LncRNA and mRNA expression of cytokine treated MDA-MB-231 cells
ABSTRACT: MDA-MB-231 cells were treated with PBS, LPS, IL1b, TNFa, IL6, and TGFb respectively and expression profile were assayed by Arraystar human lncRNA array 2.0 We designed this experiment to screen for lncRNAs whose expressions are responsive to inflammatory stimuli.
Project description:Using the highly sensitive lncRNA array, we screened the lncRNAs abundant in the human bladder cancer and Adjacent normal bladder tissues, and the function of differentially expressed lncRNAs were analyzed by bioinformatics. The Arraystar Human lncRNA Array (8x15K, Arraystar) and whole human mRNA Array (4x44K, Arraystar) and was used to profile differentially expressed lncRNAs and genes in bladder cancer vs. normal tissues following the manufacturer’s instructions. Briefly, extracted RNA template (1mg) was reversely transcribed into cDNA and digested into fragments with endonucleases. These fragments were labeled with DNA labeling reagent and labeled cDNAs were hybridized to the microarray via incubation at 45°C and rotated at 60 rpm for 17 h. Following washing and staining, the arrays were scanned using a GeneChip Scanner3000 with GeneChip Operating Software.
Project description:Using high sensitive ArrayStar Human, we detected differentially expressed genes and circRNAs, these part of data is the aberrent expressed genes. 12 Male NOD/SCID mice were obtained from the Animal Center of the Chinese Academy of Medical Science (Beijing, China). For xenograft generation, 1×10^6 LNCaP cells were subcutaneously injected into the backs of NOD/SCID mice (n=24). When tumors reached a diameter of 5 mm after 3 d, mice were randomly divided into two groups without castration (12 per group). Mice in the treatment group were administered with cisplatin at a dose of 5 mg/kg every 3 d for 30 d. Mice in the control group were treated with vehicle PBS. Tumors were taken out for microarray assay after 30 d.
Project description:The expression of lncRNAs in cutaneous squamous cell carcinoma (cSCC) were determined with a commercially available microarray (Arraystar Inc.,Rockville, Maryland USA). The Arraystar human lncRNA Microarray V3.0 containing 30,586 LncRNAs and 26,109 coding transcripts (mRNAs) A total of three patients with cSCC were biopsied. A total of three control (non-lesional skin) were biopsied.
Project description:ASPP2, also known as 53BP2L, belongs to ASPP family of proteins. ASPP2 is proved to be a haploinsufficient tumor suppressor in ASPP2-deficient mouse models with ASPP2+/- mice having a high incidence of spontaneous tumors and γ-irradiation-induced tumors. Clinical data reveals that ASPP2 is frequently decreased in a variety of cancers. We have previously showed that ASPP2 was frequently down-regulated by methylation and decreased expression of ASPP2 was positively correlated with recurrence and poor prognosis in HCC patients. We also investigated that ASPP2 may induce apoptosis, inhibit cell migration and invasion in vitro, but the underlying molecular mechanism remains unknown.This chip experiment was carried out to investigation of whole genome gene expression level changes induced by ASPP2 knockdown. HCC-LM3 cells were infected with LV-shASPP2 or LV-shNon control virus, one week later total RNA was extracted using TRIzol (Invitrogen) and the RNeasy kit (Qiagen). Three biological replicates were included .Six samples were amplified and labeled using a NimbleGen One-Color DNA Labeling Kit.
Project description:Dermal fibroblasts represent a heterogeneous population of cells with diverse features that remain largely undefined due to a lack of functional subclasses. Here we reveal the presence of multiple lineages of dermal fibroblasts within the dorsal back. Genetic lineage tracing and transplantation assays demonstrate that the bulk of connective tissue deposition during embryonic development, cutaneous wound healing, radiation fibrosis, and cancer stroma formation is carried out by a single, somitic-derived fibroblast lineage. Reciprocal transplantation of distinct fibroblast lineages between the dorsal back and oral cavity induced ectopic dermal architectures that mimic their place–of-origin. These studies demonstrate that intra and inter-site diversity of dermal architectures are set embryonically and maintained postnatally by distinct lineages of fibroblasts. Lineage-specific cell ablation using transgenic-mediated expression of the simian diphtheria toxin receptor in conjunction with localized administration of diphtheria toxin led to diminished connective tissue deposition in wounds and significantly reduced melanoma growth in the dorsal skin of mice. Using flow cytometry and in silico approaches, we identify CD26/DPP4 as a surface marker that allows for the isolation of this fibrogenic, scar-forming lineage. Small molecule-based inhibition of CD26/DPP4 enzymatic activity during wound healing results in diminished cutaneous scarring. The identification and prospective isolation of these lineages holds promise for translational medicine aimed at in vivo modulation of their fibrogenic behavior. Dermal fibroblasts were harvested for FACS from the oral dermis and cranial dermis of Wnt1Cre; R26mTmG mice, and from ventral and dorsal dermis of En1Cre; R26mTmG mice as previously described. For all microarray analysis, EPFs and ENFs where harvested from backskin of mice at 30 days of age. Positivity for GFP or RFP allowed for the separation of EPFs from ENFs and WPFs from WNFs. RNA was precipitated via chloroform-phenol extraction. Samples were processed for cleanup and concentration using Rneasy MinElute cleanup kit (cat. 74204, QIAGEN). RNA yield was typically 0.5-1 µg RNA/sorted subpopulations. RNA samples from all sorted populations were converted to cDNA using SuperScript III first strand synthesis system for RT-PCR (cat. 18080-051, Invitrogen), and hybridized to Affymetrix Mouse Genome 430 2.0 arrays. Microarrays were normalized by robust multichip average (RMA) and quantile normalization in R. Cluster analysis was performed with AutoSOME (33), using the following settings for gene expression clustering: p-value threshold of 0.05, 100 ensemble iterations, unit variance normalization of arrays, median centering of genes, and sum of squares=1 normalization for both genes and arrays.
Project description:Global protein coding gene and miRNA expression profiling studies in uterine leiomyoma showed their aberrant expression and involvement in the pathogenesis of uterine leiomyoma. But the global expression patterns and potential clinical value of long noncoding RNA (lncRNA) in uterine leiomyoma have not been explored.In this study, we performed lncRNA expression profiles analysis of uterine leiomyoma using microarray(Arraystar Human LncRNA Array v2.0) to evaluate the genome-wide expression of lncRNAs and mRNAs and their potential role in the pathogenesis of uterine leiomyoma. Expression profiling analysis of the 15 samples including 5 large fibroids, 5 small fibroids and 5 matched myometrium by Arraystar Human LncRNA Array v2.0.
Project description:To identify genes activated under hypoxia (1%O2) and serum-free treatment of a cancer cell line, we performed cDNA microarray analysis with an ovarian cancer cell line, OVSAYO. Cells were cultured under normoxia /hypoxia (1%O2) and serum-plus/serum-minus conditions for 16 hours. Total RNA was isolated for cDNA microarray analysis.
Project description:Hypoxic microenvironment plays important roles in the progression of solid tumors including oral squamous cell carcinoma (OSCC). Long noncoding RNAs (lncRNAs) have gained much attention in the past few years. However, it is not clear whether lncRNAs could regulate hypoxia-adaptation of OSCC, and which lncRNAs participate in this process. Using an lncRNA microarray, we analyzed the aberrant lncRNA expression profiles in OSCC tissues compared with paired normal oral mucosa as well as in hypoxic OSCC cells compared with normoxic OSCC cells. Our data revealed 2053 differentially expressed (Fold Change >= 2.0, P-value <= 0.05) lncRNAs, among which 934 lncRNAs were significantly up-regulated and 1119 lncRNAs were down-regulated in OSCC compared with paired normal mucosa. Six OSCC tissues and paired normal oral mucosa were obtained from 6 patients with OSCC. LncRNA expression profiles were evaluated by an Agilent Human LncRNA Array v3.0 (8 x 60K, Arraystar).
Project description:Epithelial ovarian cancer (EOC) constitutes a major gynecological malignancy, with a reported incidence rate of 3-12/100 000 woman annually. As early symptoms of ovarian cancer are often clinically atypical or absent, the majority of ovarian cancer patients are diagnosed at a late stage, when the five-year survival rate is extremely low. This condition underscores the urgency of early detection of these patients and establishment of new therapeutic targets for successful intervention. Considering that the predominant biological characteristic that differentiates malignant from benign tumors is the ability to metastasize, it is necessary to identify novel metastasis-related molecules for ovarian cancer. In this study, we found that CAFs could significantly increase the metastatic potential of ovarian cancer cells compared with non-cancer associated fibroblasts(NAFs), which is associated with over-expression of CXCL14 in CAFs. We examined the impact of CAF-secreted CXCL14 on the lncRNA expression profiles in ovarian cancer during metastasis. We treated A2780s ovarian cancer cell line with recombinant CXCL14 protein and control respectively and subjected them to Arraystar Human LncRNA microarray v3.0 to profile differential lncRNAs in ovarian cancer upon treatment of CXCL14