Transcription profiling of human hepatocytes in response to copper overload at nine time points
ABSTRACT: Nine time points for microarray analysis were chosen to study early and late transcriptional responses in copper metabolism upon copper overload in HepG2 cells. Samples of copper-treated cells were hybridized using non-treated samples as a reference.
INSTRUMENT(S): G2565AA DNA microarray scanner [Agilent]
Project description:In order to study the physiological consequences of a high-copper diet on hepatic gene expression, 6 mM CuCl2 was added to the drinking water for a period of 1 month. After this period, livers of seven control mice and eight copper-treated mice were isolated and were subjected to microarray analysis and copper measurements. The hepatic gene expression profile of copper-treated mice was compared to non-treated mice using a pooled reference.
Project description:A gene expression study using microarray analysis was performed to elucidate the underlying mechanism leading to embryonic lethality in homozygous Commd1 null (Commd1-/-) mouse embryos. A gene expression profile of 9.5 dpc Commd1-/- embryos were generated and were compared to a gene expression profile of both 8.5 dpc and 9.5 dpc normal embryos.
Project description:Cross-platform target gene screening in colorectal cancer (CRC): we have compared 25 tumoural CRC biopsies against their normal counterpart in 30 hybridizations with a home-made cDNA array (CNIO oncochip) and 16 hybridisations with a custom oligoarray (Agilent Technologies).
Project description:Identification of new genes regulated by RDR6 and SGS3 (two genes involved in PTGS) by analysis of the transcriptome of rdr6-1 and sgs3-1 mutants compared to wild-type plants in different tissues (flower and leaves). The comparison between transcriptome of rdr6-1 and sgs3-1 mutant alleles impaired in PTGS and development (juvenile-to-adult transition) and transcriptome of rdr6-5 and sgs3-3 alleles impaired only in PTGS would allowed identification of genes involved in the developmental default (zip phenotype) of the null alleles (rdr6-1 and sgs3-1 mutants).
Project description:Mice were obtained from in house breeding of C57BL/6J and C57BL/6J-Chr 1A/Na breeding pairs (Jackson Laboratories, USA). To produce F1 hybrids, C57BL/6J females were mated with C57BL/6J-Chr 1A/Na males. The F1 hybrids were intercrossed, producing 82 F2 progeny (41 males and 41 females). Microarray analysis was performed on six pairs of affected and non-affected male animals from the F2 progeny selected on the basis of their motor activity levels (average daily levels of distance moved over a 3 days recording: 768±74 cm/hr (affected) versus 1765±175 cm/hr (non-affected)(p<0.0001).
Project description:In this study, we employ high-density oligonucleotide microarrays to characterize the MutaMouse FE1 cell line at various stages of cell growth, in primary MutaMouse lung epithelial cell cultures, and in whole lung. Global transcriptional analysis and real-time RT-PCR was applied to (1) further define the cellular origin of the FE1 cell line and its responses under different culture conditions (media and substratum), (2) provide insight into the transcriptional differences in cellular processes between FE1 cultures compared to whole lung tissues, more specifically in toxicological response, and (3) preliminarily examine FE1 culture response to exposure of benzo(a)pyrene compared to whole animals. Total RNA samples from 3 cell culture types (50% FE1, %100 FE1, and Primary lung) or MutaMouse lung were labeled with Cyanine 5-CTP, and universal reference total RNA (Stratagene, CA, USA) was labeled with Cyanine 3-CTP (Perkin Elmer Life Sciences, Woodbridge, ON, Canada) using Agilent linear Amplification kits (Agilent Tech. Inc. Mississauga, ON, Canada) following the manufacturer's instruction. Briefly, double-stranded cDNA was synthesized using MMLV-RT with T7 promoter primer, starting with 5 ug total RNA. Cyanine-labeled cRNA targets were in vitro transcribed using T7 RNA polymerase. The synthesized cRNA was precipitated by LiCl and fragmented at 60 degrees C for 30 min with fragmentation solution. Cy5- sample cRNA and Cy3- reference cRNA were hybridized to Agilent mouse development microarrays (containing ~20,000 unique 60 mer oligonucleotides; Agilent Tech. Inc. Mississauga, ON, Canada) at 60 degrees C overnight with Agilent hybridization solution and washed according to manufacturer's instruction. Arrays were scanned on a VersArray ChipReader (BioRad Laboratories Ltd., Waterloo, Ontario, Canada), and data were acquired with ImaGene 5.5 (BioDiscovery, Inc. CA, USA). Present calls were determined as signals that were greater than the mean plus three times the standard deviation of the average of the negative control spots.