Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of human A2780 ovarian cancer cell lines treated (TRT) with two compounds (A and B) vs. untreated (CTRL) sampled at 6 different time points and processed on different days to summarize probe levels of Affymetrix arrays taking into account day-to-day variability

ABSTRACT: Day-to-day variability in microarray experiments is a recognized source of variation that can impede the analysis of large microarray studies where samples are processed on different days. In this study, we have applied an algorithm, called D2Dsum, which is based on a log-linear fixed effect model to cope with this kind of issues on a data set of 45 microarrays. Experiment Overall Design: A2780 human ovarian cancer cell lines have been treated (TRT) with two different chemical compounds (A and B) or left untreated (CTRL). RNA was collected form 1 to 6 hour every hour. For each time point a technical duplicate or triplicate has been performed. Samples were subjected to complete randomisation experimental design and the effect of hybridisation day has been evaluated. Experiment Overall Design: processed on 4 different days

ORGANISM(S): Homo sapiens

SUBMITTER: Roberta Bosotti

PROVIDER: E-GEOD-9826 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Summarizing probe intensities of affymetrix GeneChip 3' expression arrays taking into account day-to-day variability.

Magni Paolo P Simeone Angela A Healy Sandra S Isacchi Antonella A Bosotti Roberta R

IEEE/ACM transactions on computational biology and bioinformatics 20110901 5

Microarray experiments are affected by several sources of variability. The paper demonstrates the major role of the day-to-day variability, it underlines the importance of a randomized block design when processing replicates over several days to avoid systematic biases and it proposes a simple algorithm that minimizes the day dependence. ...[more]

PMID: 21778528

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Project description:One µg of total RNA from either an individual rat or from a pooled sample was amplified and labeled with a fluorescent dye (either Cy3 or Cy5) using the Low RNA Input Linear Amplification Labeling kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol. The amount and quality of the resulting fluorescently labeled cRNA was assessed using a Nanodrop ND-100 spectrophometer and an Agilent Bioanalyzer. Equal amounts of Cy3- or Cy5-labeled cRNA were hybridized to the Agilent Rat Oligo Microarray (Agilent Technologies, Inc., Palo Alto, CA) for 17 hrs, prior to washing and scanning. Data was extracted from the resulting images using Agilent’s Feature Extraction Software (Agilent Technologies, Inc., Palo Alto, CA). For day/night comparisons, two types of complementing hybridizations were performed: hepatic RNA from individual day rats was hybridized against a pool made up of RNA from 12 hour offset night rats, and RNA from individual night rats was hybridized against a pool made up of RNA from 12-hour offset day rats. Specifically, hepatic RNA samples from three individual day rats collected ten hours after light on (CT10) were hybridized against a pooled RNA sample composed of equal aliquots of RNA from the livers of six night rats collected ten hrs after lights off (CT22); and RNA samples from three individual night rats collected at CT22 were hybridized against a pooled RNA sample composed of equal aliquots of RNA from the livers of six day rats collected at CT10. This was replicated in a second study for a total of 24 hybridizations of 12 hour offset samples. For time of day comparisons, equal aliquots of RNA from the livers of six rats collected at each of four different times of the circadian day (CT4, CT10, C16 and CT22) were pooled. The two replicate studies thus resulted in 8 pools (two replicate pools/time point times four time points); each pool was hybridized against a Universal Rat Reference RNA Standard (Stratagene, La Jolla, CA). Keywords: time-course

Dataset Information

Transcription profiling of human A2780 ovarian cancer cell lines treated (TRT) with two compounds (A and B) vs. untreated (CTRL) sampled at 6 different time points and processed on different days to summarize probe levels of Affymetrix arrays taking into account day-to-day variability

Publications

Summarizing probe intensities of affymetrix GeneChip 3' expression arrays taking into account day-to-day variability.

Similar Datasets

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