Adaptation During Ovarian Cancer Metastasis Reveals a Predictive Gene Signature
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ABSTRACT: We characterized the genetic copy number and expression differences between matched ovarian primary tumors and omental metastases. Differentially expressed genes revealed that metastases proliferate more and are less apoptotic. Differentially expressed genes revealed a predictive expression signature when applied to other gene expression datasets. 18 samples from 9 matched pairs of primary ovarian tumors and metastases from the omentum were collected.
Project description:Xenograft ovarian tumors are useful model to test therapeutic candidates in vivo. We used microarrays to gain insight into the expression changes during tumor growth and induced by the vitamin D analog, MT19C at multiple time points. SKOV-3 cells were grown in 10% FBS/DMEM before injection into mice. Total RNA was collected using standard methods.
Project description:Analysis of estrogen receptor (ER)-positive MCF7 cell total RNA expression and polysome-assiciated RNA expression following treatment with estradiol (E2) and vehicle (etoh). We used expression microarrays to measure polysome association and total RNA abundance in E2 treated MCF7. These data, along with previously published data, show that genes that are upregulated by estrogen treatment are biased towards association with polysomes. MCF7 cells were grown in hormone depleted media for three days before a 1 hour treatment with E2 or 0.1 % ethanol (vehicle). Total RNA was collected using standard methods and polysome-association RNA from the same cells were collected using sucrose gradient fractionation. Both RNA populations were purified, labeled, and hybridized to Affymetrix Human Genest arrays.
Project description:Endothelial cells from nine steady state tissues and two regenerating tissues (bone marrow and liver) were intravitally labeld, isolated via flow sorting, and immediately processed for RNA extraction. When of sufficient quality, the RNA was amplified and hybridized. For comparison, Human Emybryonic Stem Cell-derived Endothelial cells (hESC-ECs) were differentiated and isolated based on similarities to the adult mouse counterparts. Endothelial cells were labeled via intravitally labeling of the vascular bed 8 minutes prior to sacrifice with minimally three markers to identify endothelial cells followed by flow sorting.
Project description:Comparison of each cell mRNA expression pattern. We generated osteoblasts like cell by direct reprogramming technique from human fibroblast. To confirm dOB gene expression pattern similarity to osteoblasts, we analyzed and compared the gene expression profiles of the samples by cDNA microarry. These analysis revealed that dOB are similar to osteoblats in comparative level to MSC-OB. 6 samples.
Project description:Comparasion of each cell mRNA expression pattern Human fibroblasts were directly converted into brown adipocytes (dBAs) by transducing some transcription factors. To characterize the dBAs more in detail, RNA extracted from the human WAs, human dBAs, and human iPS-derived brown adipocytes (iBAs) were subjected to DNA microarray analysis, and global gene expression profiles of the cells were compared. 6 samples
Project description:A collection of 100 ovarian cancer sample gene expression data from Singapore. Frozen archival epithelial ovarian cancer tumors samples from Department of Obstetrics & Gynecology, National University of Singapore dated from 2006 to 2014 were collected and subjected to microarray analysis.
Project description:Mononucleotide A and T repeats are abundant in human genome. Many of A repeats are bound by Argonaute proteins (AGOs). To evaluate the role of AGOs and A repeats in gene regulation, HEK293 cells were treated with 8-amino-3,6-dioxaoctanoic acid added peptide nucleic acid (PNA) AAAAAAAAAAAAAAA oligo (OO-A(15)). Matched two sets of two individual HEK293 cells were transfected with OO-A(15) and scramble OO-PNA oligo, and were analyzed as biological duplicates. Cells were grown in DMEM (Gibco-BRL) according to the manufacturer’s protocol. OO-A(15) and scramble oligo were dilute with dH2O to reach 10μM. Cells were transfected in 6-well plates, seed 6 x 105 cells per well with 50 nM OO-A(15) and scramble oligo using TransIT-siQUEST transfection reagent (Mirus). The transfected cell lines were cultured for 48 h post-transfection and harvested total RNA by Trizol reagent (Invitrogen). All RNA integrity assays were performed and hybridized on beadchip according to the protocol.
Project description:Regeneration of human cartilage is inherently inefficient; an abundant autologous source like human induced pluripotent stem cells (hiPSC) is therefore attractive for engineering cartilage. Here, we report a defined growth factor based protocol for differentiating hiPSC into articular-like chondrocytes within two weeks with a high efficiency. The hiPSC-derived chondrocytes (hiChondrocytes) are stable and comparable to adult articular chondrocytes in global gene expression, extracellular matrix production and in their ability to generate cartilage tissue in vitro and in immune-deficient mice. Molecular characterization identified an early Sox9lowCD44lowCD140low pre-chondrogenic mesodermal population during hiPSC differentiation that eventually generates a homogenous population of Sox9highCD44highCD140high hiChondrocytes. Additionally, global gene expression analyses revealed two distinct Sox9-regulated gene networks in the Sox9low and Sox9high populations providing novel molecular insights into chondrogenic fate commitment and differentiation. Our findings present a favorable method for generation of hiPSC-derived articular chondrocytes in terms of safety and efficiency. 10 samples were analysed (duplicate sets of 5 time points) to assess changing gene expression over the course of differentiation from iPSC to hiChondrocyte. All samples were compared relative to the undifferentiated iPSC. Adult chondrocytes (2 samples) were also included for comparison. We analyzed the changes in gene expression with differentiation; genes with a fold-change â?¥ or â?¤1.5, with a difference in intensity of >100 and within the lower 90% confidence bound were selected.
Project description:Examination of the genome-wide distribution of 5hmC in osteoarthritic chondrocytes compared to normal chondrocytes in order to elucidate the effect on OA-specific gene expression. 5hmC-sequencing was performed and data was compared with microarray gene expression data to identify genes with differential expression between normal and OA chondrocytes that are potentially under epigenetic regulation. Gene expression patterns were examined by comparing the 5 normal samples to the 2 OA samples to assess the changing expression profiles between normal and OA chondrocytes. We analyzed the changes in gene expression in OA; genes with a fold-change ≥ or ≤1.5 or 1.2, with a difference in intensity of >100 and within the lower 90% confidence bound, were selected.