Choosing between miR-124 and miR-143 depends on various factors, including

• your research interests,
• available resources,
• and the specific goals of your study.

However, based on the their roles in colorectal cancer, here are a few points you may want to consider:

1. miR-124

- There should be significant literature available in the context of neuronal development and cancer.

- Well known to have a tumor-suppressive role in colorectal cancer.

- Targets genes involved in :

• cell proliferation,
• migration, and invasion,
• offering potential therapeutic avenues for intervention.

2. miR-143

- Also implicated as a tumor suppressor in colorectal cancer, with important roles in

• regulating cell proliferation and metastasis.
• Regulates key signaling pathways such as RAS-MAPK and PI3K-AKT, making it a promising therapeutic target.

Considering both their similar tumor-suppressive roles in colorectal cancer as well as their potential therapeutic results , either miR-124 or miR-143 could prove to be a solid choice for your research.

You may want to consider factors such as

A few notable differences:

miR-124

If you’re interested in:

• Establishing therapeutic targets
• elucidating the underlying mechanisms of tumor suppression,

miR-143

If you’re interested in:

• studying signaling pathways and
• regulatory networks involved in colorectal cancer progression

Ultimately , I recommend further assessing the literature and resources available to you, consulting with your colleagues or mentors, and considering the specific objectives of your research to make an informed decision on which miRNA to focus on for your study.

Good luck! I look forward to following your research.

Making real time PCR primers for microRNA isn't too difficult nowadays. First make sure your RNA is isolated with columns that will retain microRNA fraction of RNA. So don't assume that your traditional RNA column which you used for mRNA expression study will have miRNA fraction. There are excellent spin columns from many vendors, QIAGEN & ThermoFisher coming to mind as top choices (though others will work as well :)). For the primers/probe target you should probably aim for the active strand of the miRNA which is either the 3' or 5' strand depending on the microRNA. A good database to screen for the active strand is miRBase, an example for hsa-miR-124-1 is here: https://mirbase.org/hairpin/MI0000443. In this case, miR-124-3p seems to be the activate strand as most NGS reads are placed on the 3' end of the miRNA (click "Show Histogram" in Sequence tab).

You will also need a miRNA reverse transcription kit, you will have to be mindful of how the miRNA is reverse transcribed as that will determine what kind of primers or probes will be possible with that assay. If you don't want to optimize much, Thermo has TaqMan assays that take away a lot of the hassle of optimization with their reverse transcription + TaqMan probe assays (https://www.thermofisher.com/order/catalog/product/4366596). If you have a decent budget and you don't feel comfortable with primer + probe design, I highly recommend looking into Thermo's Taqman and Exiqon LNA assays by QIAGEN. Exiqon makes it very convenient to run plate assays (96/384) with all the necessary normalization/QC checks in an assay setup for a decent price. After that, microRNA interpretation is very similar to mRNA expression analysis so follow all the best practices that you are familiar with for real time PCR.