Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PBMCs exposed to the Mycobacterium tuberculosis H37Ra strain

ABSTRACT: Human peripheral blood mononuclear cells were cultured in presence of H37Ra strain at 37oC, 5%CO2. Cellular aggregates were collected at 24h, and RNA extracted and hybridized to Affymetrix microarrays (HG-U133). Raw data from microarray experiments was analyzed with dCHIP and SAM programs to determine the significance of changes at the biological context. PBMCs were exposed in triplicate to H37Ra strain. PBMCs from the same donor were cultured in triplicate at the same conditions than treated samples. RNA was extracted from each sample and hybridized to Affymetrix Human arrays.

ORGANISM(S): Homo sapiens

SUBMITTER: Niradiz Reyes

PROVIDER: E-GEOD-16250 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

FACS-array profiling in retinal endothelial cells from living mouse retinas

Project description:Deregulated retinal angiogenesis directly cause vision loss in many ocular diseases, such as diabetic retinopathy and retinopathy of prematurity. To identify endothelial-specific genes expressed in angiogenic retinal vessels, we purified genetically labeled endothelial cells from Tie2-GFP transgenic mice and performed gene expression profiling using DNA microarray. To find out genes associated with angiogenesis, comparisons of microarray data were carried out between GFP-negative non-endothelial retinal cells and GFP-positive retinal endothelial cells in angiogenic P8 retina. Eighteen arrays are included. Utilizing fluorescence-activated cell sorting (FACS), we isolated endothelial cells as GFP-positive cells from P8 retina in homozygous Tie2-GFP transgenic mice. GFP-negative cells were served as non-endothelial control. RNA extracts from sorted cells were amplified and then hybridized to Affymetrix MGU74v2 series arrays in triplicate.

2011-04-17 | E-GEOD-27238 | biostudies-arrayexpress

Expression data from breast cancer FNA and surgical specimens from patients

Project description:The behavior of breast cancers and their response to neoadjuvant systemic therapy depend on their phenotype which is to a large extent determined by gene expression programs within the cancer cell. The purpose of the analysis was to compare matched gene expression profiles of pretreatment cancer with post-neoadjuvant systemic therapy, residual cancer. Pre-treatment FNA from primary tumors or post-treatment surgical specimens were obtained and RNA extracted and hybridized to afymetrix microarrays according to manufacturer protocol.

2012-01-17 | E-GEOD-32072 | biostudies-arrayexpress

Expression data from breast cancer FNA biopsies from patients

Project description:We assess if distinct biological processes might be associated with chemotherapy sensitivity in the different clinical subsets of breast cancers. We performed gene set analysis (GSA) using functionally annotated gene sets corresponding to almost all known biological processes in ER-positive/HER2negative and ER-negative/HER2-negative breast cancer, respectively. Pre-treatment FNA from primary tumors were obtained and RNA extracted and hybridized to afymetrix microarrays according to manufacturer protocol.

2010-12-31 | E-GEOD-22093 | biostudies-arrayexpress

Geminin-regulated genes during neural fate acquisition of mouse embryonic stem cells

Project description:Formation of the complex vertebrate nervous system begins when pluripotent cells of the early embryo are directed to acquire a neural fate. Although cell intrinsic controls play an important role in this process, the molecular nature of this regulation is not well defined. Here we assessed the role for Geminin, a nuclear protein expressed in embryonic cells, in neural fate acquisition from mouse embryonic stem (ES) cells. While Geminin knockdown does not affect the ability of ES cells to maintain or exit pluripotency, we found that it significantly impairs their ability to acquire a neural fate. Conversely, Geminin overexpression promotes neural gene expression, even in the presence of growth factor signaling that antagonizes neural transcriptional responses. These data demonstrate that Geminin’s activity contributes to mammalian neural cell fate acquisition. We investigated the mechanistic basis of this phenomenon and found that Geminin maintains a hyperacetylated and open chromatin conformation at neural genes. Interestingly, recombinant Geminin protein also rapidly alters chromatin acetylation and accessibility even when Geminin is combined with nuclear extract and chromatin in vitro. These findings define a novel activity for Geminin in regulation of chromatin structure. Together, these data support a role for Geminin as a cell intrinsic regulator of neural fate acquisition that promotes expression of neural genes by regulating chromatin accessibility and histone acetylation. Mouse embryonic stem cells were differentiated for two days in N2B27 medium, with or without Doxycycline-inducible shRNAmir knockdown of Geminin and compared by microarray. Three independent experiments were conducted, using two different mouse embryonic stem cell lines for Doxycycline-inducible knockdown of Geminin. The two ES lines express unique shRNAmir sequences targeting Geminin (shRNAmir #9 and #11) to control for off-target effects.

2011-03-18 | E-GEOD-25737 | biostudies-arrayexpress

Expression data from Fine Needle Aspiration (FNA) biopsies from breast cancer patients

Project description:This is a stage-matched case control study. Cases with clinical diagnosis of Inflammatory Breast Cancer (IBC) were selected after reviewing all medical records of the 440 FNA samples. IBC was defined as signs of erythema and edema (peau d’orange) involving at least one third of the skin and rapid clinical presentation. Presence of tumor emboli in the dermal lymphatics of the involved skin in the pathology report was not required for inclusion as IBC. Controls were selected to match for T stage, all T4a-c tumors in the data set were included as controls. IBC breast cancer are all T4d breast cancer. We examined if gene expression differences exist between IBC and stage-matched Non-IBC stratified according to hormone receptor and HER2 status. Pre-treatment FNA from primary tumors were obtained and RNA extracted and hybridized to Affymetrix microarrays according to manufacturer protocol.

2011-07-01 | E-GEOD-22597 | biostudies-arrayexpress

Expression data from breast cancer FNA biopsies from patients (US samples)

Project description:This is Phase II Trial of 4courses of 5-fluorouracil, doxorubicin and cyclophosphamide follwed by 4 additional courses of weekly docetaxel and capecitabine administered as Preoperative Therapy for Patients with Locally Advanced Breast Cancer, Stages II and III by US oncology (PROTOCOL 02-103) We performed gene set analysis (GSA) using functionally annotated gene sets corresponding to almost all known biological processes in ER-positive/HER2negative and ER-negative/HER2-negative breast cancer, respectively. Pre-treatment FNA from primary tumors were obtained and RNA extracted and hybridized to afymetrix microarrays according to manufacturer protocol.

2011-02-07 | E-GEOD-23988 | biostudies-arrayexpress

Analysis of gene expression in co-culture of PBMCs with breast cancer cell lines by High-Throughput Sequencing

Project description:The goal of this study is to investigate paracrine effect of peripheral blood mononuclear cells (PBMCs) on breast cancer cell lines. Transcription profiles of PBMCs (control) and PBMCs co-cultured with breast cancer cell lines (treatment) were generated by deep sequencing, in triplicate for MCF7 and duplicate for T47D, using Illumina HiSeq 4000. Transcriptome analysis of PBMCs has shown the gene expression changed when co-cultured with breast cancer cell lines. The result revealed significantly up- and down-regulated genes.

2021-12-31 | GSE112280 | GEO

Analysis of gene expression in co-culture of PBMCs with colon cancer cell lines by High-Throughput Sequencing

Project description:(Objectives) The goal of this study is to investigate paracrine effect of peripheral blood mononuclear cells (PBMCs) on colon cancer cell lines. (Method) Transcription profiles of PBMCs (control) and PBMCs co-cultured with colon cancer cell lines (treatment) were generated by deep sequencing, in triplicate for SW480 and duplicate for HT29, using Illumina HiSeq 4000. (Results and conclusion) Transcriptome analysis of PBMCs has shown the gene expression changed when co-cultured with colon cancer cell lines. The result revealed significantly up- and down-regulated genes.

2020-12-31 | GSE110989 | GEO

Expression data from HAART interruption in HIV patients

Project description:We evaluated longitudinal changes in viral replication and emergence of viral variants in the context of T cell homeostasis and gene expression in GALT of three HIV-positive patients who initiated HAART during primary HIV infection but opted to interrupt therapy thereafter. Longitudinal viral sequence analysis revealed that a stable proviral reservoir was established in GALT during primary HIV infection that persisted through early HAART and post-therapy interruption. Proviral variants in GALT and peripheral blood mononuclear cells (PBMCs) displayed low levels of genomic diversity at all times. A rapid increase in viral loads with a modest decline of CD4 T cells in peripheral blood was observed, while gut mucosal CD4 T cell loss was severe following HAART interruption. This was accompanied by increased mucosal gene expression regulating interferon (IFN)-mediated antiviral responses and immune activation, a profile similar to those found in HAART-naive HIV-infected patients. Gut mucosal responses to HAART interruption were evaluated with Affymetrix arrays

2011-03-25 | E-GEOD-28177 | biostudies-arrayexpress

CD40-activation of human B cells

Project description:Antibody-independent effector functions of B cells, such as antigen presentation and cytokine production, have been shown to play an important role in a variety of immune-mediated conditions such as autoimmune diseases, transplant rejection and graft-versus-host disease. Therapeutic strategies, which interfere with B cell activation could therefore be a useful addition to the current immunosuppressive armamentarium. CD40 is one of the strongest activation stimuli for B cells. The aim of this study was to characterise the gene expression changes that occurr after B cell activation via CD40. Purified B cells isolated from PBMCs from four donors were compared to B cells which

2014-01-14 | E-GEOD-54017 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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