297484773;C:7271108187;G:7092330543;T:8034542269;N:780303", 8, 28, 91, null, 8297484773, 7271108187, 7092330543, 8034542269, 780303, "SRX9353789", "SRS7576887", "SRA1147613", "GEO", "Pediatric Nephrology, Indiana University School of Medicine", 1, 0.94674, null, 0.11144, null, 0.79107, null, 0.5211, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "India", "2020-10-25", "Larval", "Larval", "Embryo Imprecise", "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": ["61615"], "units": {}, "query_ms": 8.417392004048452}