Filters
Technology
Platform
GSE97743
Homo sapiens
332 Downloadable Samples
Illumina HumanHT-12 V4.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Host Transcription Profile in Nasal Epithelium and Whole Blood of Hospitalized Children Under 2 Years of Age With Respiratory Syncytial Virus Infection.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
RPS19 mutations are the most common cause of the human disorder Diamond Blackfan Anemia. The R62W mutation was hypothesized to act in a dominant negative fashion and mice expressing RPS19R62W have many of the characteristics of Diamond Blackfan Anemia.
Publication Title
A transgenic mouse model demonstrates a dominant negative effect of a point mutation in the RPS19 gene associated with Diamond-Blackfan anemia.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 7 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Loss of function of the tumor suppressor BRCA1 (Breast Cancer 1) protein is responsible for numerous familial and sporadic breast cancers. We previously identified PABP1 as a novel BRCA1 partner and showed that BRCA1 modulates translation through its interaction with PABP1. We showed that the global translation was diminished in BRCA1-depleted cells and increased in BRCA1-overexpressing cells. Our findings raised the question whether BRCA1 affects translation of all cytoplasmic cellular mRNAs or whether it specifically targets a subset of mRNAs.
Publication Title
BRCA1-Dependent Translational Regulation in Breast Cancer Cells.
Sample Metadata Fields
Cell line
View Samples- Rattus norvegicus
- 13 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Glucosamine proved to be a potent, broad-spectrum inhibitor of IL-1beta. Of the 2,813 genes whose transcription was altered by IL-1beta stimulation (p<0.0001), glucosamine significantly blocked the response in 2,055 (~73%). Glucosamine fully protected the chondrocytes from IL-1-induced expression of inflammatory cytokines, chemokines and growth factors as well as proteins involved in PGE2 and NO synthesis. It also blocked the IL-1-induced expression of matrix specific proteases such as MMPs -3,-9,-10,-12 and ADAMTS-1.
Publication Title
Exogenous glucosamine globally protects chondrocytes from the arthritogenic effects of IL-1beta.
Sample Metadata Fields
Age
View Samples- Homo sapiens
- 8 Downloadable Samples
NextSeq 500
Description
We used an IL4-capture assay followed by FACS sorting, to isolate IL4-secreting TFH cells from a human tonsil and compared their transcriptomic profiles with CXCR5hi PD1hi IL4-negative tonsillar TFH cells and IL4-producing CXCR5neg non-TFH cells (TH2 cells). Our studies validate the notion of functionally distinct TFH subsets and identify genes that are specifically expressed in and define the human IL-4 secreting TFH cell subset. Overall design: T follicular helper cell subset mRNA profiles from human tonsils were generated by deep sequencing. Naive CD4 T cells, IL4-producing nonTFH CD4 T cells (i.e. TH2), and IL4-producing TFH cells and PD1hi TFH cells were analyzed. DOI: 10.26508/lsa.201800050
Publication Title
The expansion in lymphoid organs of IL-4<sup>+</sup> BATF<sup>+</sup> T follicular helper cells is linked to IgG4 class switching in vivo.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 173 Downloadable Samples
- Affymetrix Human Gene 1.1 ST Array (hugene11st)
Description
Changes in the respiratory microbiome are associated with disease progression in Idiopathic pulmonary fibrosis (IPF). The role of the host response to the respiratory microbiome however remains unknown. The role of this study is to explore the host-microbial interaction in IPF. Network analysis of gene expression data identified two gene modules that strongly associate with a diagnosis of IPF, BAL bacterial burden (determined by 16S quantitative PCR) and specific microbial OTUs, as well as lavage and peripheral blood neutrophilia. Genes within these modules that are involved in the host defence response include NLRC4, PGLYRP1, MMP9, DEFA4. The modules also contain two genes encoding specific antimicrobial peptides (SLPI and CAMP). Many of these particular transcripts were associated with survival and showed longitudinal over expression in subjects experiencing disease progression, further strengthening their relationship with disease. Integrated analysis of the host transcriptome and microbial signatures demonstrates an apparent host response to the presence of an altered or more abundant microbiome. These responses remain elevated on longitudinal follow up, suggesting that the bacterial communities of the lower airways may be acting as persistent stimuli for repetitive alveolar injury in IPF.
Publication Title
Host-Microbial Interactions in Idiopathic Pulmonary Fibrosis.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage
View Samples- Homo sapiens
- 40 Downloadable Samples
- IlluminaGenomeAnalyzer
Description
We report an applicaton of small RNA sequencing using high throughput next generation sequencing to identify the small RNA content of cell lines. By sequencing over 30 million reads we could identify a new class of small RNAs previousy observed with tiling arrays and mapping to promoter regions of coding genes. We also identified a large number of small RNAs corresponding to internal exons of coding genes. By using different enzymatic treatments and immunoprecipitation experiments, we have determined that both the promoter associated small RNAs as well as ones within the body of the genes bear 5'' cap structures. Overall design: Examination of the expression of small RNAs (<200nt).
Publication Title
Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 7 Downloadable Samples
- Illumina HiSeq 2000
Description
Gene expression analysis of wid type and Lmnb1-/- epicardial cells Overall design: Total RNA was isolated from wild type and Lmnb1-/- epicardial explants and subject ot sequencing on the Illumina platform
Publication Title
Lamin-B1 contributes to the proper timing of epicardial cell migration and function during embryonic heart development.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 26 Downloadable Samples
- Illumina humanRef-8 v1.0 expression beadchip
Description
Schizophrenia-associated miRNA were bidirectionally modulated in HEK-293, HeLa, and SH-SY5Y cell models. Results provide important insights into the current understanding of miRNA function in various cellular environments.
Publication Title
Alternative mRNA fates identified in microRNA-associated transcriptome analysis.
Sample Metadata Fields
Cell line, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
IL-10 is an anti-inflammatory cytokine that has been shown to be produced by antigen-specific CD8 T cells at the peak of viral encephalitis. We found that IL-10+CD8 T cells are more activated and cytolytic than IL-10-CD8 T cells.
Publication Title
Highly activated cytotoxic CD8 T cells express protective IL-10 at the peak of coronavirus-induced encephalitis.
Sample Metadata Fields
Specimen part
View Samples