Example Projects

• A customer was researching the differential expression of normal and diseased tissue.


• A proposal was drawn up and sent to the customer within three days of requesting it.


• The customer had decided to perform the labelling and fragmentation of RNA samples in their Labs using recommended Affymetrix protocols.


• The customer sent the signed proposal, a purchase order number and their samples (20ug of labelled and fragmented cRNA in 40ul) back to us immediately.


• A 3ul aliquot of labelled cRNA (minimum concentration 120ng/ul) was also sent for additional QC.

• The 12 cRNA samples were assessed for quality by Agilent bioanalyser. A good cRNA sample will be represented by a smear of products falling between 50 and 3000 bases long. An example profile can be seen below:

• The fragmented cRNA samples were also assessed using the Agilent bioanalyser. The standard fragmentation procedure should produce a distribution of RNA fragment sizes from approximately 35-200 bases (see below):

• All of the samples then passed QC and were hybridised to an Affymetrix Genechip Human Genome U133 Plus 2.0 Array and incubated overnight for 16 hours.


• The arrays were then washed and stained using the Affymetrix Fluidics Station and scanned using the Affymetrix GCS 3000 scanner.

• After the arrays are scanned the resulting image is analysed by Genechip Operating software (GCOS) which generates an expression report file that lists the quality control parameters.


• Basic analysis of the data was performed. This included normalisation of data and selection of differentially expressed genes.


• All the raw data and associated files were returned to the customer along with an Excel spreadsheet presented together with the corresponding Affymetrix functional annotations, allowing for additional searches and analysis.


• This data was then placed onto a secure FTP server, with the customer being supplied with a username and password so that they can remotely access and download their data.


• The entire process took 5 working days from receipt of RNA to making the data available on the FTP site.

• A customer was researching the differential expression of normal and diseased tissue.


• A proposal was drawn up and sent to the customer within three days of requesting it.


• The customer sent the signed proposal, a purchase order number, sample annotation form and their samples (minimum concentration of 120ng/ul and a minimum volume of 13ul) back to us immediately.

• The samples were assessed quantitatively and qualitatively by the nanodrop spectrophotometer and the Agilent bioanalyser. A good Total RNA sample will have an A260/A280 ratio close to 2.0 as well as a bioanalyser trace similar to the one below (i.e with two strong ribosomal peaks with a 28S/18S ratio close to 2.0 and a low baseline indicating little degradation)

• The samples were taken through the following processes: cDNA synthesis, In-vitro transcription labelling, cRNA QC (by agilent bioanalyser and nanodrop spectrophotometer) and fragmentation before being hybridised to a Mouse Genome microarray and incubated overnight for 16 hours (3 - 4 day process).


• The microarrays were then washed and stained and subsequently scanned using the Applied Biosystems 1700 Microarray analyser.

• The Resulting array image was analysed by the Applied Biosystems analyzer software and the QC parameters scrutinised by an experienced Project Scientist


• Basic analysis of the data was performed. This included normalisation of data and selection of differentially expressed genes.


• All the raw data and associated files were returned to the customer together with an Excel spreadsheet presented along with the corresponding functional annotations, allowing for additional searches and analysis.


• This data was then placed onto a secure FTP server, with the customer being supplied with a username and password so that they can remotely access and download their data.


• The entire process took 7 working days from receipt of RNA to making the data available on the FTP site.

• A customer was researching Loss of Heterozygosity and contacted us about sending 24 samples to be processed on the 50k Hind 240 arrays


• A proposal was drawn up and sent to the customer within three days of requesting it.


• The customer sent the signed proposal, a purchase order number and their samples (20ul of each at 50ng/ul) back to us immediately.

• Five samples failed to produce the recommended 260/230 and 260/280 ratios of 1.8 - 2.0. Uniquely, Geneservice are in a position to rescue these samples by Whole Genome Amplification,


• WGA was carried out (after the with the customers approval) on the 5 samples which took an additional 3 days (the WGA material was sent back to the customer on completion of the project)


• All of the samples then passed QC and were taken through the following processes: restriction digest, ligation, PCR, purification, quantification, fragmentation and labelling, before being hybridised to a 50k Hind 240 chip and incubated overnight for 16 hours (3 - 4 day process)


• The chips were then washed and stained using the Affymetrix Fluidics Station and scanned using the Affymetrix GCS 3000 scanner.

• After analysis with GDAS software, array images and data looked like this:

• This data was then placed onto a secure FTP server, with the customer being supplied with a username and password so that they can remotely access and download their data.


• The entire process took 14 working days from receipt of DNA to making the data available on the FTP site.


• A total of 1.17 million genotypes were supplied.


• The WGA procedure rescued 5 samples or 21% of the data which would otherwise have been lost to the study.