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Effect of the amount of input total RNA on T7 amplification

ABSTRACT: Zhao et al. Amplification Table 9 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. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

ORGANISM(S): Homo sapiens

PROVIDER: GSE3557 | GEO | 2005/11/04

SECONDARY ACCESSION(S): PRJNA104827

REPOSITORIES: GEO

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Effect of the amount of input total RNA on T7 amplification

Project description:Zhao et al. Amplification Table 9 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. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computed

2005-11-03 | E-GEOD-3557 | 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

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

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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 column cleanup on T7 based RNA linear amplification

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

Effect of ligase on T7 based RNA linear amplification

Project description:Zhao et al. Amplification Table 3 This experiment was designed to evaluate the effect of ligase used in the second strand cDNA synthesis on the fidelity of T7 based RNA linear amplification. BC2 total RNA was amplified with or without ligase using Affymetrix protocol. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2005-11-04 | GSE3561 | GEO

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

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

Effect of ligase on T7 based RNA linear amplification

2005-11-03 | E-GEOD-3561 | biostudies-arrayexpress

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

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

Project description:Abstract: BACKGROUND: 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. RESULTS: Using an optimized protocol, the average correlation coefficient of gene expression of 11,123 cDNA clones between amplified and unamplified samples is 0.82 (0.85 when a virtual array was created using repeatedly amplified samples to minimize experimental variation). Less than 4% of genes show changes in expression level by 2-fold or greater after amplification compared to unamplified samples. Most changes due to amplification are not systematic both within one tumor sample and between different tumors. Amplification appears to dampen the variation of gene expression for some genes when compared to unamplified poly(A)+ RNA. The reproducibility between repeatedly amplified samples is 0.97 when performed on the same day, but drops to 0.90 when performed weeks apart. The fidelity and reproducibility of amplification is not affected by decreasing the amount of input total RNA in the 0.3-3 micrograms range. Adding template-switching primer, DNA ligase, or column purification of double-stranded cDNA does not improve the fidelity of amplification. The correlation coefficient between amplified and unamplified samples is higher when total RNA is used as template for both experimental and reference RNA amplification. CONCLUSION: T7 based linear amplification reproducibly generates amplified RNA that closely approximates original sample for gene expression profiling using cDNA microarrays. This SuperSeries is composed of the SubSeries listed below.

2006-03-07 | GSE4349 | GEO

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