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  • #1

    RNA-seq samples from different numbers of cells - effects on differential expression?

    Hi All!

    I have been given a number of RNA samples for an upcoming RNA-seq experiment, but I've recently discovered that the number of cultured cells used for RNA extraction was not consistent (i.e., each extracted sample consisted of a different number of cells). I'm worried that using RNA extracted from different cell densities will have an effect on downstream differential expression analyses. I've searched around a decent amount, but am having trouble finding any solid information regarding my situation. Before I move forward with this experiment, I'm wondering:
    1. How concerned about this should I be?
    2. If I move forward with sequencing, should I try to control for cell number by adding it as a covariate in my analyses (if I can get this data)?
    3. Are there any other potential solutions that I should consider?
    Thanks in advance for any help!
    Tags: None
  • #2
    Hello RNasymetrical that's a good observation. I unfortunately don't have the answer, but it seemed to me that it could be potentially answered using one of the two papers I've included links for below.

    If that doesn't help then let me know and I'll do some more digging!

    Batch effect detection and correction in RNA-seq data using machine-learning-based automated assessment of quality - BMC Bioinformatics
    https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-022-04775-y
    Background The constant evolving and development of next-generation sequencing techniques lead to high throughput data composed of datasets that include a large number of biological samples. Although a large number of samples are usually experimentally processed by batches, scientific publications are often elusive about this information, which can greatly impact the quality of the samples and confound further statistical analyzes. Because dedicated bioinformatics methods developed to detect unwanted sources of variance in the data can wrongly detect real biological signals, such methods could benefit from using a quality-aware approach. Results We recently developed statistical guidelines and a machine learning tool to automatically evaluate the quality of a next-generation-sequencing sample. We leveraged this quality assessment to detect and correct batch effects in 12 publicly available RNA-seq datasets with available batch information. We were able to distinguish batches by our quality score and used it to correct for some batch effects in sample clustering. Overall, the correction was evaluated as comparable to or better than the reference method that uses a priori knowledge of the batches (in 10 and 1 datasets of 12, respectively; total = 92%). When coupled to outlier removal, the correction was more often evaluated as better than the reference (comparable or better in 5 and 6 datasets of 12, respectively; total = 92%). Conclusions In this work, we show the capabilities of our software to detect batches in public RNA-seq datasets from differences in the predicted quality of their samples. We also use these insights to correct the batch effect and observe the relation of sample quality and batch effect. These observations reinforce our expectation that while batch effects do correlate with differences in quality, batch effects also arise from other artifacts and are more suitably corrected statistically in well-designed experiments.


    https://academic.oup.com/nargab/article/2/3/lqaa078/5909519



    Batch effect detection and correction in RNA-seq data using machine-learning-based automated assessment of quality | BMC Bioinformatics | Full Text
    https://bmcbioinformatics.biomedcentral.com
    The constant evolving and development of next-generation sequencing techniques lead to high throughput data composed of datasets that include a large number of biological samples. Although a large number of samples are usually experimentally processed by batches, scientific publications are often elusive about this information, which can greatly impact the quality of the samples and confound further statistical analyzes. Because dedicated bioinformatics methods developed to detect unwanted sources of variance in the data can wrongly detect real biological signals, such methods could benefit from using a quality-aware approach. We recently developed statistical guidelines and a machine learning tool to automatically evaluate the quality of a next-generation-sequencing sample. We leveraged this quality assessment to detect and correct batch effects in 12 publicly available RNA-seq datasets with available batch information. We were able to distinguish batches by our quality score and used it to correct for some batch effects in sample clustering. Overall, the correction was evaluated as comparable to or better than the reference method that uses a priori knowledge of the batches (in 10 and 1 datasets of 12, respectively; total = 92%). When coupled to outlier removal, the correction was more often evaluated as better than the reference (comparable or better in 5 and 6 datasets of 12, respectively; total = 92%). In this work, we show the capabilities of our software to detect batches in public RNA-seq datasets from differences in the predicted quality of their samples. We also use these insights to correct the batch effect and observe the relation of sample quality and batch effect. These observations reinforce our expectation that while batch effects do correlate with differences in quality, batch effects also arise from other artifacts and are more suitably  corrected statistically in well-designed experiments.

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