{"database": "metadata", "table": "run_metadata", "rows": [[38039, "SRR1342218", "SRX573022", "SRS627979", "SRP042975", "PRJNA251728", "Phagocytosis of mycobacteria by zebrafish macrophages is dependent on the scavenger receptor Marco  a key control factor of pro inflammatory signalling", "GSE58230", "Transcriptome Analysis", "Scavenger receptors on the cell surface of macrophages play an important role in host defence through their ability to bind microbial ligands and induce phagocytosis. Concurrently  signal transduction pathways are initiated that aid in defence mechanisms against the invading microbe. Here we report on the function of scavenger receptor Marco macrophage receptor with collagenous structure during infection of zebrafish embryos with Mycobacterium marinum  a close relative of Mycobacterium tuberculosis. Morpholino knockdown demonstrates that Marco is required for the rapid phagocytosis of M. marinum following intravenous infection.  Furthermore  gene expression analysis shows that Marco controls the initial transient pro inflammatory response to M. marinum and remains a determining factor for the immune response signature at later stages of infection. Increased bacterial burden following marco knockdown indicates that this scavenger receptor is important for control of M. marinum growth  likely due to delayed phagocytosis and reduced pro inflammatory signalling observed under conditions of Marco deficiency Overall design: Embryos were injected at the one cell stage with a morpholino targeting marco  or with the standard control morpholino from GeneTools for comparison. Subsequently  at 24 hpf the morphants and their controls were manually dechorionated at 24 hpf and at 28 hpf they were infected by injecting 200 colony forming units of M. marinum Mma20 into the caudal vein  or mock injected with PBS/2%PVP. post injections embryos were transferred into fresh egg water containing 0.003% 1 phenyl 2 thiourea Sigma Aldrich to prevent melanization and incubated for 4 days at 28\u00b0C. post the incubation period  infected and uninfected morphants  mutants and their controls were imaged and groups of 30 embryos were snap frozen in liquid nitrogen and RNA was isolated for Illumina RNAseq analysis.", null, "pubmed:25086293", null, "marco morphant uninfected rep4", "GSM1404383", null, "tissue:zebrafish embryo injected with marco morpholino  not infected|morpholino injection at 1 cell stage:marco morpholino 0.02 mM|blood island injection at 28 hpf:PBS/2%PVP", "marco morphant uninfected rep4", "Image analysis and base calling was done by the Illumina HCS version 1.15.1; One sequencing run for sample 1 was performed while the raw data from 3 sequencing runs samples 2  9 and 10 were combined to generate one fastq file and one tsv file each. The generated fastq files were used to calculate average insert sizes and standard deviations for paired end experiments. Sequence reads were quality trimmed using the quality trim module in the CLCbio Assembly Cell v4.0.6. Filtered reads were mapped to Ensembl transcripts Danio rerio.Zv9.67.dna.toplevel / Danio rerio.Zv9.67.cdna.all.fa http://www.ensembl.org/info/data/ftp/index.html using the ref assemle short module in the CLCbio Assembly Cell v4.0.6. Accumulation of transcripts to Ensembl genes was done by first converting the mapping files to a table with the assembly table module in the CLCbio Assembly Cell v4.0.6. Secondly  a custom script was used that sums all reads belonging to the same gene. Non uniquely mapped reads were divided between genes according to their ratio of uniquely mapped reads. Finally  read counts of transcripts belonging to the same gene were summed to obtain count data at Ensembl gene level. Fold change and differential expression significance values were calculated from gene level read counts using the DESeq package version 1.8.3 available in Bioconductor version 2.10. Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "zebrafish embryo injected with marco morpholino  not infected", "Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 200 CFU of M. marinum Mma20 bacteria suspended in PBS/2%PVP or mock injected with PBS/2%PVP as a control. At 5 dpf 4 days post infection pools of 30 embryos per treatment group were snap frozen in liquid nitrogen  and total RNA was isolated using QIAZOL reagent.", "Pools of embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at  80\u00b0C. Embryos were homogenized in 0 7 ml of QIAzol\u00ae Reagent Qiagen and subsequently total RNA was extracted and on column DNase digestion was performed with a miRNeasy Mini Kit Qiagen according to the manufacturer\u2019s instructions. The integrity of the RNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. A total of 3 \u03bcg of RNA was used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer\u2019s instructions two modifications were made. In the adapter ligation step 1 \u00b5l instead of 2.5 \u00b5l adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer\u2019s description with a read length of 2 x 50 nucleotides.", "Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5\u00b0C in egg water 60\u00b5g/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea Sigma Aldrich", "morpholino injection at 1 cell stage:marco morpholino 0.02 mM|blood island injection at 28 hpf:PBS/2%PVP|developmental stage rna isolation:4 dpi", "GSM1404383", "GSM1404383: marco morphant uninfected rep4; Danio rerio; RNA Seq", "GSM1404383", null, "1", "Pools of embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at  80\u00b0C. Embryos were homogenized in 0 7 ml of QIAzol\u00ae Reagent Qiagen and subsequently total RNA was extracted and on column DNase digestion was performed with a miRNeasy Mini Kit Qiagen according to the manufacturer\u2019s instructions. The integrity of the RNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. A total of 3 \u03bcg of RNA was used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer\u2019s instructions two modifications were made. In the adapter ligation step 1 \u00b5l instead of 2.5 \u00b5l adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer\u2019s description with a read length of 2 x 50 nucleotides.", "GEO Accession:GSM1404383", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP042975", null, null, "IL-12-05_9_GAGTGG_L003_R1_001.fastq.gz IL-12-05_9_GAGTGG_L003_R2_001.fastq.gz", "fastq fastq", 1248563028.0, 12240814.0, "GSM1404383 r1", "0:51 1:51", "A:337777282;C:290967808;G:281893529;T:337006324;N:918085", 51, 51, null, null, 337777282, 290967808, 281893529, 337006324, 918085, "SRX573022", "SRS627979", "SRA169358", "GEO", "Animal Sciences and Health, Institute of Biology, Leiden University", 2, 0.91949, 0.91263, 0.11016, 0.11021, 0.67241, 0.67136, 0.47526, 0.47587, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Netherlands", "2014-06-04", "Multi-stage", "Multi-stage", "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": ["38039"], "units": {}, "query_ms": 9.37550600792747}