High-throughput biological research such as chip and sequencing from clinical samples is the most commonly used idea, but the sample collection process is subject to factors such as pathological features and number of cases, which is time-consuming and labor-intensive. Numerous expectations have come to look forward to the clinical samples, and an RNA extraction is often done...
The RNA integrity of the degraded sample is low, and the long-chain RNA becomes a short chain. In the conventional amplification process, the loss of the target fragment detected by the probe occurs, resulting in inaccurate chip results.
What if I encounter RNA degradation?
If you have the conditions, it will be a better choice to re-sample. Pay attention to the rapid and stable operation of the sample, and quickly freeze the liquid nitrogen. RNA preservation reagents such as RNAlater can also be used, but it is also necessary to strictly follow the operation specifications of such reagents, otherwise the protection effect on RNA will not be achieved. For example, before soaking the RNAlater, the tissue sample should be cut into small pieces of less than 0.5 cm in any direction to ensure that the soaking is as full as possible.
But how can a precious sample be easily retrieved? Can the precious samples of degradation really only be thrown away? No!
Affymetrix officially launched an excellent degrading RNA amplification labeling kit for the degradation sample: SensationPlusTM FFPE Amplification and 3' IVT Labeling Kit. The kit uses a combination of random primers and OligodT primers to efficiently amplify 20-200 ng of degraded sample RNA, even FFPE sample RNA, allowing these low-degradation samples to survive, saving researchers a large amount of sample collection. The end of the time to pay.
Test this kit. Different gene manipulation treatments were performed on the same cell, and a 3vs3 chip expression profile was detected. After receiving the sample, the RIN value of the extracted product 2100 was about 2 due to some treatment. The hybridization chip was amplified by the SensationPlus kit and the results were very beautiful.
The data quality is excellent, and more than 600 differential genes (more than 2 times difference) are up-regulated, and more than 500 are down-regulated. Subsequent GO/Pathway enrichment analysis results are also very good.
Attached to the analysis process:
The well-preserved FFPE sample extraction product RIN value is usually between 1.8 and 2.8, so the FFPE sample can also be revived with this kit. However, the FFPE sample will be affected by the storage conditions and time, resulting in certain data instability. Therefore, it is recommended that the chip be targeted for FFPE samples, and the samples with shorter time will be preferred. Of course, it is best to sort out a batch of samples and try to extract a few to see the degradation of RNA.
What are you waiting for, the paraffin blocks that fall asleep in the sample library, let them play a bigger role~~~ 
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