{"database": "metadata", "table": "run_metadata", "rows": [[61983, "SRR13080692", "SRX9527457", "SRS7734428", "SRP293088", "PRJNA679243", "A Non Canonical Type 2 Immune Response Coordinates Tuberculous Granuloma Formation and Epithelialization", "GSE161712", "Other", "Using the zebrafish M. marinum model  we identify the basis of granuloma macrophage transformation. Single cell RNA seq analysis of zebrafish granulomas as well as analysis of M. tuberculosis infected macaques reveal that  even in the presence of robust type 1 immune responses  countervailing type 2 signals associate with macrophage epithelialization. We find that type 2 immune signaling  mediated via stat6  is absolutely required for epithelialization and granuloma formation. Overall design: Wildtype zebrafish M. marinum granuloma single cell RNAseq profile.", null, "pubmed:33761328", null, "*AB wildtype zebrafish M.marinum granuloma cells", "GSM4913139", null, "source name:WT Zebrafish granuloma cels|tissue:Granulomas|cell type:Granuloma cells|zebrafish strain:*AB", "*AB wildtype zebrafish M.marinum granuloma cells", "10X Cell Ranger was used to demultiplex raw base call BCL files generated by an Illumina sequencer into FASTQ before aligning them to the Ensembl zebrafish genome assembly GRCz11.96  performed filtering  barcode and UMI counting. Genome build: GRCz11.96 Supplementary files format and content: WTGran.matrix.mtx:  Gene barcode matrix in Market Exchange Format MEX for Mus musculus Uninjured Control & Injured1d  tibialis anterior muscle cells. Columns correspond to individual cellsbarcodes  while rows correspond to genes. Supplementary files format and content: WTGran.features.tsv: Genes corresponding to row indices in matrix.mtx. Gene ID and gene name are stored in the first and second column. Supplementary files format and content: WTGran.barcodes.tsv: Barcode sequences that correspond to column indices in matrix.mtx.", "WT Zebrafish granuloma cels", null, "Granulomas were microdissected from of tissues 14 days post infection and cells dissociated using 30 minute incubation with 0.05% trypsin/EDTA Library preparation was done using Chromium Single Cell 3\u2019 GEM  Library and Gel Bead Kit v3.", "Adult  wildtype *AB zebrafish were infected with 350 fluorescent bacteria of M. marinum.", "tissue:Granulomas|cell type:Granuloma cells|zebrafish strain:*AB", "GSM4913139", "GSM4913139: *AB wildtype zebrafish M.marinum granuloma cells; Danio rerio; RNA Seq", "GSM4913139", null, "1", "Granulomas were microdissected from of tissues 14 days post infection and cells dissociated using 30 minute incubation with 0.05% trypsin/EDTA Library preparation was done using Chromium Single Cell three prime GEM  Library and Gel Bead Kit v3.", "GEO Accession:GSM4913139", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP293088", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=5761 S1 L001 I1 001.fastq.gz   read2PairFiles=5761 S1 L001 R1 001.fastq.gz   read3PairFiles=5761 S1 L001 R2 001.fastq.gz", "5761_S1_L001_I1_001.fastq.gz 5761_S1_L001_R1_001.fastq.gz 5761_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 13295345266.0, 104687758.0, "GSM4913139 r1", "0:8 1:28 2:91", "A:3755348831;C:2900888340;G:2979576059;T:3656820253;N:2711783", 8, 28, 91, null, 3755348831, 2900888340, 2979576059, 3656820253, 2711783, "SRX9527457", "SRS7734428", "SRA1160946", "GEO", "Tobin, Molecular Genetics and Microbiology, Duke University", 1, 0.92709, null, 0.13791, null, 0.81929, null, 0.57724, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-11-18", "Adult", "Adult", "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": ["61983"], "units": {}, "query_ms": 10.363850999965507}