Gene expression profiles in cancer stem cells isolated as ALDHhigh cells from human endometrioid adenocarcinoma cells, HEC-1.
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ABSTRACT: ALDHhigh cells were isolated as aldehyde dehydrogenase high active cells from HEC-1 cells by aldefluor assay. Aldehyde dehydrogenase low cells were isolated as ALDHlow cells. ALDHhigh cells showed higher tumor-initiating ability compared with those in ALDHlow cells. Thus ALDHhigh cells were enriched with cancer stem cells. The gene expression profiles were analyzed by cDNA microarray. ALDHlow cells were used as non-cancer stem cells.
Project description:Cancer stem-like cells are defined as small population of cancer cells which has, higher tumor-initiating ability, self-renewing ability and differentiation ability. In this experiment, transcription profile of cancer stem-like cells derived from human colon cancer line cell SW480 was investigated. Cancer stem-like cells were isolated as side population (SP) cells by Hoechst33342 dye staining from human colon cancer line cell SW480. Non-cancer stem-like cells were isolated as main population (MP) cells. RNAs were isolated from SP cells and MP cells derived from SW480 cells and array experiment was perfromed in dye swaped fashion.
Project description:We used the commercially available amino-allyl RNA amplification Kit ver,2 (High Yield Type) (SIGMA-ALDRICH). Purified total RNA (3 ?g) was reverse-transcribed to generate double-stranded cDNA using an oligo dT T7 promoter primer and reverse transcriptase. Next, cRNA was synthesized using T7 RNA polymerase, which simultaneously incorporated Cy3- or Cy5-labeled cytidine triphosphate. During this process, the samples of SP cells were labeled with Cy5, whereas the non-SP cells were labeled with Cy3 as control cells. Quality of the cRNA was again checked using the Nano Drop. Cy3-labeled cRNA and Cy5-labeled cRNA were combined and then fragmented in a hybridization cocktail (SIGMA-ALDRICH). Then the labeled cRNAs were hybridized to a 60-mer probe oligonucleotide microarray and incubated for 20 h ours at 50 ?C. The fluorescent intensities were determined by a Genepix 4000B Microarray Scanner (Axon, US).
Project description:Expression profiling of HeLa cells transduced stably with pre-miR-31 mimic, miR-31 inhibitor and parental HeLa cells was performed using Human Whole Genome OneArray v6.1 (Phalanx Biotech Group, Taiwan, China). Four hybridizations for each group were performed, with two biological and two technical replicates. Briefly, the signal intensity of each spot was loaded into the Rosetta Resolver System (Rosetta Biosoftware, Cambridge, MA, USA) for data analysis. The technical repeat data were tested by Pearson's correlation coefficient calculation to check the reproducibility (R>0.95). Normalized spot intensities were transformed to gene expression log2 ratios between the control and treatment groups.
Project description:The present study reports the genetic and biochemical characterization of a dominant glossy mutant allele (BnaA. GL) in B. napus that results in a glossy phenotype. Results from transmission electron microscopy and scanning electron microscopy revealed the GL mutant exhibits reduced deposition of the cuticle layer, which was confirmed by a cuticular wax analysis. The wax compositional analysis revealed an increase in aldehydes but a severe decrease in alkanes, ketones and secondary alcohols. Genetic mapping narrowed the BnaA. GL gene to the end of A9 chromosome, where a gene homologous to ECERIFERUM1 (CER1) in Arabidopsis locates.<br><br>Then, we conducted a microarray analysis to find the differentially expressed genes between normal phenotype and glossy plants. Two comparisons were performed: wild type parent VS. the GL parent, and the bulked normal phenotype DH lines VS. the bulked glossy DH lines. The DH lines are generated from F1 plants of two parents, and RNA samples from three DH lines were combined to make a bulked sample for each phenotype. <br><br>Although no discernible mutation was apparent in the B. napus gene, this cDNA microarray chip assay revealed coordinated down regulation of genes encoding enzymes of the cuticular wax biosynthetic in the glossy mutant with BnCER1 being one of the most severely suppressed genes.
Project description:LSECs were grown in culture medium supplemented with 10% FBS (depleted of endogenous exosomes by overnight centrifugation at 100,000 g) and were treated with or without 1,000 U/ml IFN-a (PBL Interferon Source, Piscataway, NJ, USA) for 48 h. The exosomes from the cell culture supernatants were isolated by differential centrifugation as follow, at 300g for 10 min, 2,000g for 10 min, 10,000g for 30 min, and 100,000g for 70 min, washed once with PBS, and purified by centrifugation at 100,000g for 70 min. Total RNA of purified exosomes were extracted and Exiqon miRCURY LNA Expression Array were used for detection of mRNA and miRNA, respectively.
Project description:We characterized the genomes of five commonly used hematopoietic cell lines: Kasumi-1, REH, U-937, BV-173 and ME-1. DNA samples from all five cell lines were compared to commercial sex-matched DNA.
Project description:Transcriptional responses in the gut of the main malaria vector Anopheles gambiae following oral bacterial infection with the entomopathogen Serratia marcescens were identified using DNA microarrays. S. marcescens is a common member of the mosquito gut microbiota, found in both laboratory reared and field collected mosquitoes, that can be potentially pathogenic as in Drosophila (Nehme et al., 2007), while it has been shown to influence the outcome of Plasmodium infections (Bando et al., 2013). S. marcescens belongs to the Enterobacteriaceae family, members of which have been shown to influence malaria transmission dynamics (Cirimotich et al., 2011, Boissiere et al., 2012). To further investigate the interactions between S. marcescens and the mosquito host, likely to shape, directly or indirectly, malaria transmission dynamics, An. gambiae mosquitoes, from the recently established N'gousso M form laboratory colony that retains much of the genetic variation of field mosquitoes, were antibiotic treated for 5 days and subsequently orally infected with the Db11-GFP strain of S. marcescens. Bacteria-fed mosquitoes were selected 2 days post infection, and, 3 days post infection, guts from bacteria-fed mosquitoes were dissected. Uninfected control mosquitoes were treated in the same way. Differential expression in the gut of S. marcescens infected mosquitoes, compared to uninfected controls, was identified by hybridizing labelled complementary RNA, derived from total RNA extracted from the respective gut pools, in customized Agilent 4x44k gene expression microarrays, comprising oligonucleotide probes encompassing all An. gambiae annotated genes of the AgamP3.6 release, with each probe represented in duplicate.
Project description:We characterized the global microRNA expression of five commonly used hematopoietic cell lines: Kasumi-1, REH, U-937, BV-173 and ME-1. RNA samples from all five cell lines were compared to reference material composed of RNA from 20 different tissues
Project description:Whole genome transcriptome analysis was performed to determine which genes were differentially expressed between strains T44625 and RB50