{"database": "metadata", "table": "run_metadata", "rows": [[36029, "SRR33397800", "SRX28640377", "SRS24910734", "SRP582598", "PRJNA1257824", "Paired single cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation in humans and zebrafish", "GSE296119", "Transcriptome Analysis", "Mycobacterial granulomas are categorical manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection  but the identities  arrangement  cellular interactions and regulation of the cells that comprise them has thus far been incompletely understood. Using the Mycobacterium marinum zebrafish model we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls. Overall design: To determine the impact of mycobacterial infection on the transcriptional response of nascent granuloma macrophages we conducted bulk RNA seq on flow sorted infected and uninfected macrophages isolated from infected larvae or uninfected controls.", null, null, null, "1C 1726", "GSM8965479", null, "source name:Larval|tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Uninfected|treatment:nonfluorescent cells from uninfected larvae|geo loc name:missing|collection date:missing", "1C 1726", "RNA seq data were processed using the fastp toolkit to trim low quality bases and Illumina sequencing adapters with default parameters. Trimmed sequence reads were pseudo aligned to GRCz11/ASM1834v1 using Salmon. Gene count was quantified by Salmon v1.4.0. Read count extraction and normalization were performed using DESeq2. Assembly: GRCz11 Supplementary files format and content: zebrafish bulkRNAseq raw count.csv; a excel csv file contains raw counts quantified by Salmon", "Larval", "Two dpf zebrafish larvae were infected with approximately 100 fluorescent expressing Mycobacterium marinum or control; Macrophages were isolated from infected or uninfected larvae post 48 hours of infection  then sorted by FACS.", "RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer\u2019s instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource", "Zebrafish larvae were maintained at 28.5 \u00b0C in E3 medium supplemented with 1 phenyl 2 thiourea #P7629  Sigma Aldrich at a final concentration of 45 \u03bcg/mL.", "tissue:Larval|cell line:Larval|cell type:macrophage|genotype:Uninfected|treatment:nonfluorescent cells from uninfected larvae", "GSM8965479", "GSM8965479: 1C 1726; Danio rerio; RNA Seq", "GSM8965479 r1", "GSM8965479", "1", "RNA extraction was carried out using the Qiagen micro RNeasy kit and manufacturer's instructions were followed with subsequent Single Cell RT PCR method for cDNA synthesis and subsequent PCR amplification developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51. Illumina Sequencing Library Preparation method developed in: Zhou T  Chien MS  Kaleem S  Matsunami H. 2016. Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol 594:4225 51.  was used whereby the amplified cDNA was purified with magnetic beads Agencourt AMPure XP and 50ng of DNA was tagmentated using the Nextera DNA sample preparation kits Illumina Inc. Sequencing was carried out by the Duke Sequencing and Genomic Technologies Shared Resource", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP582598", null, null, "1C_1726.fastq.gz", "fastq", 2116510506.0, 41500206.0, "GSM8965479 r1", "0:51", "A:580244434;C:475940957;G:474848964;T:585459729;N:16422", 51, null, null, null, 580244434, 475940957, 474848964, 585459729, 16422, "SRX28640377", "SRS24910734", "SRA2148962", "Duke University", "Duke University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "bulk", "bulk", "bulk", null, "United States", "2025-05-01", "Larval", "Larval", "Multi-tissue", "Multi-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": ["36029"], "units": {}, "query_ms": 11.765444000047864}