Genome-Wide Gene Expression Profiling Using Microarray

Global cDNA Whole-Human Genome 4 × 44 K Microarray (Agilent) gene expression profiling was performed on the same tissue specimens previously mentioned, as described elsewhere^{36 (link)}. Briefly, 100 ng of mRNA were reverse transcribed using Superscript II reverse transcriptase (Invitrogen Canada, Burlington, ON) while incorporating Cy3-dCTP or Cy5-dCTP (NEN, Boston, MA, USA). Raw microarray image files were extracted using Agilent Feature Extraction Software (v9.5). Microarray data were pre-processed and normalised using agilp v3.4.0 (bioconductor v3.3); only probes that matched to a gene symbol were included. In case of multiple ID mappings, the average was calculated between the matching probes, with no filtering on variance or expression threshold. Six samples (4_D1, 4_O1, 8b_T, 10_D1, 10_D2 and 22_D1) were excluded, after QC, and were defined as outliers using a sum of standard error boxplot.

Free full text: Click here

Abdalla M., Tran-Thanh D., Moreno J., Iakovlev V., Nair R., Kanwar N., Abdalla M., Lee J.P., Kwan J.Y., Cawthorn T.R., Warren K., Arneson N., Wang D.Y., Fox N.S., Youngson B.J., Miller N.A., Easson A.M., McCready D., Leong W.L., Boutros P.C, & Done S.J. (2017). Mapping genomic and transcriptomic alterations spatially in epithelial cells adjacent to human breast carcinoma. Nature Communications, 8, 1245.

Publication 2017

Whole-Human Genome 4 × 44 K Microarray Superscript II Feature Extraction Software (v9.5).

Cdna microarray Cy5 dctp Dctp Gene Human genome Microarray Mrna Reverse transcriptase Tissue Variance

Corresponding Organization :

Other organizations : Princess Margaret Cancer Centre, University Health Network, University of Toronto

Top 5 similar protocols

Variable analysis

independent variables

None explicitly mentioned

dependent variables

Gene expression levels measured by Global cDNA Whole-Human Genome 4 × 44 K Microarray (Agilent)

control variables

Tissue specimens previously mentioned
Reverse transcription of 100 ng of mRNA using Superscript II reverse transcriptase (Invitrogen Canada, Burlington, ON)
Incorporation of Cy3-dCTP or Cy5-dCTP (NEN, Boston, MA, USA) during reverse transcription
Extraction of raw microarray image files using Agilent Feature Extraction Software (v9.5)
Pre-processing and normalization of microarray data using agilp v3.4.0 (bioconductor v3.3)
Inclusion of only probes that matched to a gene symbol
Calculation of average for multiple ID mappings
Exclusion of 6 samples (4_D1, 4_O1, 8b_T, 10_D1, 10_D2 and 22_D1) identified as outliers after quality control

positive controls

None explicitly mentioned

negative controls

None explicitly mentioned

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!