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GSE32893
Homo sapiens
6 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This present study is the first to investigate the global changes in host gene expression during the interaction of human bronchial epithelial cells and live Alternaria spores. Human bronchial epithelial cells (BEAS2-B) were exposed to spores or media alone for 24 hours. RNA was collected from three biological replicates/treatment and used to assess changes in gene expression patterns using Affymetrix Human Genome U133 Plus 2.0 Arrays. Interestingly, many cytokine/chemokine immune response genes were upregulated. Genes involved in cell death, retinoic acid signaling, TLR3, and interferon response pathways were also significantly upregulated.
Publication Title
Analysis of global gene expression changes in human bronchial epithelial cells exposed to spores of the allergenic fungus, Alternaria alternata.
Sample Metadata Fields
Cell line, Treatment
View Samples- Homo sapiens
- 5 Downloadable Samples
IlluminaHiSeq2000
Description
Total RNA extracted from differentiated mesenchymal stem cells at four time points (T1,T2,T3,T4) and sequenced using Illumina Hi-seq 2000 platform to generate RNA sequencing with 101bp in read length. Nearly 50 million raw reads were yielded from each sample respectively. We used FastQC to confirm the quality of raw fastq sequencing data, and SOAPfuse software to detect fusion transcripts. Overall design: Discovering fusion genes from muscle differentiated mesenchymal stem cells
Publication Title
Fusion transcriptome profiling provides insights into alveolar rhabdomyosarcoma.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- IlluminaHiSeq2000
Description
Total RNA extracted from prostate cancer LNCaP cells transfected with siRNA against CTCF(siCTCF), or negative control siRNA (si-)were processed, and sequenced by two different companies using Illumina Hi-seq 2000 platform to generate RNA sequencing with two output sequences: paired-end 50bp and 101bp in read length. Nearly 100 million and 50 million raw reads were yielded from each sample respectively. We used FastQC to confirm the quality of raw fastq sequencing data, and SOAPfuse software to detect fusion transcripts. Overall design: Discovering fusion genes from siCTCF and si- in LNCaP cells.
Publication Title
Discovery of CTCF-sensitive Cis-spliced fusion RNAs between adjacent genes in human prostate cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 86 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Time series of eleven breast cancer samples subjected to different cold ischemic stress of up to 3 hr post tumor excision.
Publication Title
Effects of tissue handling on RNA integrity and microarray measurements from resected breast cancers.
Sample Metadata Fields
Subject
View Samples- Danio rerio
- 18 Downloadable Samples
- NextSeq 500
Description
Low incubation temperature during early development negatively affects survival and related innate immune processes in zebrafish larvae exposed to lipopolysaccharide Overall design: Zebrafish embryos were collected from 28 °C, and divided into three temperature groups (24 °C, 28 °C, 32 °C) for incubation. At the first-feeding stage, larvae from each incubation temperature group were further split into three temperature groups in a full-factorial way for LPS challenge. In total, nine temperature groups (three incubation temperatures x three challenge temperatures) were generated. At 24 h post LPS challenge, mortality of larvae were recorded. Larvae originating from 24 °C incubation temperature group had higher mortality rate than larvae from the other two temperature groups. LPS-treated larvae from three temperature groups, incubation 24 °C x challenge 24 °C, incubation 24 °C x challenge 32 °C, and incubation 32 °C x challenge 24 °C, together with their respective control were chosen for transcriptomic analyses using mRNA sequencing. A total of 722 genes were determined differentially expressed (DEGs) by DESeq2 (adjusted p-value < 0.05) in LPS-challenged larvae compared to control, and 605 of them had a fold change greater than 1.5, including 294 DEGs (144 up-/150 down-regulated) in larvae incubated and challenged with LPS at 24 °C; 33 DEGs (20 up-/13 down-regulated) in larvae incubated at 32 °C and challenged at 24 °C; and 278 DEGs (190 up-/88 down-regulated) in larvae incubated at 24 °C and challenged at 32 °C. Larvae incubated and challenged with LPS at 24 °C had stimulated innate immune response compared to control, while they also showed down-regulated innate immune processes and genes. In larvae incubated at 32 °C and challenged at 24 °C, the innate immune processes were up-regulated in larvae exposed to LPS compared to control, and theses processes were even much stronger (with higher enrichment values) than larvae from incubation and challenge temperature of 24 °C. In larvae incubated at 24 °C and challenged with LPS at 32 °C, limited innate immune response were up-regulated, and additional hypoxia and oxidative processes were observed. Genes annexin A2a, S100 calcium binding protein A10b, and lymphocyte antigen-6, epidermis were identified as promising candidates for LPS recognition and signal transduction.
Publication Title
Low incubation temperature during early development negatively affects survival and related innate immune processes in zebrafish larvae exposed to lipopolysaccharide.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Saccharomyces cerevisiae
- 15 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Gene expression in eukaryotes is an essential process that includes transcription, pre-RNA processing and RNA export. All these steps are coupled and normally, any failure in one step affects the other steps and could cause nuclear mRNA retention. One important player in this interface is the poly(A)-RNA binding protein Nab2, which regulates the poly(A)-tail length of mRNAs protecting their 3-ends from a second round of polyadenylation and facilitating their nucleo-cytoplasmic export. Interestingly, here we show that Nab2 has additional roles in mRNA transcription elongation, tRNA metabolism and rRNA export.
Publication Title
Nab2 functions in the metabolism of RNA driven by polymerases II and III.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 6 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Gene expression in eukaryotes is an essential process that includes transcription, pre-RNA processing and RNA export. All these steps are coupled and normally, any failure in one step affects the other steps and could cause nuclear mRNA retention. One important player in this interface is the poly(A)-RNA binding protein Nab2, which regulates the poly(A)-tail length of mRNAs protecting their 3-ends from a second round of polyadenylation and facilitating their nucleo-cytoplasmic export. Interestingly, here we show that Nab2 has additional roles in mRNA transcription elongation, tRNA metabolism and rRNA export.
Publication Title
Nab2 functions in the metabolism of RNA driven by polymerases II and III.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
Cytomegaloviruses express large amounts of viral miRNAs during lytic infection, yet, they only modestly alter the cellular miRNA profile. The most prominent alteration upon lytic murine cytomegalovirus (MCMV) infection is the rapid degradation of the cellular miR-27a and miR-27b. Here, we report that this regulation is mediated by the <1.7 kb spliced and highly abundant MCMV m169 transcript. Specificity to miR-27a/b is mediated by a single, apparently optimized, miRNA binding site located in its 3''-UTR. This site is easily and efficiently retargeted to other cellular and viral miRNAs by target site replacement. Expression of the 3''-UTR of m169 by an adenoviral vector was sufficient to mediate its function, indicating that no other viral factors are essential in this process. Degradation of miR-27a/b was found to be accompanied by 3''-tailing and -trimming. Despite its dramatic effect on miRNA stability, we found this interaction to be mutual, indicating potential regulation of m169 by miR-27a/b. Most interestingly, three mutant viruses no longer able to target miR-27a/b, either due to miRNA target site disruption or target site replacement, showed significant attenuation in multiple organs as early as 4 days post infection, indicating that degradation of miR-27a/b is important for efficient MCMV replication in vivo. Overall design: Small RNA sequencing from total RNA or Ago2 associated small RNAs extracted from mock- or MCMV-infected NIH-3T3 cells
Publication Title
Degradation of cellular mir-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 11 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
RORt+ innate lymphoid cells (ILC) are crucial players of innate immune responses and represent a major source of IL-22, which has an important role in mucosal homeostasis. The signals required by RORt+ ILC to express IL-22 and other cytokines, including TNF, have only partially been elucidated. Here we show that RORt+ ILC can directly sense the environment by the engagement of the activating receptor NKp44. NKp44 triggering in RORt+ ILC selectively activates a coordinated pro-inflammatory program, including TNF, while cytokine stimulation induces preferentially IL-22 expression. However, combined engagement of NKp44 and cytokine receptors results in a strong synergistic effect. These data support the concept that NKp44+ RORt+ ILC can be activated without cytokines and are able to switch between IL-22 or TNF production, depending on the triggering stimulus.
Publication Title
RORγt⁺ innate lymphoid cells acquire a proinflammatory program upon engagement of the activating receptor NKp44.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Pseudomonas aeruginosa
- 9 Downloadable Samples
- Illumina HiSeq 2500
Description
Extremely slow growth imposed by energy limitation is a ubiquitous but poorly understood physiological state for microbes. We used oxygen limitation to impose this state on Pseudomonas aeruginosa and measured newly synthesized proteins using a time-selective proteome labeling method (BONCAT) to identify relevant regulators and metabolic pathways. We further characterized one upregulated protein that has no homology to any known protein domains. This small, acidic protein is post-transcriptionally regulated and physically interacts with RNA polymerase, binding near the secondary channel during transcription elongation, and leading to widespread effects on gene expression. For some genes, the impacts on transcript and protein levels are different, suggesting possible modulation of translation as well. These effects have phenotypic consequences, as deletion of the gene affects biofilm formation, secondary metabolite production, and fitness in fluctuating conditions. Based on these phenotypes, we have designated the protein SutA (survival under transitions). Overall design: Profiles of rRNA-depleted total RNA from WT, ?sutA (PA14_69770), and SutA-overexpressing cells grown late exponential phase in minimal medium containing pyruate as the carbon source, in triplicate
Publication Title
SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa.
Sample Metadata Fields
Cell line, Subject
View Samples