Formalin-fixed, paraffin-embedded (FFPE) samples are valuable resources for translational medicine studies.
Global gene expression profiling of FFPE material is challenging as the quality and availability of recovered RNA is heavily hampered. ArrayXS Human FFPE compensates for this deficit and enables reliable and robust detection of the expression of 39,975 protein coding genes in FFPE samples -
even in tiny amounts as obtained from laser capture microdissection (LCM).
―ArrayXS Human FFPE Workflow
Who is Array-To-Go developed for?―
checkA single curl of your FFPE material is sufficient for the analysis on ArrayXS Human FFPE
checkRNA is attained out of the FFPE sample material
checkAn optimised pre-amplification is employed to yield sufficient cDNA for subsequent labelling
checkA dual colour labelling is performed
checkFFPE samples are hybridised in a dye swap setup to achieve high quality reliable results of superior significance
checkData are analysed and visualised according to OakLabs' proven strategy for gene expression analysis in FFPE and facilitated data interpretation
―Your Benefits at a Glance
star_borderDesign for High Quality
Perfect harmonisation of experimentally validated probes, RNA isolation from FFPE and processing are key to high-quality data which you receive for every project. Combined with our dedicated sample processing protocol for FFPE, ArrayXS Human FFPE delivers highest
data quality for FFPE materials.
Sourced from Annotation Release 106 based on the genome assembly GRCh38; 33,975 genes are represented on ArrayXS Human FFPE.
Our turnaround times starting from 2 weeks including data analysis guarantee fast progress in your research project.
Agilent’s superior sensitivity, the extended dynamic range over 5 logs and OakLabs’ proven validation strategy allow for the detection of subtle biological changes with confidence. For example, our FFPE tissue preparation process is very exact, whether it be an FFPE tumor or any other FFPE specimen at your disposal. Our specialized lab team can even work with tiny amounts as obtained from laser capture microdissection (LCM).
check_circleValid Proof Certified
ArrayXS Human FFPE is validated and certified for new strong features creating an outstanding experience to fit your your research and development process and protocol.
Bundled with a comprehensive data analysis package, the ArrayXS FFPE service enables a rapid interpretation of results.
We have successfully completed projects from LCM samples. However, such projects are quite challenging and we ensure its feasibility in a small pilot project. Here we typically process two to four representative samples. Based on the quality controls during the sample processing we are able to predict whether the analysis on ArrayXS Human FFPE would be successful.
The FFPE material’s RNA unterwent a torture during the process of embedding. This becomes obvious by a electrophoretic separation, e.g. a bioanalyzer run. For paired samples (e.g. if a study contains two samples for each patient, such as a tumor and a normal tissue) we recommend to perform paired technical replicate dye-swap corrections for increased significance of the data.
Yes it is. However, you will need to consider that due to the heterogenous sample consisting of tumor and normal cells, the measured fold changes of significantly differentially expressed genes will be smaller than in reality. Assuming that your tissue sample contains 50% normal tissue, a measured 2-fold up-regulation means a 3-fold up-regulation in the tumor cells. If the portion of tumor tissue in the sample is very small, only strongly differentially expressed genes can be identified.
A microarray analysis always requires samples that are used as a reference. For gene expression analysis on ArrayXS Human FFPE, tumor samples are usually compared to normal tissue. However, you also can choose any other suitable reference for your study, e.g. choose a particular tumor entity as a reference or a certain time point, such as before chemotherapy.
The minimum number of samples is 8 in a 1-colour setup as well as in a 2-colour dye swap setup. This could for example be 4 patients with a tumor and a normal tissue sample (1-colour setup), or 4 sample pairs (e.g. tumor and adjacent tissue). In a 2-colour setup without dye swap, the minimal number of samples is 8 sample pairs.
You can either use the Request Order form on this page or send us an e-mail to email@example.com stating the number of samples you would like to submit. In many cases it is helpful to discuss the project on the phone in more detail. You can either call us at +49 33 02 2 07 13 91 or request a call back by e-mail.
After receiving your personal quote for FFPE analysis, you can accept it by fax or email.
The service including RNA isolation starts from EUR 1,200 / $ 1,300 per sample pair in a dye swap setup, and from EUR 950 / USD 1,040 per sample pair in a single colour setup (e.g. tumor and normal tissue of one patient).
―Specifications ArrayXS Human FFPE for gene expression analysis
OakLabs product number
GEO Platform ID
to be announced
Design creation date
8 x 60K
33,975 target IDs (coding genes)
Replicates of biological probes
300 x 10
35 x 12 ERCC control oligonucleotides
35 x 10 E1A spike-in control oligonucleotides
An initial large microarray was developed to detect 33,975 coding transcripts. Every sequence was represented by up to 20 different probes. In addition, all probes of Agilent’s SurePrint G3 Human Gene Expression 8x60K v2 Microarray (ID 039464) as well as OakLabs ArrayXS Human (ID 079407) were added.
looks_twoHybridisation of various samples
FFPE samples of various sources and ages were processed and hybridised onto the initial microarrays.
looks_3Selection of the best probes
Based on the hybridisation data, the best suited probes were selected to reliably measure gene expression in FFPE samples according to our FFPE protocol.
―How ArrayXS perfectly matches the challenge of FFPE sequencing
Each probe on ArrayXS Human FFPE was selected from a variety of different probes, including those of the 8x60K Agilent microarray and OakLabs' ArrayXS Human, both not developed specifically for formalin-fixed, paraffin-embedded tissue. For the majority of genes, neither the Agilent nor the ArrayXS Human's probe was the best choice.
Figure 1 illustrates, exemplarily for one gene, the probes’ signals on ArrayXS Human FFPE (green shadowed) compared to other tested probes including the one on Agilent’s 8x60K (red shadowed) as well as on OakLabs ArrayXS for gene expression in FFPE (blue shadowed).
The importance of harmonisation of probe design and sample processing and hybridisation to achieve high data quality is also illustrated in figures 2 and 3. The histograms show the signal distributions of the same sample hybridised to ArrayXS Human FFPE (blue) compared to the alternative microarrays (grey), Agilent's 8x60K (Fig 2) and ArrayXS Human (Fig 3). In both comparisons, the histograms of the signals obtained from ArrayXS Human FFPE are shifted to the right towards larger signals and at the same time, the peak on the left is significantly smaller indicating that the expression of a large portion of genes can be detected only with ArrayXS Human FFPE.
Colour DYE Swap approach for stringent and confident gene identification―
In gene expression studies from fresh material, a 1-colour approach is preferred over a 2-colour approach due to its large flexibility and the lower costs.
In contrast, a 2-colour dye swap analysis of FFPE material is capable of increasing the confidence of the identified genes, as demonstrated in a pilot project that has been performed on FFPE tumor tissue and normal tissue of 10 patients.
The mean log2 fold changes of tumor versus normal are visualised in a scatter plot (figure 4). The x-axis shows the data with the tumor tissue cy5-labeled and the normal tissue cy3-labelled, and y-axis vice versa.
Genes which have been identified to be significantly (at a p-value of 0.05) differentially expressed in both labelling orientations appear green. Those ones that are not significantly differentially expressed in either orientation appear in the middle of the plot and grey.
Those genes with detection of signficant differential expression in only one labelling orientation appear red. Those genes illustrate the portion of potentially false positive identifications if a dyes swap approach is being avoided. Therefore, by a 2-colour dye swap approach the significance of the identified genes (DNA and RNA) will be increased.