Biomedical Engineering Reference
In-Depth Information
DNA extraction (DNA isolation kits).
Labeling.
Sample loading onto the aCGH chip.
Scanning and image analysis for the raw data.
Raw data processing and result loading.
Sequencing
Specimen tracking.
DNA extraction (DNA isolation kits).
Sequencing (some instrument specific files and formats).
Data file processing and loading.
As seen earlier, mRNA-based analyses involve total RNA preparation and
reverse transcription, and then the samples are loaded onto the experimental plat-
form. Similarly, DNA-based analyses involve DNA extraction and labeling (some-
times with DNA amplification, which is not discussed here), and then the prepared
samples are applied to the experimental platforms. If the tracking system is of a
modular structure, the modules from sample tracking to molecule preparation can
be reused again and again, simplifying the development of the entire workflow. Of
course, there might be some subtle differences in the sample preparation steps for
different experiments using the same type of molecules, so the tracking modules will
need to be developed in a generalized form for easy adaptation to different needs.
7.3.4.4 Requirements for Proteomics Experiments
Similar to genomic studies, for proteomic studies the specimen needs to be uniquely
tracked to allow proper tracing of the information back to the clinical data of the
donor. Multiple tissue types, including multiple blood sample subtypes, are
involved in proteomic studies. However, sample preparation in proteomic studies is
typically not as complicated as in genomic studies.
Protein expression studies are often carried out with different protein separation
and identification technologies depending on the tissue type and the goal of study, as
described in Chapter 6. As discussed there, proteomic technologies are not as mature
as genomic technologies and, thus, flexibility of the tracking system is more impor-
tant in proteomic studies. Data generated in different experimental steps, as well as
the output files from the instruments and platform-specific data analysis software,
should be captured in the tracking system. Data types from example proteomic
experimental platforms that need to be tracked are described next. (More detailed
description of these experimental platforms can be found in Chapter 6.)
2D-DIGE/MS
Specimen tracking.
Sample preparation.
Protein labeling (with Cy2, Cy3 or Cy5) and sample pooling.
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