{"database": "metadata", "table": "run_metadata", "rows": [[39666, "SRR2027910", "SRX1029314", "SRS937773", "SRP058376", "PRJNA284108", "RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures", "GSE68920", "Transcriptome Analysis", "We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28\u00b0C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.", null, "pubmed:31832066", null, "6dpf mpeg1:mCherryPosMmarinumGFPPos rep2", "GSM1686458", null, "source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu", "6dpf mpeg1:mCherryPosMmarinumGFPPos rep2", "Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample", "zebra fish larvae", "Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.", "Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer\u2019s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were 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 1 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 SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich", "tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu", "GSM1686458", "GSM1686458: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep2; Danio rerio; RNA Seq", "GSM1686458", null, "1", "Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer\u2019s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were 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 1 x 50 nucleotides.", "GEO Accession:GSM1686458", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP058376", null, null, "ZFG-14-09_05_ACTGAT_L003_R1_001.fastq.gz", "fastq", 846771207.0, 16603357.0, "GSM1686458 r1", "0:51", "A:268435928;C:150903620;G:153931870;T:273331733;N:168056", 51, null, null, null, 268435928, 150903620, 153931870, 273331733, 168056, "SRX1029314", "SRS937773", "SRA268539", "GEO", "Institute of Biology, Leiden University", 1, 0.72025, null, 0.17943, null, 0.87937, null, 0.5683, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "poly_a", "smarter", "bulk", "unknown", "unknown", null, "Netherlands", "2015-05-15", "Larval", "Larval", "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": ["39666"], "units": {}, "query_ms": 10.356271995988209}