ERCC (External RNA Controls Consortium) spike-in controls are synthetic RNA molecules used in RNA-seq experiments to assess the performance
of the assay, monitor technical variability, and quantify gene expression. Here’s a breakdown of the differences, pros, and cons of ERCC ExFold and ERCC RNA Spike-In Mix:

 ERCC ExFold RNA Spike-In Mixes (with Mix1 and Mix2):

  • Purpose: ERCC ExFold is
    a set of ERCC spike-ins designed for use in
    fold-change experiments. These spike-ins consist of a mix of 92 transcripts, each at a different known concentration, spanning a wide dynamic range.
  • Pros:
    • Ideal for experiments where you want to assess the fold-change accuracy of your RNA-seq assay.
    • Provides a range of known concentration levels, allowing you to test the ability of your assay to accurately measure fold changes across a broad dynamic range.
    • Useful for benchmarking and quality control in experiments with a focus on differential gene expression analysis.
  • Cons:
    • May not be as suitable for experiments where absolute quantification of gene expression is the primary goal, as the ERCC ExFold spike-ins are designed to assess
      relative fold changes.

ERCC RNA Spike-In Mix (with only Mix1):

  • Purpose: The ERCC RNA Spike-In Mix consists of a set of 92 synthetic RNA molecules, each at a known concentration. These spike-ins are intended for use in absolute quantification experiments.
  • Pros:
    • Ideal for experiments where you need to accurately quantify the absolute expression levels of genes in your sample.
    • Allows you to estimate the absolute abundance of RNA molecules in your sample, which is valuable for applications such as biomarker discovery.
  • Cons:
    • May not be as informative for fold-change experiments, as the spike-ins are primarily designed for absolute quantification.

In summary, the choice between ERCC ExFold and ERCC RNA Spike-In Mix depends on the goals of your RNA-seq experiment. If you’re primarily interested in assessing the accuracy of fold-change measurements, ERCC ExFold is a better choice. On the other hand, if your focus is on absolute quantification of gene expression, the ERCC RNA Spike-In Mix is more suitable.

It’s worth noting that you can use both types of ERCC controls in the same experiment if you want to assess both fold-change accuracy and absolute quantification. However, keep in mind that adding too many spike-ins to your experiment can increase its complexity and cost. Therefore, it’s important to carefully plan your spike-in strategy based on your research objectives.

Understanding the Role of ERCC Spike-Ins in Your RNA-seq Experiment

  • No ERCC Spike-Ins:
    • In many cases, you may not need ERCC spike-ins if your primary goal is to detect differentially expressed (DE) genes without a specific requirement for absolute measurements. In this scenario, the focus is on comparing the relative abundance of genes across samples, typically achieved through normalization based on library size. This
      approach is commonly used when the emphasis is on identifying which genes are differentially expressed without needing precise absolute measurements.
  • With ERCC RNA Spike-In Mix (Mix1):
    • When your research involves samples with genome-wide overexpressed or knocked-down genes, you may find value in incorporating ERCC RNA Spike-In Mix1. These spike-ins serve as a control, enabling you to assess the accuracy of absolute measurements in your RNA-seq experiment, particularly in cases where large-scale gene expression alterations are expected.
  • With ERCC ExFold Spike-Ins (Mix1 and Mix2):
    • For experiments targeting the measurement of fold changes in low-expressed genes, ERCC ExFold Spike-Ins provide an additional layer of confidence. Mix1 and Mix2 together create a positive control system for assessing the accuracy of fold changes in RNA-seq data. It’s important to note that this method doesn’t recalibrate your
      measurements but rather enhances your confidence in the fold change estimates, especially for genes expressed at lower levels. It’s a valuable tool when precision in measuring fold changes is essential to your research objectives.

In summary:

  • No ERCC Spike-Ins: Suitable for DE gene detection without the need for absolute measurements, focusing on relative gene expression.
  • ERCC RNA Spike-In Mix (Mix1): Beneficial when studying genome-wide gene expression changes, offering confidence in absolute measurements.
  • ERCC ExFold Spike-Ins (Mix1 and Mix2): Ideal for experiments involving low-expressed genes, enhancing confidence in fold change measurements.

Your choice of ERCC spike-ins depends on your specific research goals and the level of precision required for your RNA-seq analysis.