run_metadata: 9765
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 |
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| 9765 | ERR3454280 | ERX3476200 | ERS360450 | ERP116513 | PRJEB33700 | Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila | ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961 | Other | Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors. | ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26 | SAMEA2224101 | SC | ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:50:06Z|External Id:SAMEA2224101|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:50:06Z|INSDC status:public|Submitter Id:ZMP phenotype 32 4 mutant sc 2013 10 17T10:16:27Z 1727408|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically abnormal embryos from ZMP phenotype32 clutch 4. A 5 base indexing sequence CGCAA is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 4 mutant sc 2013 10 17T10:16:27Z 1727408|scientific name:Danio rerio|strain:mixed | Illumina HiSeq 2500 sequencing | ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 5 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | ERP116513 | Illumina HiSeq 2500 sequencing | ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26 | 1031629900.0 | 20632598.0 | ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 5 | 0:50 | A:266496533;C:234318648;G:214719546;T:316013013;N:82160 | 50 | 266496533 | 234318648 | 214719546 | 316013013 | 82160 | ERX3476200 | ERS360450 | ERA2051096 | CIRI-Inserm-U1111|European Nucleotide Archive | CIRI-Inserm-U1111 | 1 | 0.003 | 0.00187 | 0.99902 | 0.27272 | 50 | T | under 1.2% mapping rate | illumina | hiseq_era | 3prime | cdna_unspecified | unknown | bulk | unknown | unknown | France | 2014-03-04 | Hatching | Embryo | Whole Organism | All anatomical structures |