Title: Transcriptional landscape of intestinal environment in DSS-induced ulcerative colitis
mouse model
Version: 2 Date: 03 Jun 2023
Reviewer:  Maziar Ganji
Reviewer's report:
The manuscript entitled “Transcriptional landscape of intestinal environment in DSS-induced
ulcerative colitis mouse model” examines the transcriptomic changes in an animal model of
Ulcerative Colitis. The following points need to be addressed:
- Grammatical edition is required.
- Although the term “Difference in Expressed Genes (DEGs)” can be applied, the “Differentially
Expressed Genes (DEGs)” seems to be more frequently used in the academic environment.
- The mRNA & microRNA sequencing processes performed on mice need to be clearly
described! Also, the sample type name and its preparation method for these molecular tests
should be noted!
- The abbreviations such as FDR, lncRNA, and miRNA should be fully described in their first
appearance in the body text.
- It would be great if the authors can explain how a 7-day treatment can result in transcriptomic
changes in the mice's body? Adding references for conducting this approach in groups with only
3 sample sizes is highly suggested.
- In the Results section, for the genes with significantly altered expression some parameters such
as p-value or fold changes should be mentioned! These would show how much such alterations
might be of importance compared to other less crucial ones.
- Another major issue is that the Discussion section is too short! These huge numbers of genes,
pathways, and novel achievements of this manuscript can be easily discussed in detail.
- As a suggestion for Figures 3 & 4, in addition to the genes shown, their critical pathways can
be demonstrated too in order to clearly define the involved dysregulated pathways and gene
networks.
Title: Transcriptional landscape of intestinal environment in DSS-induced ulcerative colitis
mouse model
Version: 2 Date: 03 Jun 2023
Reviewer:  Maziar Ganji
Reviewer's report:
The manuscript entitled “Transcriptional landscape of intestinal environment in DSS-induced
ulcerative colitis mouse model” examines the transcriptomic changes in an animal model of
Ulcerative Colitis. The following points need to be addressed:
- Grammatical edition is required.
- Although the term “Difference in Expressed Genes (DEGs)” can be applied, the “Differentially
Expressed Genes (DEGs)” seems to be more frequently used in the academic environment.
- The mRNA & microRNA sequencing processes performed on mice need to be clearly
described! Also, the sample type name and its preparation method for these molecular tests
should be noted!
- The abbreviations such as FDR, lncRNA, and miRNA should be fully described in their first
appearance in the body text.
- It would be great if the authors can explain how a 7-day treatment can result in transcriptomic
changes in the mice's body? Adding references for conducting this approach in groups with only
3 sample sizes is highly suggested.
- In the Results section, for the genes with significantly altered expression some parameters such
as p-value or fold changes should be mentioned! These would show how much such alterations
might be of importance compared to other less crucial ones.
- Another major issue is that the Discussion section is too short! These huge numbers of genes,
pathways, and novel achievements of this manuscript can be easily discussed in detail.
- As a suggestion for Figures 3 & 4, in addition to the genes shown, their critical pathways can
be demonstrated too in order to clearly define the involved dysregulated pathways and gene
networks.
Please review this paper.
user
Title: Transcriptional landscape of intestinal environment in DSS-induced ulcerative colitis
mouse model
Version: 2 Date: 03 Jun 2023
Reviewer:  Maziar Ganji
Reviewer's report:
The manuscript entitled “Transcriptional landscape of intestinal environment in DSS-induced
ulcerative colitis mouse model” examines the transcriptomic changes in an animal model of
Ulcerative Colitis. The following points need to be addressed:
- Grammatical edition is required.
- Although the term “Difference in Expressed Genes (DEGs)” can be applied, the “Differentially
Expressed Genes (DEGs)” seems to be more frequently used in the academic environment.
- The mRNA & microRNA sequencing processes performed on mice need to be clearly
described! Also, the sample type name and its preparation method for these molecular tests
should be noted!
- The abbreviations such as FDR, lncRNA, and miRNA should be fully described in their first
appearance in the body text.
- It would be great if the authors can explain how a 7-day treatment can result in transcriptomic
changes in the mice's body? Adding references for conducting this approach in groups with only
3 sample sizes is highly suggested.
- In the Results section, for the genes with significantly altered expression some parameters such
as p-value or fold changes should be mentioned! These would show how much such alterations
might be of importance compared to other less crucial ones.
- Another major issue is that the Discussion section is too short! These huge numbers of genes,
pathways, and novel achievements of this manuscript can be easily discussed in detail.
- As a suggestion for Figures 3 & 4, in addition to the genes shown, their critical pathways can
be demonstrated too in order to clearly define the involved dysregulated pathways and gene
networks.
assistant