cdna microarray facility (AECOM International Development)

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AECOM International Development cdna microarray facility

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 <t>FFPE-cDNA</t> 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.)

Cdna Microarray Facility, supplied by AECOM International Development, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/complementary+dna+(cdna)+microarray/cdna+microarrays/pmc01976468-129-11-19
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cdna microarray facility - by Bioz Stars, 2026-09

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1) Product Images from "Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)"

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

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkm510

Figure Legend 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.)

Techniques Used: Reverse Transcription, Purification, Amplification, In Vitro

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.

Figure Legend 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.

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

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.

Figure Legend 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.

Techniques Used: Amplification, Expressing, Microarray, Hybridization

Microarray:

Article Title: IL-1beta regulates blood-brain barrier permeability via reactivation of the hypoxia-angiogenesis program.
Article Snippet: .. Human cDNA arrays were obtained from the Albert Einstein College of Medicine cDNA Microarray Facility ( http://microarray1k.aecom.yu.edu ), and each slide contained an unbiased, random collection of 27K cDNA probe elements (Incyte Genomics). ..

Article Title: Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)
Article Snippet: The UHR Cy3 (Green) and the FFPE-RNA Cy5 (Red) images were acquired and gridded with GenePix Pro 6.0 Software to generate signal intensities. .. Arrays used for the studies were designed and printed at the cDNA Microarray Facility, Albert Einstein College of Medicine (AECOM), Bronx, NY. ..

Article Title: Apoptotic Sensitivity of Colon Cancer Cells to Histone Deacetylase Inhibitors Is Mediated by an Sp1/Sp3-Activated Transcriptional Program Involving Immediate-Early Gene Induction
Article Snippet: .. We thank Dr. Geoff Childs and Aldo Massimi at the AECOM cDNA microarray facility for generation of cDNA microarrays and assistance with array scanning and David Reynolds at the AECOM DNA sequencing facility. ..

Article Title: Interleukin-11 Potentiates Oligodendrocyte Survival and Maturation, and Myelin Formation
Article Snippet: .. Human cDNA arrays were obtained from the Albert Einstein College of Medicine cDNA Microarray Facility (http:// microarray1k.aecom.yu.edu/), and each slide contained an unbiased, random collection of 27K cDNA probe elements (Incyte Genomics, Palo Alto, CA). ..

Article Title: Spectrum and Range of Oxidative Stress Responses of Human Lens Epithelial Cells to H 2 O 2 Insult
Article Snippet: .. RNAs were analyzed by cDNA microarray hybridizations on human gene chips containing 9700 genes (developed at Albert Einstein College of Medicine [AECOM]). ..

Article Title: Characterization of monocyte maturation/differentiation that facilitates their transmigration across the blood–brain barrier and infection by HIV: Implications for NeuroAIDS
Article Snippet: Five micro grams of total RNA were used to amplify antisense RNA (aRNA) copies of each mRNA in the sample using the Ambion MessageAmp aRNA Amplification Kit (Austin, TX). .. Human cDNA arrays (27,323 cDNA clones) were obtained from the AECOM cDNA Microarray Facility. ..

DNA Sequencing:

other:

Article Title: Restoration of nucleic acid from degraded or formalin-fixed and paraffin-embedded tissue and uses thereof
Article Snippet: These cDNAs were designed and built at the Albert Einstein College of Medicine (AECOM), Bronx, N.Y.

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