RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata: 59222

This data as json

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
59222 SRR11777252 SRX8330119 SRS6649606 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.   pubmed:34991725   Wide type in conventionally raised condition rep2 [WT CV 2] GSM4547719   source name:Wide type in conventionally raised condition|strain background:AB|age:7 dpf type|treatment:conventionally raised condition|tissue:larvae intestine Wide type in conventionally raised condition rep2 [WT 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 Wide type 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℃ 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 type|treatment:conventionally raised condition|tissue:larvae intestine GSM4547719 GSM4547719: Wide type in conventionally raised condition rep2 [WT CV 2]; Danio rerio; RNA Seq GSM4547719   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:GSM4547719 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP261275     WT-CV-2_1.fastq.gz WT-CV-2_2.fastq.gz fastq fastq 8458913418.0 41875809.0 GSM4547719 r1 0:101 1:101 A:2076906648;C:2150093093;G:2142972201;T:2088851553;N:89923 101 101     2076906648 2150093093 2142972201 2088851553 89923 SRX8330119 SRS6649606 SRA1074703 GEO Genome structure research center, Korea Research Institute of Bioscience and Biotechnology 2 0.70042 0.63598 0.13488 0.12346 0.82731 0.83402 0.70617 0.63904 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   South Korea 2020-05-12 Larval Larval Gut Digestive System