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Homo sapiens
8 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Using microarray analysis, we explored the differences in gene expression profiles between individual and combined stimulation of Toll-like receptor 4 (TLR4) and Nucleotide oligomerization domain (NOD)-like receptor (NOD2) in THP-1 cells. Analysis was performed 3 hours post addition of TLR4 agonist MPLA and the NOD2 agonist MDP to THP-1 cells.
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 71 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Based on the assumption that molecular mechanisms involved in cancerogenesis are characterized by groups of coordinately expressed genes, we developed and validated a novel method for analyzing transcriptional data called Correlated Gene Set Analysis (CGSA). Using 50 extracted gene sets we identified three different profiles of tumors in a cohort of 364 Diffuse large B-cell (DLBCL) and related mature aggressive B-cell lymphomas other than Burkitt lymphoma. The first profile had high level of expression of genes related to proliferation whereas the second profile exhibited a stromal and immune response phenotype. These two profiles were characterized by a large scale gene activation affecting genes which were recently shown to be epigenetically regulated, and which were enriched in oxidative phosphorylation, energy metabolism and nucleoside biosynthesis. The third and novel profile showed only low global gene activation similar to that found in normal B cells but not cell lines. Our study indicates novel levels of complexity of DLBCL with low or high large scale gene activation related to metabolism and biosynthesis and, within the group of highly activated DLBCLs, differential behavior leading to either a proliferative or a stromal and immune response phenotype.
Publication Title
Massive transcriptional perturbation in subgroups of diffuse large B-cell lymphomas.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 32 Downloadable Samples
Illumina Genome Analyzer IIx
Description
In the current study, we investigated the collective roles of protein tyrosine phosphatases (PTPs) and histone deacetylases (HDACs) on regulation of IRG expression in human choriocarcinoma cells by genome-wide transcriptional profiling. Logic-rules were optimized to derive rules governing gene expression patterns observed upon different combinations of treatment with PTP and HDAC inhibitors. The data reveal that IRGs can be divided into distinct subsets that are differentially modulated by co-treatment of Jar cells with IFN-? and PTP versus HDAC inhibitors, respectively. Furthermore, promoter analysis of the genes governed by the rules identifies transcription factor binding sites associated with the different gene subsets. Thus, the regulatory modes identified in this study provide insights into the complex regulation of inflammatory pathways at the fetal-maternal interface, as well as mechanisms that choriocarcinoma cells may utilize to promote their survival.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 32 Downloadable Samples
- Illumina HiSeq 2500
Description
Retinoic acid-inducible gene-I (RIG-I) is a cytosolic pathogen recognition receptor that initiates the innate immune response against many RNA viruses. RIG-I also has been shown to sense some DNA viruses, and host RNA polymerase III (RNA Pol III), a cytosolic DNA sensor, converts cytosolic AT-rich DNA into RNA to be sensed by RIG-I. We previously showed that the RIG-I restricts Kaposi Sarcoma-associated herpesvirus (KSHV) reactivation (J Virol. 2014 May;88(10):5778-87). In this study, we report that KSHV stimulates the RIG-I signaling pathway in an RNA Pol III-independent manner and subsequently induces type I IFN responses. Knockdown or inhibition of RNA Pol-III had no effect on IFN-ß induction by KSHV. By using CLIP (Cross-Linking and Immunoprecipitation) and RNA deep sequencing technologies, we identified multiple KSHV regions that give rise to RNA fragments binding to RIG-I, such as ORF810420-10496, ORF6411058-110675, Repeat region (LIR1)119059-119204, and ORF2543561-43650. The sequence dissimilarity between these fragments suggests that RIG-I detects a particular structure rather than a specific sequence motif. Synthesized ORF810420-10496 RNA stimulated RIG-I-dependent but RNA Pol III-independent IFN-ß signaling. In summary, some KSHV viral RNAs are sensed by RIG-I in an RNA Pol III-independent manner.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Disease, Cell line, Treatment, Race
View Samples- Mus musculus
- 32 Downloadable Samples
- Illumina HiSeq 2500
Description
No description.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Cell line, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
- NextSeq 500
Description
Fresh splenic Treg cells (CD4+CD25+YFP+) were isolated from 6-week-old Senp3+/+Foxp3-Cre and Senp3fl/flFoxp3-Cre mice and stimulated with anti-CD3 and anti-CD28 for 24 hours. Activated Treg cells were used for total RNA isolation with TRIzol and subjected to RNA-sequencing.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples- Mus musculus
- 5 Downloadable Samples
- NextSeq 500
Description
Single NG2-glia with GFP fluorescence labeling from PDGFRaCreER; mGFP mice was selected and aspirated into a glass pipette from hippocampal acute slices. In brief, cells were picked promptly by micromanipulation and immediately placed in lysis buffer. All NG2 glial cells were collected within 3 h after slice preparation. The selected NG2-glia were processed for single-cell RNA extraction and reverse transcription within 1 h and were subjected to RNA-sequencing.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Mus musculus
- 4 Downloadable Samples
- NextSeq 500
Description
B cell mRNA profiles of 18-week-old wild type (WT) and B cell-specific SHIP1 knockout (SHIP?B) mice were generated by deep sequencing, in duplicate, using Illumina Nextseq500.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Danio rerio
- 2 Downloadable Samples
- Illumina HiSeq 2500
Description
Determination of the genes that can be important for the defense of the host to infection for Mucorales fungi, using zebrafish and the fungus Mucor circinelloides as host and pathogen model, respectively. Total RNA was sequenced (RNA-seq) from abdominal organs of infected fish.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
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GSE9735- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Dataset of IL-12+IL-18 trated and Yersinia enterocolitica infected C57BL/6 NK cells
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples