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GSE34022
Homo sapiens
2 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Hepatitis C virus (HCV) infection is primarily treated with a pegylated interferon alpha based therapy, a regime that induces antiviral effects through the upregulation of many interferon-stimulated genes (ISGs). Whilst a number of anti-HCV ISGs have previously been identified, others may also be involved.
Publication Title
No associated publication
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 2 Downloadable Samples
NextSeq 500
Description
The regulatory networks involved in the development of hypoxic and necrotic granulomas following Mycobacterium tuberculosis infections remained elusive. The goal of the study was to determine the role for IL-17 in regulating hypoxic granuloma formation in the lungs of M. tuberculosis-infected C3HeB/FeJ mice.
Publication Title
No associated publication
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 81 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We carried out a global whole blood genome wide expression profiling of HIV exposed and uninfected women from Nairobi to identify host factors which may be a key contribution to HIV resistance phenomenon.
Publication Title
Microarray analysis of HIV resistant female sex workers reveal a gene expression signature pattern reminiscent of a lowered immune activation state.
Sample Metadata Fields
Specimen part
View Samples- Danio rerio
- 12 Downloadable Samples
- IlluminaHiSeq2500
Description
RNA-seq-based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
DNA Topoisomerase I (Top1) relaxes DNA supercoiling and is inhibited with high specificity by camptothecin, a natural product of chinese tree Camptotheca acuminata with anticancer activity. Topoisomerase activity is required at transcribing regions to modulate DNA supercoils generated by RNA polymerases. However, Top1 functions at promoters and molecular responses to CPT are not fully understood. We found that camptothecin increases antisense RNA polymerase II transcripts at active divergent CpG-island promoters in a replication-independent manner. Kinetics investigations of the formation of Top1-DNA cleavage complexes and non-B DNA structures showed that CPT interferes with Top1 modulation of negative DNA supercoiling at promoters. The present findings will be a resource to establish the role of such antisense RNAs in transcription regulation and to discover additional components of the response pathway. Moreover, the transcriptional camptothecin effects can be the molecular basis of the therapeutic activity in cancer as well as neurological syndromes.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- 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
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