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Biological replicates

I have few conditions. Please tell me if these are biological replicates or not-

  1. RNASeq expression from 3 different strains of same bacteria under same condition.
  2. RNASeq expression from 3 different bacteria under same condition.
  3. RNASeq expression from 1 bacterial strain under different conditions.
  4. RNASeq expression from 1 bacteria, 1 nematode and 1 protozoa under same condition.
biological replicates
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written by prs • prs

Is this a homework question?

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written by rpolicastro rpolicastro

This is what ChatGPT has to say about it ;-) :

I'd be happy to help you understand what constitutes a biological replicate in experimental design, but it's important to note that it's not ethical for me to complete your homework for you.

In general, a biological replicate refers to a sample or experimental unit that is independently grown, collected, or prepared from the same biological source, under identical conditions.

For example, if you are studying the effect of a particular treatment on a group of mice, and you want to compare the gene expression in their liver tissue, then each mouse would be a biological replicate. You would need to ensure that each mouse is genetically similar, housed in the same conditions, and given the same diet and treatment regimen.

On the other hand, if you take multiple samples from a single mouse, such as different regions of the liver or different time points after treatment, those would not be considered biological replicates because they are not independent units from the same biological source.

It nonetheless provides an assignment, which I however think is plain wrong everywhere:

Sure, here's how each of these cases can be considered in terms of biological replicates:

  • RNASeq expression from 3 different strains of the same bacteria under the same condition: In this case, each strain of bacteria would be considered a biological replicate as they are independent samples collected from different biological sources (i.e., different bacterial strains).
  • RNASeq expression from 3 different bacteria under the same condition: Each of the three bacteria would be considered a biological replicate in this case because they are independent samples collected from different biological sources.
    • RNASeq expression from 1 bacterial strain under different conditions: Each condition would be considered a technical replicate because they are different measurements taken from the same biological sample. However, if the bacteria are grown separately under each condition, then each biological replicate would be considered independent and should be analyzed separately.
    • RNASeq expression from 1 bacterial strain, 1 nematode, and 1 protozoa under the same condition: Each organism would be considered a biological replicate in this case because they are independent samples collected from different biological sources.
    • RNASeq expression from 1 bacterial strain under different conditions: Each condition would be considered a technical replicate
      because they are different measurements taken from the same biological sample. However, if the bacteria are grown separately under each condition, then each biological replicate would be considered independent and should be analyzed separately.
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written by Matthias Zepper Matthias Zepper

No. I am trying to understand the basics. So I created these questions as these might help me to understand the minute differences.

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written by prs • prs

1 answer

Start with first principles. What constitutes a biological replicate? If this is a homework question (and it sounds like one), look through your notes for what your professor has given as a definition for "biological replicate".

It may be helpful, also, to consider also the difference between "biological replicate" and "technical replicate". A technical replicate means you're repeating (replicating) an experimental technique, usually on different aliquots (sub-samples) of the same sample. A biological replicate usually means you have taken independent biosamples that are "the same" in some relevant trait of interest. The thing that you're replicating, or repeating, is that trait or condition of interest.

What you're being asked to do here is make an argument, in each case, for why or WHY NOT the set of samples in consideration constitute a biological replicate. You need to do that with reference to the definition for biological replication that your instructor is using. Do please note that ChatGPT's answers in the second part, as Matthias above suggested, are probably mostly wrong. I wouldn't ever consider the penultimate set to be biological replicates because they have very little in common -- what are you "replicating" there?

Good luck -- you can puzzle it out, I believe in you.

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written by Cera • Cera

Thank you. But, these are not homework questions and I don't have any definition given by professor. I created the questions myself so to understand the meaning of biological replicates properly. I have watched videos and tried chatgpt as well (which answered me quite differently than the above mentioned answer), but I didn't get any clear logic anywhere. So I framed the questions and asked here.

I'll try to answer the questions myself and would request others to correct and clarify me-

  1. Under same conditions, 3 different strains of 1 bacteria which are almost similar genetically, are considered biological replicates
  2. If 3 bacteria are grown under similar condition, and the bacteria are closely related, say all three are coccus/vibrio, then these are biological replicates
  3. If data is taken from 1 bacteria under different conditions, they are also biological replicates
  4. If expression is from 1 bacteria, 1 nematode and 1 protozoa, it is not a biological replicate since all three are from different phylum.
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written by prs • prs

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