ArrayXS Human FFPE

No compromise in analysing archived tissue

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 to access high data quality.

Human FFPE gene expression

SERVICE WORKFLOW ON ARRAYXS HUMAN FFPE

FFPE workflow

a single curl of your FFPE material is sufficient for the analysis on ArrayXS Human FFPE
RNA is attained out of the FFPE material
an optimised pre-amplification is employed to yield sufficient cDNA for subsequent labelling
a dual colour labelling is performed
samples are hybridised in a dye swap setup to achieve high quality reliable results of superior significance
data are analysed and visualised according to OakLabs' proven analysis strategy for facilitated data interpretation

ARRAYXS HUMAN FFPE: THE KEY TO BETTER DATA


DESIGNED FOR HIGH QUALITY

Perfect harmonisation of experimentally validated probes, RNA isolation and processing are key to high-quality data which you receive for every project.



UP-TO-DATE

Sourced from Annotation Release 106 based on the genome assembly GRCh38; 33,975 genes are represented on ArrayXS Human FFPE.



FAST

Our 2-weeks turnaround times including data analysis guarantee fast progress in your research project.

SENSITIVE

Agilent’s superior sensitivity, the extended dynamic range over 5 logs and OakLabs’ proven validation strategy allow to detect subtle biological changes with confidence.



VALID PROOF CERTIFIED

ArrayXS Human FFPE is validated and certified for new strong features creating an outstanding experience for your R&D.



CARE-FREE

Bundled with a comprehensive data analysis package, the ArrayXS service enables a rapid interpretation of results.





FREQUENTLY ASKED QUESTIONS

Q: When do you recommend a 2-colour dye swap?

A: 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.

Q: Can you isolate the tumor cells out of my sections?

A: Unfortunately, we can’t offer this service.

Q: There are normal cells in the tumor samples I'd like to analyse. Is it worth to submit those samples to gene expression analysis service on ArrayXS Human FFPE?

A: 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.

Q: Is it possible to just analyse tumor samples without normal tissue?

A: 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.

Q: Is there a minimum number of samples I need to order?

A: The minimum number of samples is 8. This could for example be 4 patients with a tumor and a normal tissue sample.

Q: How do I place an order?

A: You can either use the Request Order form on this page or send us an e-mail to sales@oak-labs.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, you can accept it by fax or email.

Q: What is the turnaround time?

A: The usual turnaround time is 2 weeks.

Q: How do I submit my samples?

A: You will find all information about that in our service guidelines for FFPE samples.

Q: What prices can I expect for ArrayXS Human FFPE?

A: The service on ArrayXS Human FFPE 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).

faq-image

Request a free consultancy

You can also reach our gene expression experts by calling +49 3302 2 07 13 91.

CEO OakLabs
Dr. Martina Schad
Gene Expression
Project Consultant
Lab Manager
Przemyslaw Dudys
Lab Manager
Administration
Stefanie Heuchel
Customer Service and
Administrative Manager
CEO OakLabs
Dr. Jim Kallarackal
Data Analysis Specialist

Specifications ArrayXS Human FFPE



Feature Specification
OakLabs product number XS-200110
Design ID 080448
GEO Platform ID to be announced
Design creation date 12/20/2015
Format 8 x 60K
Subarrays/slide 8
Biological features 33,975 target IDs (coding genes)
Replicates of biological probes 300 x 10
Positive controls 35 x 12 ERCC control oligonucleotides 35 x 10 E1A spike-in control oligonucleotides
Gene list, annotations, design files, probe sequences Contact service(at)oak-labs.com.
Composition Sequence content sourced from: genome build GRCh38, probe design and protocol adapted to FFPE samples
Validation details OakLabs’ approved MyArray strategy (details: Development of ArrayXS Human FFPE)
Manufacturing Agilent 60-mer SurePrint technology, details: Agilent’s Microarray Technology
Compatibility 1- and 2-colour hybridisations




DEVELOPMENT OF ARRAYXS HUMAN FFPE IN THREE STEPS

1. DEVELOPMENT OF AN INITIAL TEST ARRAY

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.

2. HYBRIDISATION OF VARIOUS SAMPLES

FFPE samples of various sources and ages were processed and hybridised onto the initial microarrays.

3. SELECTION OF THE BEST PROBES

Based on the hybridisation data, the best suited probes were selected to reliably measure gene expression in FFPE samples.



RESULTS

VPC logo
33,975 genes are represented on ArrayXS Human FFPE
better performance of ArrayXS Human FFPE for FFPE samples than that of ArrayXS Human and 8x60K Agilent microarray (see the comparison)






HOW ARRAYXS HUMAN FFPE PERFECTLY MATCHES THE CHALLENGE OF ANALYSING ARCHIVED TISSUE

ARRAYXS HUMAN FFPE'S PROBES PERFORM BETTER


Comparison

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 FFPE samples. 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 Human (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. > .


Comparison

Comparison Agilent

2-COLOUR DYE SWAP APPROACH FOR STRINGENT AND CONFIDENT GENE IDENTIFICATION


Comparison

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 tumor 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 will be increased.