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Transcription profiling of different tumors (BC2 and BC91) measured by poly(A)+RNA and aRNA for each tumor

ABSTRACT: This experiment was designed to determine the correlation between expression levels of defferent tumors (BC2 and BC91) measured by poly(A)+RNA and aRNA for each tumor. Total RNA was amplified using the Jeffrey lab protocol with G50 cleanup.

ORGANISM(S): Homo sapiens

SUBMITTER: Janos Demeter

PROVIDER: E-SMDB-1764 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis.

Zhao Hongjuan H Hastie Trevor T Whitfield Michael L ML Børresen-Dale Anne-Lise AL Jeffrey Stefanie S SS

BMC genomics 20021030 1

<h4>Background</h4>T7 based linear amplification of RNA is used to obtain sufficient antisense RNA for microarray expression profiling. We optimized and systematically evaluated the fidelity and reproducibility of different amplification protocols using total RNA obtained from primary human breast carcinomas and high-density cDNA microarrays.<h4>Results</h4>Using an optimized protocol, the average correlation coefficient of gene expression of 11,123 cDNA clones between amplified and unamplified ...[more]

PMID: 12445333

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Correlation between expression levels of different tumors measured by poly(A)+RNA and aRNA

Project description:Zhao et al. Amplification Table 7 This experiment was designed to determine the correlation between expression levels of defferent tumors (BC2 and BC91) measured by poly(A)+RNA and aRNA for each tumor. Total RNA was amplified using the Jeffrey lab protocol with G50 cleanup. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2005-11-04 | GSE3563 | GEO

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Effect of column cleanup on T7 based RNA linear amplification

Project description:Zhao et al. Amplification Table 4 This experiment was designed to evaluate the effect of column cleanup on the fidelity and yield of T7 based RNA linear amplification. BC2 total RNA was amplified using the Jeffrey lab protocol with or without G50 cleanup. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2005-11-04 | GSE3562 | GEO

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2005-11-03 | E-GEOD-3562 | biostudies-arrayexpress

Effect of in vitro transcription time on the fidelity of T7-based RNA linear amplification

Project description:Zhao et al. Amplification Figure 1 This experiment was designed to evaluate the effect of in vitro transcription time on the fidelity, reproducibility, and yield of T7 based linear amplification. Duplicate reactions were performed at 37 degree for 2, 3, 4, 5, and 6 hours. Two additional 5-hour incubation reactions were stored at 4 degree overnight to determine the effect of low temperature incubation on amplification. BC2 total RNA was amplified using the Jeffrey lab protocol with the G50 column cleanup step. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2005-11-04 | GSE3558 | GEO

Effect of in vitro transcription time on the fidelity of T7-based RNA linear amplification

2005-11-03 | E-GEOD-3558 | biostudies-arrayexpress

Transcription profiling to analyse the effect of the amount of human input total RNA on the fidelity, reproducibility, and yield of T7 based RNA linear amplification

Project description:This experiment was designed to evaluate the effect of the amount of input total RNA on the fidelity, reproducibility, and yield of T7 based RNA linear amplification. BC2 total RNA was amplified using the Jeffrey lab protocol. Different amounts of T7 primer were used according to the quantity of input total RNA. Multiple amplifications were done for each quantity of input total RNA to minimize experimental variations.

2005-09-30 | E-SMDB-1609 | biostudies-arrayexpress

Variation in cDNA microarray analysis of gene expression using unamplified poly(A)+ RNA

Project description:Zhao et al. Amplification BC2 uM This experiment was designed to assess the reproducibility of microarray hybridization using poly(A)+RNA. BC2 total RNA was isolated from which poly(A)+RNA was subsequently isolated. Three arrays were hybridized on the same day using arrays from the same batch. Two were done three months later using poly(A)+RNA freshly isolated from the same total RNA. A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. Keywords: replicate_design

2005-11-04 | GSE3559 | GEO

Effect of the amount of input total RNA on T7 amplification

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2005-11-03 | E-GEOD-3559 | biostudies-arrayexpress

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