With the advent of microarray technology, it is possible to analyze thousands of gene expression values with a single experiment to identify markers of a target phenotype. Thus, to assess the quality of the analyses and improve further integration tasks, it is fundamental to track both the biological information related to the sample source and the entire experimental process. The Microarray Module aims to track all the steps of a microarray experiment. The main functionalities it provides are listed in the following.
Microarray experiment can be planned for both internal and external aliquots. The internal aliquots are all the aliquots stored in the Biobank module. By using the “Experiment” functionality in the Biobank module, the user can defines the set of aliquots on which the microarray experiment will be performed, the title and a description (optional) for this request. To manage aliquots collected only for the microarray facility, the system allows the insertion of external requests. For this kind of requests, the user should associate an unique identifier and provide a minimum set of information (i.e., volume and concentration) for each aliquot. It is possible to upload a file containing the description of these aliquots.
The first step of the microarray experiment is the hybridization of samples positioned on chips. The user should define the instrument and hybridization protocol that will be used. Then, she should define many (virtual) chips, also with different layout (i.e., number of positions), and position the aliquots belonging to several requests. The visualized requests are those assigned to the user or with no assignment and they can be external requests (see External request paragraph) or the ones defined in the Experiment procedure of the Biobank. The system suggests how to prepare the aliquots positioned on the virtual chips.
Before apply the hybridization procedure, the user should validate all the planned aliquots and confirm the used quantity. After selecting an hybridization plan, the user should insert the barcode of each aliquot to perform the validation procedure. The system automatically update the volume of each aliquot according to the hybridization protocol. Although, the user can modify the used volume.
The hydrization procedure is used to prepare the chips before the scanning by positioning the aliquots on them. In this functionality all the hybridization plans for which the aliquots have been validated are visualized. After selecting a plan, the user should insert the barcode of the chips. The system automatically move the planned aliquots on the chip according to the chip layout and the virtual hybridization plan. The user can modify the position of each aliquot by using the drag & drop function.
The hybridized chips are ready to be insert into the scanner. The user selects the scan protocol which defines the scanner and its settings. By inserting the chip barcode the system shows the chip content (i.e., aliquot identifiers) and positions automatically the chip in the first available position of the scanner. The chip location can be changed by using the drag & drop function.
Some scan procedures requires a Q/C evaluation. For the chips scanned with this kind of protocols, the user should associated to each aliquot if the scan failed or not. After selecting one scan, the system show the chips belonging to the experiment of interest. For each aliquot in each chip, the system automatically set all the aliquots with the successful flag, but the user can change this status by simply clicking on the target aliquot.
The chip used in the experiments should be described by the following set of information: (i) barcode, (ii) type, (iii) owner, (iv) expiration date , (v) lot number, (vi) link to Dmap file.
Each chip inherits some characteristics from the chip type. For instance, all the chips with the same type have the same layout. During the new chip type definition, the user defines the number of positions and the system suggests the identifier for each position.
The hybridization protocols are used to define the rules applied to prepare the aliquots and the chip before the scan. An hybridization protocol includes the following features: (i) unique name, (ii) load quantity (ng), (iii) hybridization buffer (ul), (iv) hybridization temperature (°C), (v) total volume (ul), (vi) hybridization time (hours) (vii) denaturation temperature (°C), and (viii) denaturation Time (minutes).
A scan protocol describes the main characteristic of the process by means of the following parameters: (i) unique name, (ii) used software, (iii) used instrument and (iv) if the Q/C evaluation of the result is required. According to the instrument information a set of scanner parameters are visualized and can be modified.
Using the chip barcode, the user can browse the files associated to the scan event and to each aliquot positioned on the chip. The file can be downloaded for further analyses. The microarray raw data coming from the scans are remotely loaded in the Document Storage Manager and linked to the corresponding sample by the provided software.