Title: Markers of immune dysregulation in response to the ageing gut: insights from aged murine
gut microbiota transplants
Version: 1 Date: 20 May 2022
Reviewer's report:
1. The manuscript is well conceptualized and well written
2. The analysis is effective and easy to comprehend.
3. It would be nice if the name of the groups being compared using DEG and the sample number
within each group is clearly mentioned in the methods. I do feel that the number of sample count
used within the manuscript (4 vs 5) is very low. Is there a reason for such low sample count
considering these are mice samples.
4. I did not see the Log2 FC threshold being used to filter out upregulated and downregulated
genes. If there isnt any threshold, please mention the base means within each group as well. A
threshold allows the reader to understand that low abundance genes were removed.
5. Line 230 - How many down-regulated genes can be classified as membrane proteins?
6. Considering the dataset has access to Log2 fold change data and q values, it would also be
nice to visualize and depict up regulated and down-regulated genes using volcano plots. That
allows to see how many genes (that are q value significant) are not low abundant.
Title: Markers of immune dysregulation in response to the ageing gut: insights from aged murine
gut microbiota transplants
Version: 1 Date: 20 May 2022
Reviewer's report:
1. The manuscript is well conceptualized and well written
2. The analysis is effective and easy to comprehend.
3. It would be nice if the name of the groups being compared using DEG and the sample number
within each group is clearly mentioned in the methods. I do feel that the number of sample count
used within the manuscript (4 vs 5) is very low. Is there a reason for such low sample count
considering these are mice samples.
4. I did not see the Log2 FC threshold being used to filter out upregulated and downregulated
genes. If there isnt any threshold, please mention the base means within each group as well. A
threshold allows the reader to understand that low abundance genes were removed.
5. Line 230 - How many down-regulated genes can be classified as membrane proteins?
6. Considering the dataset has access to Log2 fold change data and q values, it would also be
nice to visualize and depict up regulated and down-regulated genes using volcano plots. That
allows to see how many genes (that are q value significant) are not low abundant.
Please review this paper.
user
Title: Markers of immune dysregulation in response to the ageing gut: insights from aged murine
gut microbiota transplants
Version: 1 Date: 20 May 2022
Reviewer's report:
1. The manuscript is well conceptualized and well written
2. The analysis is effective and easy to comprehend.
3. It would be nice if the name of the groups being compared using DEG and the sample number
within each group is clearly mentioned in the methods. I do feel that the number of sample count
used within the manuscript (4 vs 5) is very low. Is there a reason for such low sample count
considering these are mice samples.
4. I did not see the Log2 FC threshold being used to filter out upregulated and downregulated
genes. If there isnt any threshold, please mention the base means within each group as well. A
threshold allows the reader to understand that low abundance genes were removed.
5. Line 230 - How many down-regulated genes can be classified as membrane proteins?
6. Considering the dataset has access to Log2 fold change data and q values, it would also be
nice to visualize and depict up regulated and down-regulated genes using volcano plots. That
allows to see how many genes (that are q value significant) are not low abundant.
assistant