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Mus musculus
36 Downloadable Samples
Illumina HiSeq 1500
Description
The goal was to characterize gene expression profiles of HSPCs in mice during Bordetella pertussis infection. Mice were immunized with acellular or whole cell pertussis vaccines. HSPCs were isolated by flow cytometric sorting and RNA was prepared for library prep and RNA seq analysis.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Cell line, Treatment
View Samples- Mus musculus
- 32 Downloadable Samples
- Illumina HiSeq 1500
Description
Total transcriptome analysis of naive or vaccinated murine lungs, post-challenge with Bordatella pertussis. Mice were immunized with PBS, whole cell pertussis vaccine, acellular pertussis vaccine, and RTX (adenylate cyclase toxoid) vaccine. The mice were then infected with B. pertussis and at 1 or 6/9 days post-challenge total lung RNA was purified for RNA-seq analysis.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Disease, Cell line, Treatment
View Samples- Homo sapiens
- 24 Downloadable Samples
- Illumina HiSeq 2500
Description
Infection of mammalian cells with vesicular stomatitis virus (VSV) results in the inhibition of cellular gene expression. This host shut-off is achieved through viral mediated inhibition of cellular gene expression at multiple levels including transcription, mRNP nuclear-cytoplasmic export, and translation. To interrogate the effects of VSV infection on translation, we infected HeLa cells at MOI 10 for 2 or 6 hours and performed polysome profiling and deep sequenced total cytoplasmic mRNA as well as monosome- and polysome-associated mRNAs. Our data support a model where viral mRNA abundance contributes to host shut-off by dominating the pool of cytoplasmic mRNA.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment, Time
View Samples- Mus musculus
- 14 Downloadable Samples
Affymetrix Mouse Expression 430A Array (moe430a)
Description
12 C57BL/6 mice were infected orogastrically with the H. pylori strain SS1. After 6 and 12 months, 3 non-infected and 3 infected mice were sacrificed and stomachs isolated. Gastric tissues were disaggregated and total RNA were isolated by TRIzol extraction and then purified on RNeasy minicolumns. After synthesis of the first cDNA strand (In vitrogen), the double-stranded cDNA was obtained and used to produce biotin-labeled cRNA (Enzo Diagnostic). FRagmented cRNA was hybridized to GeneChip Mouse expression array 430A (Affymetrix).
Publication Title
Interferon gamma-signature transcript profiling and IL-23 upregulation in response to Helicobacter pylori infection.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Subject, Time
View Samples- Saccharomyces cerevisiae
- 14 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Yeast knockout strains were constructed by the Yeast Deletion Project. Three biological replicates were analyzed for each strain. 5 ml cultures were inoculated at OD600 = 0.2 from saturated overnight cultures and grown to mid-log phase (OD600 = 0.6 - 0.8) in YPD media 37 or in phosphate-depleted media 38 at 30C. Cells were harvested by centrifugation and washed with nuclease-free water (Ambion). Total RNA was isolated immediately after harvest using the Ribopure Yeast RNA Isolation Kit (Ambion). 5 mg of total RNA was used to generate labeled probes with standard Affymetrix protocols.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Pseudomonas aeruginosa
- 10 Downloadable Samples
- Affymetrix Pseudomonas aeruginosa Array (paeg1a)
Description
Effect of acyl-HSL signal or ectopic lasR, rhlR, or rpoS expression on the advancement of quorum sensing gene expression during the logarithmic phase of growth
Publication Title
Early Activation of Quorum Sensing in Pseudomonas aeruginosa Reveals the Architecture of a Complex Regulon
Sample Metadata Fields
Compound
View Samples- Homo sapiens
- 10 Downloadable Samples
- Illumina HiSeq 2500
Description
Cells were transfected with control, TIF-IA, or UBF siRNAs prior to transfection of no DNA or dsDNA. The impact of TIF-IA depletion on gene expression and the impact of TIF-IA and UBF depletion on dsDNA-induced gene expression were assayed.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Pseudomonas aeruginosa
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
Global Transcriptomic Analysis for Interactions between Pseudomonas aeruginosa and Bacteriophage PaP3
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Disease
View Samples- Zea mays
- 2 Downloadable Samples
- Illumina HiSeq 2500
Description
Plant growth-promoting rhizobacteria (PGPR) offer several benefits to host plants such as plant growth and development, elimination of deleterious pathogens and tolerance to abiotic stresses, including drought stress. Root colonization by PGPR alters the plant gene expressions, which result in enhanced tolerance to abiotic stresses. Here we aim to study the effects of the association between the Pseudomonas putida strain FBKV2 and maize (Zea mays L. var DHM117) during water depletion by characterizing differential transcriptome profiles of maize leaf. The present study helps in understanding the mechanisms of drought tolerance during plant interaction with PGPR and could provide tools to maximize the benefits of PGPR for crop production.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Treatment
View Samples
E-MEXP-1020- Saccharomyces cerevisiae
- 1 Downloadable Sample
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
Gene regulations that are affected by TBP1(E186D) at 28°C
Publication Title
TFIIB/SUA7(E202G) is an allele-specific suppressor of TBP1(E186D).
Sample Metadata Fields
Sex
View Samples