{"database": "metadata", "table": "run_metadata", "rows": [[59226, "SRR11777248", "SRX8330115", "SRS6649602", "SRP261275", "PRJNA631936", "mRNA seq of WT and tp53 e7/e7 mutant in zebrafish intestine with or without xxx microbiota.", "GSE150376", "Transcriptome Analysis", "In order to explore host factor provided by tp53 e7/e7 mutants that supports the colonization of specific microbiota  comparative transcriptomic analyses of intestines of WT vs. tp53 mutants or CV vs. GF conditions at 7 dpf were performed. Overall design: intestinal mRNA profiles of wild type WT and tp53 e7/e7 mutant zabrafish at 7 dpf Zebrafish larvae intestine at 7dpf were dissected and pooled 25 larvae intestine per group using fine pins and forceps manually.", null, "pubmed:34991725", null, "tp53 mutant in conventionally raised condition rep2 [P53 CV 2]", "GSM4547715", null, "source name:tp53 mutant in conventionally raised condition|strain background:AB|age:7 dpf mutant|treatment:conventionally raised condition|tissue:larvae intestine", "tp53 mutant in conventionally raised condition rep2 [P53 CV 2]", "Illumina Casava1.7 software used for basecalling. The reads were mapped to danRer10 using STAR v2.5.1. Read counts were calculated using a STAR standard protocol. Heat map was constructed using Mev v. 4.9.0. Statistical analyses were performed using R v. 3.3.0 and PYTHON v. 2.7.6. Genome build: hg19 Supplementary files format and content: tab delimited text files include log2CPM count per million values for each sample", "tp53 mutant in conventionally raised condition", "germ free condition was carried out as previously describedPham et al.  2008.", "Total RNA was isolated from cells using the RNeasy RNA extraction Mini Kit Qiagen and the quality of the RNA was confirmed by agarose gel electrophoresis. TruSeq Stranded mRNA Sample Preparation Guide  Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit Illumina. The mRNA derived from total RNA using poly T oligo attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.", "embryos were incubated at 28.5\u2103 in E3 egg water 5 mM NaCl  0.17 mM KCl  0.33 mM CaCl2  0.33 mM MgSO4", "strain background:AB|age:7 dpf mutant|treatment:conventionally raised condition|tissue:larvae intestine", "GSM4547715", "GSM4547715: tp53 mutant in conventionally raised condition rep2 [P53 CV 2]; Danio rerio; RNA Seq", "GSM4547715", null, "1", "Total RNA was isolated from cells using the RNeasy RNA extraction Mini Kit Qiagen and the quality of the RNA was confirmed by agarose gel electrophoresis. TruSeq Stranded mRNA Sample Preparation Guide  Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit Illumina. The mRNA derived from total RNA using poly T oligo attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.", "GEO Accession:GSM4547715", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP261275", null, null, "P53-CV-2_2.fastq.gz P53-CV-2_1.fastq.gz", "fastq fastq", 11447791268.0, 56672234.0, "GSM4547715 r1", "0:101 1:101", "A:2899821061;C:2807713057;G:2785490114;T:2954649447;N:117589", 101, 101, null, null, 2899821061, 2807713057, 2785490114, 2954649447, 117589, "SRX8330115", "SRS6649602", "SRA1074703", "GEO", "Genome structure research center, Korea Research Institute of Bioscience and Biotechnology", 2, 0.7899, 0.76325, 0.16845, 0.16179, 0.79338, 0.80119, 0.6617, 0.65495, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "South Korea", "2020-05-12", "Larval", "Larval", "Gut", "Digestive 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": ["59226"], "units": {}, "query_ms": 11.642393001238815}