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.
Microarray analysis of the in vitro granulomatous response to Mycobacterium tuberculosis H37Ra.
Specimen part
View Sampleswe analyzed the gene expression profiles of Mat-Lylu cell lines (in duplicate) compared to G cell lines (in duplicate) using Affymetrix tools and dChip software. The objective was to find metastasis-associated genes in prostate cancer, using this in vitro model.
DNA microarray analysis reveals metastasis-associated genes in rat prostate cancer cell lines.
No sample metadata fields
View SamplesTo explore how PKC regulates tumorigenesis, we performed mRNA expression analysis of four KRAS mutant NSCLC cell lines that stably express scrambled shRNA or PKC targeted shRNA
PKCδ regulates integrin αVβ3 expression and transformed growth of K-ras dependent lung cancer cells.
Disease, Cell line, Treatment
View SamplesWild type, pkl, pkr2 and pkl pkr2 plants were grown, and gene expression in roots was compared at the age of 5 days. <br></br>
CHD3 proteins and polycomb group proteins antagonistically determine cell identity in Arabidopsis.
Age, Specimen part, Time
View SamplesHow chromatin controls transcription elongation and splicing is an open question. Here we determine the transcriptomic changes of cells partially depleted of core histones. For that we construct a cell line with Doxycycline-controlled levels of the histone regulatory protein SLBP (HCT-shSLBP). HCT-shSLBP is derived from the human colon cancer cell line HCT116.
Defective histone supply causes changes in RNA polymerase II elongation rate and cotranscriptional pre-mRNA splicing.
Specimen part, Cell line
View SamplesC33-A is a Homo sapiens cervix carcinoma cell line. In this experiment we determine the level of gene expression under exponentially growing conditions.
The chromatin remodeller CHD8 is required for E2F-dependent transcription activation of S-phase genes.
Cell line
View SamplesWe identified RNA targets of Matrin3 using SH-SY5Y by PAR-CLIP analysis. Because Matrin3 mainly bound to intron of pre-mRNA, in order to find the effect of Matrin3 on splicing pattern and expression, we knocked down Matrin3 using SH-SY5Y cells by electroporation and extracted total RNAs from those cells. The total RNAs were subjected to whole transcripts microarray GeneChip Affymetrix Human Transcriptome array 2.0.
Matrin3 binds directly to intronic pyrimidine-rich sequences and controls alternative splicing.
Cell line, Treatment
View SamplesTo understand the underlying cause for the observed apoptosis in E2f1-3 deficient myeloid cells. We compared gene expression profiles of Cd11b+ sorted myeloid cells isolated from bone marrow of control (E2F1-/- ) and experimental (Mxcre;E2F1-/-2-/-3f/f ) mice.
E2f1-3 are critical for myeloid development.
Age, Specimen part
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Dissecting Low Atmospheric Pressure Stress: Transcriptome Responses to the Components of Hypobaria in Arabidopsis.
Age, Specimen part
View SamplesControlled hypobaria presents biology with an environment that is never encountered in terrestrial ecology, yet the apparent components of hypobaria are stresses typical of terrestrial ecosystems. High altitude, for example, presents terrestrial hypobaria always with hypoxia as a component stress, since the relative partial pressure of O2 is constant in the atmosphere. Laboratory-controlled hypobaria, however, allows the dissection of pressure effects away from the effects typically associated with altitude, in particular hypoxia, as the partial pressure of O2 can be varied. In this study, whole transcriptomes of plants grown in ambient (97 kPa/pO2 = 21 kPa) atmospheric conditions were compared to those of plants transferred to five different atmospheres of varying pressure and oxygen composition for 24 h: 50 kPa/pO2 = 10 kPa, 25 kPa/pO2 = 5 kPa, 50 kPa/pO2 = 21 kPa, 25 kPa/pO2 = 21 kPa, or 97 kPa/pO2 = 5 kPa. The plants exposed to these environments were 10 day old Arabidopsis seedlings grown vertically on hydrated nutrient plates. In addition, 5 day old plants were also exposed for 24 h to the 50 kPa and ambient environments to evaluate age-dependent responses. The gene expression profiles from roots and shoots showed that the hypobaric response contained more complex gene regulation than simple hypoxia, and that adding back oxygen to normoxic conditions did not completely alleviate gene expression changes in hypobaric responses.
Dissecting Low Atmospheric Pressure Stress: Transcriptome Responses to the Components of Hypobaria in Arabidopsis.
Age, Specimen part
View Samples