Transcriptomic tools

From Listeriomics Wiki
Revision as of 10:12, 11 September 2015 by Cbecavin (talk | contribs) (→‎How-to directly vizualize transcriptome datasets ?)

Jump to: navigation, search

General organization

A total of 492 files, 150 absolute value data, 342 relative expression data, were created and integrated in the Listeriomics website. For every experiment, relative expression data were always available whereas absolute expression data was found only in a quarter of the data.

The transcriptomics tools can be accessed by clicking on the button on the right of the banner of the Listeriomics website.

Transcriptomic datasets summary page


Filter panel

With this panel one can filter out the list of transcriptomics datasets by different key properties: Genome, Data type, intracellular growth. A earch bar is available to do so, or by clicking on the check box. In parenthesis is displayed the number of datasets available for each property.

List of all Listeria transcriptomes with biological condition information

All transcriptome datasets available are displayed with all additional information: “TimePoint” for growth time; “Mutant” if a gene is removed or over-expressed; “Growth” indicates the growth phase from which the bacteria were extracted; “Temperature” for the growth media; “Media” gives the media properties for example if Glucose was added, or if bacteria were extracted from macrophages; “Strain used” and “Strain array” indicates the strain used for the experiment, and the strain used for designing the arrays or mapping RNASeq reads.

Link to Genome and Heatmap viewers

If transcriptome datasets are selected in the summary table, there are two possibility: Display them on the genome viewer for direct vizualization, or look at fold-change values from dataset comparisons in the heatmap viewer.

How-to directly vizualize transcriptome datasets ?

TranscriptomeGene annotation panel of the Gene webpage
 Click on General information on the Omics selection panel
  • Genome viewer: Displays the gene in the genome viewer to see surrounding genome features.
  • General information: Every general information available on gene position, product, Cluster of Orthologous Gene (COG) and summary of gene conservation.
  • Supplementary information: All supplementary information available on the gene annotation such as conserved motif or alternative annotation.
  • Sequences: DNA and amino acid sequences are available here for copy/paste.
  • Localization information: A graphical representation of the predicted localization of the protein is displayed. Sub-cellular localization prediction was performed in Listeria monocytogenes EGD-e strain in Renier et al. Plos One 2012. For proteins from a strain different from EGD-e, the localization of its homolog EGD-e protain is shown.
Gene annotation panel of the Gene webpage
 Click on General information on the Omics selection panel
  • Genome viewer: Displays the gene in the genome viewer to see surrounding genome features.
  • General information: Every general information available on gene position, product, Cluster of Orthologous Gene (COG) and summary of gene conservation.
  • Supplementary information: All supplementary information available on the gene annotation such as conserved motif or alternative annotation.
  • Sequences: DNA and amino acid sequences are available here for copy/paste.
  • Localization information: A graphical representation of the predicted localization of the protein is displayed. Sub-cellular localization prediction was performed in Listeria monocytogenes EGD-e strain in Renier et al. Plos One 2012. For proteins from a strain different from EGD-e, the localization of its homolog EGD-e protain is shown.

Transcriptomic database

We downloaded the 64 Listeria related ArrayExpress experiments in MAGE-TAB standard. Every MAGE-TAB file included an IDF (Investigation Description Format) file giving general information about the experiment, SDRF (Sample and Data Relationship Format) file giving data relationship, and processed data. We manually curated every SDRF file and integrated the different information about the data.

IDAccessionTitleTypeOrganismAssaysYear month / dayProcessed DataRaw Data
1E-MEXP-1118Transcription profiling of Listeria monocytogenes EGD-e after heat-shock for 3, 10, 20, and 40 mintranscription profiling by arrayListeria monocytogenes242007 10 / 9http://www.ebi.ac.uk/arrayexpress/files/E-MEXP-1118/E-MEXP-1118.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-MEXP-1118/E-MEXP-1118.raw.1.zip
2E-BUGS-46Transcription profiling of Listeria monocytogenes relA and codY mutantstranscription profiling by arrayListeria monocytogenes62007 3 / 7http://www.ebi.ac.uk/arrayexpress/files/E-BUGS-46/E-BUGS-46.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-BUGS-46/E-BUGS-46.raw.1.zip
3E-GEOD-12143Listeria monocytogenes EGD after growth BHI vs. LB vs. MMtranscription profiling by arrayListeria monocytogenes92008 11 / 30http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-12143/E-GEOD-12143.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-12143/E-GEOD-12143.raw.1.zip
4E-GEOD-12145Listeria monocytogenes EGD?prfApPrfA and EGD?prfApPrfA* compared to the wild type strain EGDtranscription profiling by arrayListeria monocytogenes122008 11 / 30http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-12145/E-GEOD-12145.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-12145/E-GEOD-12145.raw.1.zip
5E-GEOD-12146Listeria monocytogenes EGD and EGD-etranscription profiling by arrayListeria monocytogenes, Listeria monocytogenes EGD-e32008 11 / 30http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-12146/E-GEOD-12146.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-12146/E-GEOD-12146.raw.1.zip
6E-GEOD-12151Modulation of PrfA activity in Listeria monocytogenes upon growth in different culture mediatranscription profiling by arrayListeria monocytogenes, Listeria monocytogenes EGD-e242008 11 / 30http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-12151/E-GEOD-12151.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-12151/E-GEOD-12151.raw.1.zip
7E-GEOD-11459Glycerol metabolism and PrfA activity in Listeria monocytogenestranscription profiling by arrayListeria monocytogenes232008 5 / 30http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-11459/E-GEOD-11459.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-11459/E-GEOD-11459.raw.1.zip
8E-MEXP-1144Transcription profiling of wild type Listera monocytogenes EGD-e and an isogenic deltahlydeltaplcA mutant strain 1 hour or 4 hours post infection into human intestinal epithelial cellstranscription profiling by arrayListeria monocytogenes122008 6 / 18http://www.ebi.ac.uk/arrayexpress/files/E-MEXP-1144/E-MEXP-1144.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-MEXP-1144/E-MEXP-1144.raw.1.zip
9E-MEXP-1162Transcription profiling of Listeria monocytogenes EGD-e versus the over-expressing strain (EGD-e+pPXrnhBtranscription profiling by arrayListeria monocytogenes62008 6 / 29http://www.ebi.ac.uk/arrayexpress/files/E-MEXP-1162/E-MEXP-1162.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-MEXP-1162/E-MEXP-1162.raw.1.zip
10E-MEXP-1170Transcription profiling of wild type and sigma B mutant Liseteria monocytogenes to characterise the EGD-e sigma B regulontranscription profiling by arrayListeria monocytogenes262008 7 / 2http://www.ebi.ac.uk/arrayexpress/files/E-MEXP-1170/E-MEXP-1170.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-MEXP-1170/E-MEXP-1170.raw.1.zip
11E-MEXP-2138Transcription profiling of Listeria monocytogenes wild type and prfA, sigB and hfq deletion mutants grown in different media and at different temperaturestranscription profiling by arrayListeria monocytogenes392009 4 / 24http://www.ebi.ac.uk/arrayexpress/files/E-MEXP-2138/E-MEXP-2138.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-MEXP-2138/E-MEXP-2138.raw.1.zip
12E-MEXP-2142Tiling path analysis of Listeria monocytogenes wild type and prfA, sigB and hfq deletion mutants grown in different media and at different temperaturestranscription profiling by tiling arrayListeria monocytogenes422009 4 / 24Data is not availablehttp://www.ebi.ac.uk/arrayexpress/files/E-MEXP-2142/E-MEXP-2142.raw.1.zip
13E-GEOD-19918Transcriptomic and phenotypic responses of L. monocytogenes with different growth efficiencies under acidic conditionstranscription profiling by arrayListeria monocytogenes142010 1 / 15http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-19918/E-GEOD-19918.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-19918/E-GEOD-19918.raw.1.zip
14E-GEOD-15651Listeria monocytogenes Transcriptome with RNA-SeqRNA-seqListeria monocytogenes42010 1 / 5http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-15651/processed/Data is not available
15E-GEOD-24107The cell envelope stress response mediated by the LiaFSRLm three-component system of Listeria monocytogenes is controlled via the phosphatase activity of the bifunctional histidine kinase LiaSLmtranscription profiling by arrayListeria monocytogenes EGD-e112010 11 / 16http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-24107/E-GEOD-24107.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-24107/E-GEOD-24107.raw.1.zip
16E-MEXP-1947Transcription profiling of Listeria monocytogenes after infection into murine macrophagestranscription profiling by arrayListeria monocytogenes552010 11 / 25http://www.ebi.ac.uk/arrayexpress/files/E-MEXP-1947/E-MEXP-1947.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-MEXP-1947/E-MEXP-1947.raw.1.zip
17E-GEOD-16336Induction of virulence genes in Listeria monocytogenes serotype 4b upon exposure to concentrations of biocidestranscription profiling by tiling arrayListeria monocytogenes str. 4b F2365342010 11 / 27http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-16336/E-GEOD-16336.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-16336/E-GEOD-16336.raw.1.zip
18E-GEOD-19014Pyruvate carboxylase and carbon metabolism in Listeria monocytogenestranscription profiling by arrayListeria monocytogenes42010 2 / 9http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-19014/E-GEOD-19014.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-19014/E-GEOD-19014.raw.1.zip
19E-TABM-663Transcription profiling of Listeria monocytogenes intracellularly replicating in mouse macrophages activated by IFN-gammatranscription profiling by arrayListeria monocytogenes122010 3 / 11http://www.ebi.ac.uk/arrayexpress/files/E-TABM-663/E-TABM-663.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-TABM-663/E-TABM-663.raw.1.zip
20E-MTAB-1677Transcription profiling by tiling array of Listeria monocytogenes EGD wild type, Listeria monocytogenes EGD-e wild-type and EGD-e PrfA*transcription profiling by tiling arrayListeria monocytogenes EGD, Listeria monocytogenes EGD-e92013 8 / 1http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-1677/E-MTAB-1677.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-MTAB-1677/E-MTAB-1677.raw.1.zip
21E-MTAB-116Transcription profiling of wild type and L forms of Listeria monocytogenestranscription profiling by arrayListeria monocytogenes42010 5 / 12Data is not availablehttp://www.ebi.ac.uk/arrayexpress/files/E-MTAB-116/E-MTAB-116.raw.1.zip
22E-GEOD-20274Transcriptome profiling of Listeria monocytogenes during growth on a RTE-meat matrixtranscription profiling by arrayListeria monocytogenes122010 5 / 14http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-20274/E-GEOD-20274.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-20274/E-GEOD-20274.raw.1.zip
23E-GEOD-19570Osmotic stress in Listeria monocytogenes serotype 4b strain F2365 grown in BHI medium and BHI medium with 1.2% NaCltranscription profiling by arrayListeria monocytogenes122010 5 / 15http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-19570/E-GEOD-19570.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-19570/E-GEOD-19570.raw.1.zip
24E-GEOD-11347Characterization of the SigB-PrfA regulatory network in Listeria monocytogenestranscription profiling by arrayListeria monocytogenes242010 5 / 19http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-11347/E-GEOD-11347.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-11347/E-GEOD-11347.raw.1.zip
25E-GEOD-12634Listeria monocytogenes SOS response determined after mitomycin C exposuretranscription profiling by arrayListeria monocytogenes EGD-e162010 5 / 19http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-12634/E-GEOD-12634.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-12634/E-GEOD-12634.raw.1.zip
26E-GEOD-18363Identification of the major PEP-phosphotransferase systems (PTS) for glucose, mannose and cellobiose of L. monocytogenestranscription profiling by arrayListeria monocytogenes EGD-e242010 5 / 19http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-18363/E-GEOD-18363.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-18363/E-GEOD-18363.raw.1.zip
27E-GEOD-21427Sigma B in Listeria monocytogenes strains from different lineagestranscription profiling by arrayListeria monocytogenes42010 6 / 1http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-21427/E-GEOD-21427.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-21427/E-GEOD-21427.raw.1.zip
28E-GEOD-6421regulation of Listeria monocytogenes internalin-like genes by ?B and PrfA as revealed by subgenomic microarray analysestranscription profiling by arrayListeria monocytogenes, Listeria monocytogenes 10403S42010 6 / 11http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-6421/E-GEOD-6421.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-6421/E-GEOD-6421.raw.1.zip
29E-GEOD-18796Physiology and genetic activity of Listeria monocytogenes during multi-hurdle stress induced cell deathtranscription profiling by arrayListeria monocytogenes82010 6 / 20http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-18796/E-GEOD-18796.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-18796/E-GEOD-18796.raw.1.zip
30E-MTAB-118Transcription profiling of wild type and SreA mutant Listeria monocytogenestranscription profiling by arrayListeria monocytogenes42010 6 / 20Data is not availablehttp://www.ebi.ac.uk/arrayexpress/files/E-MTAB-118/E-MTAB-118.raw.1.zip
31E-GEOD-13057In vivo transcriptome of Listeria monocytogenes EGDetranscription profiling by arrayListeria monocytogenes EGD-e82010 6 / 25http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-13057/E-GEOD-13057.processed.1.zipData is not available
32E-MEXP-2279Transcription profiling of Listeria monocytogenes following oxygen restrictiontranscription profiling by arrayListeria monocytogenes32010 7 / 1http://www.ebi.ac.uk/arrayexpress/files/E-MEXP-2279/processed/http://www.ebi.ac.uk/arrayexpress/files/E-MEXP-2279/E-MEXP-2279.raw.1.zip
33E-GEOD-25195Transcriptional response of Listeria monocytogenes h7858 and f6854 to lactate and acetatetranscription profiling by arrayListeria monocytogenes322011 11 / 3http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-25195/E-GEOD-25195.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-25195/E-GEOD-25195.raw.1.zip
34E-GEOD-34083Intracellular transcription by multiple Listeria monocytogenes strainstranscription profiling by arrayListeria monocytogenes42011 12 / 2http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-34083/E-GEOD-34083.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-34083/E-GEOD-34083.raw.1.zip
35E-GEOD-16887Identification of sigB inhibitors in L. monocytogenestranscription profiling by arrayListeria monocytogenes 10403S12011 12 / 6http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-16887/E-GEOD-16887.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-16887/E-GEOD-16887.raw.1.zip
36E-GEOD-26690Transcriptomic Response of Listeria monocytogenes throughout the Life Cycletranscription profiling by arrayListeria monocytogenes serotype 4b str. F2365122011 2 / 24http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-26690/E-GEOD-26690.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-26690/E-GEOD-26690.raw.1.zip
37E-GEOD-28507Listeria monocytogenes transcriptional response to biletranscription profiling by arrayListeria monocytogenes62011 4 / 12http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-28507/E-GEOD-28507.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-28507/E-GEOD-28507.raw.1.zip
38E-BUGS-110Global Transcriptional Analysis of Spontaneous Sakacin P-Resistant Mutant Strains of Listeria monocytogenes during Growth on Different Sugarstranscription profiling by arrayListeria monocytogenes162011 4 / 15http://www.ebi.ac.uk/arrayexpress/files/E-BUGS-110/processed/http://www.ebi.ac.uk/arrayexpress/files/E-BUGS-110/E-BUGS-110.raw.1.zip
39E-GEOD-22819Gene expression profiling of a pressure-tolerant Listeria monocytogenes Scott A ctsR deletion mutanttranscription profiling by arrayListeria monocytogenes42011 6 / 10http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-22819/E-GEOD-22819.processed.1.zipData is not available
40E-GEOD-22672Listeria monocytogenes Grown at Refrigeration Temperature Shows Reduced Acid Survival and an Altered Transcriptional Response to Acid Shocktranscription profiling by arrayListeria monocytogenes102011 6 / 30http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-22672/E-GEOD-22672.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-22672/E-GEOD-22672.raw.1.zip
41E-GEOD-27521Temporal changes in Listeria monocytogenes gene expression during salt stresstranscription profiling by arrayListeria monocytogenes602011 7 / 1http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-27521/E-GEOD-27521.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-27521/E-GEOD-27521.raw.1.zip
42E-MTAB-329non-coding RNA-Seq of Listeria monocytogenes from bacteria growing extracellularly and in macrophagesRNA-seqListeria monocytogenes EGD-e22011 7 / 21http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-329/E-MTAB-329.processed.1.zipData is not available
43E-GEOD-32434Analysis of ?L dependent traits based on phenotypic and transcriptomic evaluation of the Listeria monocytogenes EGDe straintranscription profiling by arrayListeria monocytogenes EGD-e362012 1 / 1http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-32434/E-GEOD-32434.processed.1.zipData is not available
44E-GEOD-27936Gene Expression Profiling of Listeria monocytogenes in monoculture and in co-culture state in the presence of Bacillus subtilis both as planktonic cells and in biofilms.transcription profiling by arrayListeria monocytogenes J016182012 1 / 15http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-27936/E-GEOD-27936.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-27936/E-GEOD-27936.raw.1.zip
45E-GEOD-32913Genome-wide transcriptional profiling of the cell envelope stress response of Listeria monocytogenestranscription profiling by arrayListeria monocytogenes162012 1 / 24http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-32913/E-GEOD-32913.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-32913/E-GEOD-32913.raw.1.zip
46E-GEOD-36060Comparative transcriptomics of pathogenic and non-pathogenic Listeria speciesRNA-seqListeria monocytogenes EGD-e, Listeria innocua641030http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-36060/E-GEOD-36060.processed.1.zip
47E-GEOD-40598Role of a GntR-family response regulator LbrA in Listeria monocytogenes biofilm formationtranscription profiling by arrayListeria monocytogenes62012 9 / 6http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-40598/E-GEOD-40598.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-40598/E-GEOD-40598.raw.1.zip
48E-GEOD-32172L. monocytogenes ctsR mutant 2-1 cells response to pressuretranscription profiling by arrayListeria monocytogenes str. Scott A22013 2 / 14http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-32172/E-GEOD-32172.processed.1.zipData is not available
49E-GEOD-41891Gene expression profiling of a nisin-sensitive Listeria monocytogenes Scott A ctsR deletion mutanttranscription profiling by arrayListeria monocytogenes str. Scott A42013 2 / 14http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-41891/E-GEOD-41891.processed.1.zipData is not available
50E-GEOD-46182Characterization of the lag-phase associated cold acclimation gene expression responses in L. monocytogenes EGD-etranscription profiling by arrayListeria monocytogenes EGD-e122013 4 / 19http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-46182/E-GEOD-46182.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-46182/E-GEOD-46182.raw.1.zip
51[ E-GEOD-60363]Sequestration of a two-component response regulator by a riboswitch regulated non-coding RNARNA-seqListeria monocytogenes EGD-e841873http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-60363/E-GEOD-60363.processed.1.zip
52E-GEOD-43052The whole genome transcription analysis reveals the regulatory network for Listeria monocytogenes biofilm formation is modified in the prfA deletion mutanttranscription profiling by arrayListeria monocytogenes EGD-e152013 5 / 1http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-43052/E-GEOD-43052.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-43052/E-GEOD-43052.raw.1.zip
53E-GEOD-46612Characterization of the transcriptomes of genetically diverse Listeria monocytogenes exposed to hyperosmotic and low temperature conditionstranscription profiling by arrayListeria monocytogenes62013 5 / 4http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-46612/E-GEOD-46612.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-46612/E-GEOD-46612.raw.1.zip
54E-GEOD-42730Listeria monocytogenes strain F2365 has reduced ability to survive stress while maintaining virulence characteristicstranscription profiling by arrayListeria monocytogenes12013 6 / 1http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-42730/E-GEOD-42730.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-42730/E-GEOD-42730.raw.1.zip
55E-GEOD-49056Listeria monocytogenes Sigma B, but not PrfA, shows strain specific contributions to growth under salt stress, and prolongated lag phase of a sigB null mutant across strainstranscription profiling by arrayListeria monocytogenes12013 20 / 7http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-49056/E-GEOD-49056.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-49056/E-GEOD-49056.raw.1.zip
56E-MTAB-1676Transcription profiling by array of Listeria monocytogenes EGD wild type, Listeria monocytogenes EGD-e wild-type and EGD-e PrfA*transcription profiling by arrayListeria monocytogenes EGD, Listeria monocytogenes EGD-e92013 8 / 1http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-1676/E-MTAB-1676.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-MTAB-1676/E-MTAB-1676.raw.1.zip
57E-GEOD-47721Transcriptomic profiling of L-rhamnose utilization in Lmo0753 deletion mutant of Listeria monocytogenes EGDe from human foodborne outbreak associated lineage LIIRNA-seqListeria monocytogenes EGD-e441472http://www.ebi.ac.uk/ena/data/view/SRP024278
58E-GEOD-52325Transcriptional adaptation of L. monocytogenes EGD to oxygen availabilitytranscription profiling by arrayListeria monocytogenes EGDe1241666http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-52325/E-GEOD-52325.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-52325/E-GEOD-52325.raw.1.zip
59E-GEOD-51487A single exposure to a sublethal pediocin concentration initiates a resistance-associated temporal cell envelope and general stress response in L. monocytogenesRNA-seqListeria monocytogenes EGDe2041670http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-51487/E-GEOD-51487.processed.1.ziphttp://www.ebi.ac.uk/ena/data/view/SRP031645
60PRJEB4644Ultra deep Sequencing of Listeria monocytogenes sRNA transcriptome revealed new antisense RNAsRNA-seqListeria monocytogenes EGD-e641680
61E-GEOD-48187Listeria monocytogenes exposure to chlorine dioxidetranscription profiling by arrayListeria monocytogenes441705http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-48187/E-GEOD-48187.raw.1.zip
62E-GEOD-51193Temperature dependent Transcriptome of L. monocytogenes EGDe in minimal mediumtranscription profiling by arrayListeria monocytogenes EGD-e1241782http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-51193/E-GEOD-51193.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-51193/E-GEOD-51193.raw.1.zip
63E-GEOD-56558Stress and adaptation of Listeria monocytogenes 08-5923 exposed to a sublethal dose of carnocyclin Atranscription profiling by arrayListeria monocytogenes 08-5923641737http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-56558/E-GEOD-56558.processed.1.ziphttp://www.ebi.ac.uk/arrayexpress/files/E-GEOD-56558/E-GEOD-56558.raw.1.zip
64PRJEB6949sRNA transcriptome of Listeria monocytogenes during extracellular growth and within macrophagesRNA-seqListeria monocytogenes EGD-e641922
Retrieved from "http://listeriomics.pasteur.fr/WikiListeriomics/index.php?title=Transcriptomic_tools&oldid=278"