E-MTAB-1238
Ontology highlight
ABSTRACT:
PROVIDER: E-MTAB-1238 | ExpressionAtlas | 2015-10-23
REPOSITORIES: ExpressionAtlas
Similar Datasets
Project description:Down syndrome (DS) (MIM 190685) is a complex disorder caused by the trisomy of either the entire, or a critical region of chromosome 21 (21q22.1-22.3). Despite representing the first genetic cause of mental retardation, the molecular bases of the syndrome are still largely unknown. We analyzed the genome-wide transcription profiles of lymphoblastoid cell lines (LCLs) from six DS and six euploid individuals and investigated differential gene expression and pathway deregulation associated with trisomy 21. RNA from six DS and six control LCLs was independently hybridized on the Affymetrix HU133 plus 2.0 oligonucleotide array (Affymetrix, Santa Clara, CA).The experimental design was a diseased versus control comparison. In a second approach, variability of gene expression among the DS and control group, respectively, was assessed by the analysis of the coefficient of variation (CV), calculated as the ratio between standard deviation and mean expression level for each gene among samples.
2012-12-06 | E-MTAB-1238 | biostudies-arrayexpress
Project description:Breast cancer brain metastasis has been recognized as one of the central issues in breast cancer research. Elucidation of the process and pathway that mediate this step is expected to provide important clues for a better understanding of breast cancer metastasis. Increasing evidence suggests that the aberrant glycosylation patterns greatly contribute to the cell invasion and cancer metastasis. Herein, we combined next generation RNA sequencing with liquid chromatograph-tandem mass spectrometry based proteomic and N-glycomic analysis from five breast cancer cell lines and one brain cancer cell line to investigate the possible mechanism of breast cancer brain metastasis. 24763 genes were identified including 14551 differentially expressed genes across six cell lines while proteomic analysis allowed the quantitation of 1096 differentially expressed proteins with approximately 83.8% proteins’ regulation matching their gene expression change. The genes/proteins associated with cell movement were highlighted in the breast cancer brain metastasis. Integrin signaling pathway and the up-regulation of α-integrin (ITGA2, ITGA3) associated with the brain metastatic process was shown through Ingenuity Pathway Analysis (IPA). Overall 91 glycosylation genes were selected from transcriptomic data and all exhibited differential expression. 12 glycogenes showed unique expression in 231BR. The regulation of these genes could result in an activation prediction of sialylation function in 231BR by ingenuity pathway analysis. In agreement with the changes of glycogenes, 60 N-glycans out of 63 identified exhibited differential expression among cell lines. The correlation of glycogenes and glycans revealed the importance of sialylation and sialylated glycans in breast cancer brain metastasis. Highly sialylated glycans, which were up-regulated in brain seeking cell line 231BR, probably contributes to brain metastasis.
2020-05-26 | PXD010506 | Pride
Project description:A comprehensive evaluation of differential gene expression on RNA-seq data of early and late passage hMSCs from three individuals, and undifferentiated and 21-day of chondrogenic differentiation hMSCs from previous publication (GSE109503). Genome-wide RNA-seq and differential expression analysis revealed that signalings such as Pulmonary Fibrosis Idiopathic (IPF) Signaling Pathway and Osteoclasts in Rheumatoid Arthritis (RA) Signaling Pathway were significant differences in early MSC. Differential FOXO1 expression, higher in Early than Late MSCs, was responsible for promoting suspension survival, and cell migration, and induces chondrogenic differentiation.
2023-02-24 | GSE225530 | GEO
Project description:Transcriptional profiling of chicken spleen tissues from Marek's disease virus (MDV) infected and non-infected control individuals from three inbred chicken lines 63, 72, RCSM with varying disease resistance characteristics. Line 63 is highly resistant; line 72 is highly susceptible; and line RCSM has intermediate resistance. Our goal was to investigate the genetic basis of systemic variation in disease resistance in these genetically similar individuals. Three time points were chosen at different stages of disease progression - 5 days post-infection (dpi) - early cytolytic phase; 10 dpi - latent phase; and 21 dpi - late cytolytic phase with 4 replicates at each stage. Two-condition experiment, MDV infected sample vs non-infected control, 3 chicken lines - 63, 72 and RCSM, 3 time points - 5, 10 & 21 dpi. Biological replicates: 4 non-infected control replicates, 4 infected replicates for each line at each time point.
2010-09-08 | E-GEOD-24017 | biostudies-arrayexpress
Project description:Transcriptional profiling of chicken spleen tissues from Marek's disease virus (MDV) infected and non-infected control individuals from three inbred chicken lines 63, 72, RCSM with varying disease resistance characteristics. Line 63 is highly resistant; line 72 is highly susceptible; and line RCSM has intermediate resistance. Our goal was to investigate the genetic basis of systemic variation in disease resistance in these genetically similar individuals. Three time points were chosen at different stages of disease progression - 5 days post-infection (dpi) - early cytolytic phase; 10 dpi - latent phase; and 21 dpi - late cytolytic phase with 4 replicates at each stage.
2010-09-08 | GSE24017 | GEO
Project description:We defined the molecular alterations associated with acquired resistance using combined treatment with BRAFi/MEKi in melanoma cell lines. After the successful establishment of six resistant cell lines, we determined the invasion properties and gene/protein expression differences between sensitive and resistant cells. We observed that the in-vasive potential of three of six resistant cell lines increased significantly compared to sensitive cell lines. We also observed that resistant cells were not drug addicted and did not exhibit significantly increased lethality following the “drug holiday”. RNA sequencing (RNA-Seq) analysis showed that the differentially expressed genes were associated with epithelial-mesenchymal tran-sition (EMT), the reactive oxygen species (ROS) pathway, and KRAS signalling
2021-12-01 | GSE186108 | GEO
Project description:We analyzed samples from fourteen deaf individuals (Affected 1 through 14), fifteen hearing maternally related family members (Unaffected 1-15), six marry-in controls (Controls 1-6) from extended pedigree from Arab-Israeli village, and nine individuals from another Arab-Israeli village (Controls 7-15). All affected and unaffected maternally-related individuals carry homoplasmic mutation in the 12S rRNA gene of the mitochondrial DNA, associated with both non-syndromic and aminoglycosides-induced deafness. Keywords: Comparison of genome-wide expression in cell lines of maternally-related individuals with mitochondrial mutation and controls carrying wild-type mitochondrial chromosome.
2009-06-01 | GSE9822 | GEO
Project description:Temproral networks of (phospho)-proteins are constructed and analyzed to infer differential interactions under insulin and IGF1 stimulation. In total, 134 antibodies are tested in 21 breast cancer cell lines. The experiments are done in triplicate. Three serum-free-condition time points (5min, 24hr, 48hr) and six stimulation time points (5min, 10min, 30min, 6hr, 24hr, and 48hr) are obtained with either 10 nM IGF1 or 10 nM insulin stimulation.
2016-07-21 | E-GEOD-80233 | biostudies-arrayexpress
Project description:Transcriptome data from six cancer cell lines passaged twenty times in normoxia (21% oxygen) or hypoxia (1% oxygen) Transcriptome analysis was conducted to determine the effect of chronic, long passaging, at 1% oxygen (hypoxia) on gene expression and alternative splicing in six cancer cell lines. The cancer cell lines included were two pancreatic (MIA PaCa-2, Capan-1), one lung (H226), one breast (MCF-7), one colon (HT-29), and one ovarian (SKOV-3). They were selected from a panel of 12 cancer cell lines since they showed the highest and lowest sensitivity to hypoxia based on their expression levels of a hypoxia 8-gene signature.
2023-03-29 | GSE222048 | GEO
Project description:Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) provide a conveniently accessible and renewable resource for functional studies in humans. The ability to accumulate multidimensional data pertaining to the same individual cell lines, from complete genomic sequences to detailed gene regulatory profiles, further enhances the utility of LCLs as a model system. A lingering concern, however, is that the changes associated with EBV transformation of LCLs reduce the usefulness of LCLs as a surrogate model for primary tissues. To evaluate the validity of this concern, we compared global promoter CpG profiles between CD20+ primary B cells and CD3+ primary T cells sampled from six individuals. Six independent replicates of transformed LCLs were derived from each sample.
2011-03-01 | GSE26211 | GEO