Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

47 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative gene expression profiling of the EBV-positive NPC cell line C666.1 and normal primary tonsillar epithelial cells

ABSTRACT: In this study, we have performed comparative gene expression profiling of primary tonsil epithelial cells with the EBV-positive NPC cell line C666.1 using a human gene array. Differences in cellular gene expression was compared using RNA isolated from C666-1 cells and primary tonsil epithelial cells grown in serum-free keratinocyte growth medium (performed in triplicate). RNA isolated from each sample was processed according to the Genechip WT sense target labelling protocol. 1μg of RNA was hybridised to human gene 1.0 ST array chips.

ORGANISM(S): Homo sapiens

SUBMITTER: Wenbin Wei

PROVIDER: E-GEOD-39826 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Epstein-Barr virus induction of the Hedgehog signalling pathway imposes a stem cell phenotype on human epithelial cells.

Port Rebecca J RJ Pinheiro-Maia Sonia S Hu Chunfang C Arrand John R JR Wei Wenbin W Young Lawrence S LS Dawson Christopher W CW

The Journal of pathology 20131101 3

Nasopharyngeal carcinoma (NPC) is a cancer common in southern China and South East Asia that is causally linked to Epstein-Barr virus (EBV) infection. Here, we demonstrate that NPC displays frequent dysregulation of the Hedgehog (HH) pathway, a pathway implicated in the maintenance of stem cells, but whose aberrant activation in adult tissues can lead to cancer. Using authentic EBV-positive carcinoma-derived cell lines and nasopharyngeal epithelial cell lines latently infected with EBV as models ...[more]

PMID: 23934731

Similar Datasets

Gene expression in human germinal center light zone and dark zone B cells

Project description:Microarrays of gene expression in human germinal center light zone and dark zone B cells sorted according to the expression of cell surface molecules CD83 and CXCR4 We used microarray data to identify genes differentially expressed by B cells in the light and dark zones of germinal centers from human tonsil specimens. Germinal center B cells (CD19+CD38+IgD-) were sorted from pediatric tonsil discard specimens into light zone (CXCR4hi/CD83lo) and dark zone (CXCR4lo/CD83hi) populations, from which RNA was extracted

2012-06-13 | E-GEOD-38697 | biostudies-arrayexpress

Expression data of human tonsilar CD4 positive T cell subsets

Project description:Type 1 regulatory T (Tr1) cells are one of the regulatory T cell subsets that are characterized by the production of high amount of IL-10 and lack of FOXP3 expression. Lymphocyte-activation gene 3 (LAG3) is a CD4 homologue molecule and we have previously reported that LAG3 is expressed on IL-10 producing regulatory T cells. However, naturally occurring Tr1 cells in human secondary lymphoid tissue have not been detected. We identified CD4+CD25-LAG3+ T cells in human tonsil. We compared mRNA expression of five CD4+ T cell subsets in tonsil using microarray analysis (CD4+CD25-LAG3+ T cells, CD4+CD25-CXCR5+PD-1+ follicular helper T cells (TFH), CD4+CD25+ T cells, CD4+CD25-LAG3-CD45RO+ cells and CD4+CD25-LAG3-CD45RO- cells). A human tonsil was obtained from a patient undergoing routine tonsillectomy, and five tonsillar CD4+ T cell subsets were sorted (each 1 x 10^5 cells). There is no biological replication.

2016-04-01 | E-GEOD-73927 | biostudies-arrayexpress

Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization

Project description:Four single consecutive murine kidney tissue specimens were prepared with the direct trypsinization with RapiGest (DTR) approach or with the filter aided sample preparation (FASP) protocol using both 10k and 30k filter devices and analyzed by label-free, quantitative liquid chromatography – tandem mass spectrometry (LC-MS/MS). Furthermore, we probed compatibility of the DTR protocol for the analysis of common histological stainings, namely hematoxylin & eosin (H&E), hematoxylin, and hemalaun. These were proteomically compared to an unstained control by analyzing four human tonsil FFPE tissues per condition.

2018-08-15 | PXD006401 | Pride

Gene expression signatures of human plasma cells isolated from different territories

Project description:In vivo antigen (Ag)-induced differentiation of B lymphocytes into plasma cells (PCs) takes place in extra-follicular foci and germinal centers of the secondary lymphoid organs (SLOs). Most of these SLO PCs are short-living and only relatively few PCs, characterized by secreting high-affinity antibodies (Ab), travel through the circulation and finally home in specialized survival niches of the bone marrow (BM) and, at a lesser extent, in the SLOs, where they become long-living Ab-secreting PCs. We have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish between human circulating Ag-induced PCs in comparison with tonsil and BM PCs distinctively regulate genes involved in cell proliferation. Gene expressions in human plasma cells isolated from tonsil (7 samples), blood (6 samples) and bone marrow (7samples) were measured. Each sample was isolated from a different donor.

2015-01-05 | E-GEOD-59697 | biostudies-arrayexpress

A framework for performing single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology

Project description:Metabolic reprogramming in cancer and immune cells occurs to support their increasing energy needs in biological tissues. Here we propose Single Cell SPAtially resolved METabolic (scSpaMet) framework for joint protein-metabolite profiling of single immune and cancer cells in male human tissues by incorporating untargeted spatial metabolomics and targeted multiplexed protein imaging in a single pipeline. We utilized the scSpaMet pipeline to profile cell types and spatial metabolomic maps of 19507, 31156, and 8215 single cells in human lung cancer, tonsil and endometrium tissues, respectively. ScSpaMet analysis revealed cell type-dependent metabolite profiles and local metabolite competition of neighboring single cells in human tissues. Deep learning-based joint embedding revealed unique metabolite states within cell types. Trajectory inference showed metabolic patterns along cell differentiation paths. Here we show scSpaMet’s ability to quantify and visualize the cell-type specific and spatially resolved metabolic-protein mapping as an emerging tool for systems-level understanding of tissue biology.

2023-10-02 | PXD045840 | Pride

Expression Data from BALB/c and Stat6-deficient bone marrow derived macrophages (BMDM)

Project description:We used microarrays to find Stat6 dependent genes in control and IL-4 exposed bone marrow derived macrophages. Alternatively activated macrophages (AAM) accumulate in tissues during Th2-associated immune responses like helminth infections and allergic disorders. These cells possess potent inhibitory activity against T cells. The differentiation of AAM depends on IL-4/IL-13-mediated activation of the transcription factor Stat6. Stat6 is also required in AAM to induce several genes, such as YM1, FIZZ1 and Arginase1. Macrophages were differentiated from bone marrow cells in supplemented RPMI 1640 for 7 days in the presence of 10% supernatant from the M-CSF producing fibroblast cell line L929. After removal of nonadherent cells, macrophages were detached using 5mM EDTA treatment, washed, counted, and replated at a density of 10x6 cells/mL. Macrophages were cultured for 24 hours in medium (control) or in the presence of IL-4 (10mg/mL). F4/80 positive macrophages were sorted with a purity of 99% and RNA was isolated (Trizol/Chloroform) according to the manufacturer's instructions. RNA was labeled (biotin), fragmented, and hybridized to the arrays according to the manufacturer's recommendations.

2010-07-19 | E-GEOD-20030 | biostudies-arrayexpress

B cell-intrinsic STAT6 controls the germinal center response in type 2 immunity

Project description:By investigating the germinal center (GC) formation in STAT6ko/WT bone marrow-mixed chimera we found that GC formation in type 2 immune responses is dependent on B cell intrinsic expression of IL-4/IL-13-induced genes. We therefore used microarrays to find Stat6 dependent genes that are important for germinal center formation and/or organization after infection with the nematode Nippostrongylus brasiliensis (N. brasiliensis). Bone marrow of STAT6ko (CD45.2+) and WT (CD45.1+) were mixed and injected in lethaly irradiated WT (CD45.1+) mice. After 8 weeks, 5 Bone marrow-mixed chimera were infected with N. brasiliensis and draining lymph nodes were collected at day 14 after the infection and pooled. RNA was isolated from sort-purified CD45.1+ or CD45.2+ GC B cells (B220+CD38loGL-7hi).

2014-05-26 | E-GEOD-47679 | biostudies-arrayexpress

Influence of neutrophils in tumor-supportive stromal cells gene expression in non-Hodgkin B-cell lymphoma

Project description:Tumor infiltrating neutrophils (TAN) have been shown to exert both pro- and anti-tumoral activities and their recruitment and polarization are triggered by tumor-derived signals. Resident mesenchymal stromal cells (MSC) could contribute to tumor-supportive cell niche and have been shown to display tumor-specific transcriptomic, phenotypic, and functional features compared to normal tissue. In our study, we investigate whether these two cell subsets establish a bidirectional crosstalk in the context of B-cell lymphoma. We used microarrays to explore how neutrophils could trigger the polarization of tumor-supportive stromal cells. Gene expression analysis were performed on stromal cells (MSC) derived from bone marrow (BM) or tonsil (Resto) of healthy donors. These BM-MSC (n=3) or Resto (n=3) were primed or not with neutrophils for 1 day to induce stromal modification.

2015-05-11 | E-GEOD-62782 | biostudies-arrayexpress

Deciphering functional tumor-immune crosstalk through highly multiplexed imaging and deep visual proteomics

Project description:Deciphering the intricate tumor-immune interactions within the microenvironment is crucial for advancing cancer immunotherapy. Here, we developed a novel approach integrating highly multiplexed imaging, laser microdissection, and deep visual proteomics to spatially profile the proteomes of 21 distinct cell populations in human colorectal and tonsil cancers with high sensitivity. In colorectal tumors, we uncovered an immunosuppressive macrophage barrier impeding T cell infiltration and regionally altering lymphocyte proteomes. Spatial proteomic analysis revealed distinct functional states of T cells in different tumor compartments. In tonsil cancer, we identified significant tumor cell proteomic heterogeneity influenced by proximity to specific T cell subtypes. Tumor-infiltrating T cells exhibited metabolic adaptations and enhanced stress resilience, enabling migration into hypoxic regions. Our spatially-resolved, highly multiplexed strategy provides a powerful tool to decipher the complex cellular interplay within the tumor microenvironment, with implications for identifying new immunotherapy targets and signatures.

2024-09-16 | PXD051891 | Pride

RORÎ³t+ Innate lymphoid cells transcriptomes after aNKp44 and cytokine stimulation

Project description:RORÎ³t+ 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 RORÎ³t+ ILC to express IL-22 and other cytokines, including TNF, have only partially been elucidated. Here we show that RORÎ³t+ ILC can directly sense the environment by the engagement of the activating receptor NKp44. NKp44 triggering in RORÎ³t+ 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+ RORÎ³t+ ILC can be activated without cytokines and are able to switch between IL-22 or TNF production, depending on the triggering stimulus. Transcriptome analysis of CD56+CD127hi tonsil ILC, Ex vivo and after stimulation with aNKp44, IL-1/IL-7/IL-23 or aNKp44/IL-1/IL-7/IL-23 for 3.5h. RNA was extracted and pooled from 2 donors each, Amplified and labeled according to manufacturerÂ´s instructions (GeneChipU133plus2Â® , Affymetrix). The analysis was performed in triplicates.

2013-10-30 | E-GEOD-43409 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data