Journal: BMC Bioinformatics

Article Title: Impact of the spotted microarray preprocessing method on fold-change compression and variance stability

doi: 10.1186/1471-2105-12-413

Figure Lengend Snippet: Correlation between Microarray and Taqman fold-changes

Article Snippet: As our study focuses on the preprocessing of spotted microarray data, we decided to perform analyses on a high density spotted oligonucleotide microarray platform (CodeLink Human Whole Genome from GE Healthcare) as well as on a low density spotted cDNA microarray platform (Dualchip Microarray from Eppendorf).

Techniques: Microarray

Journal: BMC Bioinformatics

Article Title: Impact of the spotted microarray preprocessing method on fold-change compression and variance stability

doi: 10.1186/1471-2105-12-413

Figure Lengend Snippet: Scatter plot between microarray and Taqman . Scatter plot of log2 fold-changes obtained from quantitative PCR versus the log2 fold-changes obtained from microarray after the best- (Standard background correction with log2 transformation) and the worst- (No background correction with glog transformation) preprocessing methods. Microarray data leads to fold-change compressions for many genes, especially with the No background correction and the glog transformation (see Figure2).

Article Snippet: As our study focuses on the preprocessing of spotted microarray data, we decided to perform analyses on a high density spotted oligonucleotide microarray platform (CodeLink Human Whole Genome from GE Healthcare) as well as on a low density spotted cDNA microarray platform (Dualchip Microarray from Eppendorf).

Techniques: Microarray, Real-time Polymerase Chain Reaction, Transformation Assay

Journal: BMC Bioinformatics

Article Title: Impact of the spotted microarray preprocessing method on fold-change compression and variance stability

doi: 10.1186/1471-2105-12-413

Figure Lengend Snippet: GE Healthcare Fold-change compression . Lowess curves of the log2 fold-change compression estimated with the GE Healtchare platform as a function of the average processed intensity. The No background correction as well as the glog transformation produce high fold-change compression at low processed intensities. The fold-change compression at low intensities affects the correlation between gold-standard fold-changes and those obtained with microarray data (see Table 2).

Article Snippet: As our study focuses on the preprocessing of spotted microarray data, we decided to perform analyses on a high density spotted oligonucleotide microarray platform (CodeLink Human Whole Genome from GE Healthcare) as well as on a low density spotted cDNA microarray platform (Dualchip Microarray from Eppendorf).

Techniques: Transformation Assay, Microarray

Journal: Nucleic Acids Research

Article Title: Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)

doi: 10.1093/nar/gkm510

Figure Lengend Snippet: Complementary-template reverse-transcription (CT-RT) of single-stranded DNA primers reverse-transcribed from FFPE-RNA. ( a ) RNA extracted from FFPE tissue is reverse-transcribed, the mRNA/DNA duplex is filtered on an YM-50 column and the DNA is single-stranded with RNase-H and column purified. The 5′-NB-Oligo-dA (24) -cT7-3′ (complementary to the T7 promoter) is annealed to the FFPE-cDNA primers. ( b ) Total RNA from universal human reference (UHR, Stratagene) is amplified using the Sense-Amp cRNA amplification kit from Genisphere to provide RNA with the same orientation as messenger RNA . ( c ) Single-stranded DNA primers are hybridized to their sense-RNA template between 70 and 42°C for 90 min. The hybridized products are reverse-transcribed by a process described as CT-RT. The restored FFPE-cDNAs are doubled stranded and transcribed in vitro using T7 polymerase. (See Supplementary Data for technical description of points 1 through 6.)

Article Snippet: Arrays used for the studies were designed and printed at the cDNA Microarray Facility, Albert Einstein College of Medicine (AECOM), Bronx, NY.

Techniques: Reverse Transcription, Purification, Amplification, In Vitro

Journal: Nucleic Acids Research

Article Title: Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)

doi: 10.1093/nar/gkm510

Figure Lengend Snippet: Experimental procedure utilized for the analysis of 10-year-old matched frozen and formalin-fixed paraffin embedded breast cancer samples. ( a ) Five micrograms of RNA extracted from the 10-year-old frozen portion of the sample, is reverse-transcribed and the cDNA is double stranded (dsDNA), in four individual reactions. The dsDNA of three reactions undergoes IVT-amplification (MessageAmpII, Ambion), which gives rise to complementary RNA (cRNA) for cDNA microarray analyses. The dsDNA of one reaction is used for PCR experiments. ( b ) Five micrograms of RNA extracted from the 10-year-old FFPE portion of the sample underwent the exact same process. ( c ) Single-stranded DNA (ssDNA) obtained by RT of 5 μg of FFPE-RNA is purified and hybridized to the sense-RNA template library. The restored ssDNA is double stranded and purified. Three of the CT-RT reactions undergo IVT-amplification, while the dsDNA of one reaction is used for PCR experiments.

Article Snippet: Arrays used for the studies were designed and printed at the cDNA Microarray Facility, Albert Einstein College of Medicine (AECOM), Bronx, NY.

Techniques: Formalin-fixed Paraffin-Embedded, Reverse Transcription, Amplification, Microarray, Purification

Journal: Nucleic Acids Research

Article Title: Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)

doi: 10.1093/nar/gkm510

Figure Lengend Snippet: Signal intensity and heat-map analysis of the correlation between the log 2 ratios measured by cDNA microarrays. ( a ) Signal intensity of one sample grid in the red channel (Cy5) across all microarrays. Top three panels display the grids obtained from three repeats using cRNA from 10-year-old frozen RNA (Frozen-Amp 1–3). Three mid-panels show the signal of three repeats using cRNA obtained by restoration and IVT-amplification of RNA from 10-year-old FFPE tissue (FFPE-Restored 1–3). Three bottom panels display the signal of three repeats using cRNA obtained by direct IVT-amplification of RNA from 10-year-old FFPE tissue. ( b ) Heat map displaying the log 2 of expression ratios ranging between 0.5 and 2 for 1044 genes detected in frozen tissue on a 28 032 features cDNA microarray and represented in the UHR library. From left to right are displayed the ratios obtained by IVT-amplification of RNA from 10-year-old frozen tissue (Frozen-Amp 1–3), restoration and IVT-amplification of RNA from 10-year-old FFPE tissue (FFPE-Restored 1–3) and direct IVT-amplification of RNA from 10-year-old FFPE tissue (FFPE-Amp 1–3). Each column represents an individual hybridization and each line a different feature. Red and blue represent up-regulated and down-regulated genes, respectively.

Article Snippet: Arrays used for the studies were designed and printed at the cDNA Microarray Facility, Albert Einstein College of Medicine (AECOM), Bronx, NY.

Techniques: Amplification, Expressing, Microarray, Hybridization