PONE-D-23-31720Transcriptomics analysis of the bovine endometrium during the perioestrus periodPLOS ONE

Dear Dr. Irwin,

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Academic Editor

PLOS ONE

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Editor Comments:

It is imperative that the resolution of the images in the figures be enhanced to meet the standards for publication. As the current images are unsuitable for publication. Furthermore, it is crucial that the manuscript be meticulously edited in compliance with the guidelines set forth by the journal.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Excellent job with this work.

Just one question.

Did you only sample intercaruncular tissue or both caruncular and intercaruncular tissue? That information would be beneficial in the methods (ln 144-145).

Reviewer #2: Alfattah et al. (PONE-D-23-31720) performed a transcriptome analysis of estrus-synchronized heifers using RNA-seq to determine changes in gene expression during peri-estrus periods in the bovine endometrium. To extract differentially expressed genes (DEGs), analysis was based on gene expression at the onset of estrus and compared the following stages: 12 hours after CIDR removal, 24 hours after CIDR removal, 12 hours after estrus onset, 48 hours after estrus onset, and 7 days after estrus onset. They found a total of 5,845 differentially expressed genes (DEGs) from all comparisons, although the number of DEGs at 12 hours post-oestrus was low. Based on the extracted gene list, the authors attempted to identify standard pathways and functional processes of biological importance using Ingenuity Pathway Analysis, revealing pathways that are distinctive at each stage.

Overall, this is a well written paper that provides some interesting results. However, this reviewer found major issues and concerns in this manuscript.

Major Comments

The reviewer basically understands that this study is based on endometrial samples collected in the previous report (Pluta et. al, 2012, Physiol Genomics). However, the description of this manuscript does not make it clear to what extent the data are from the past and to what extent they were conducted in this study.

Pluta et. al (2012, Physiol Genomics) also performs RNA-seq. Are you using their RNA-seq data for IPA analysis?　Or are RNA extraction, library preparation and RNA-seq also performed in this study?　These should be clearly stated.

Figures and tables should be grouped together at the end of the manuscript. In the current version of the manuscript, reviewers were unable to understand the main text or legend. Are L276-278, L376-377 and L384-388 main text in Results section? It is very difficult to read.

Please provide a more detailed explanation of Figure legends for the benefit of the readers. In the current version of legends, it takes time to understand the figures and tables.

Minor Comments

L137: …according to the methods of Cooke et. al (43) and Forde et. al (20).

L246-247: What is differences in “multiple locations” and “many locations” ?

L262-268: The number of increased and decreased genes listed in parentheses should be deleted, because there were listed already in Figure 1A.

L364, 370, 378, 390 and 397: Are “Network 1” in each sections meaning the rank 1 network analyzed by IPA in each comparison? If so, should be described more clearly in the Figure legends.

L405: HDAC

L407: Remove space before “S7”.

L445: (40, 68)

L461: …by Bauersachs et. al (64) and Mitko et. al (3) ...

L566: HDAC

L953-954: Ref. 68 Is this journal, book or thesis?

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Reviewer #1: No

Reviewer #2: No

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Transcriptomics analysis of the bovine endometrium during the perioestrus period

PONE-D-23-31720R1

Dear Dr. Irwin,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Birendra Mishra, DVM, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

All comments have been addressed.

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: (No Response)

Reviewer #2: This manuscript, Transcriptomics analysis of the bovine endometrium during the perioestrus period, has been revised and resubmitted to PLOS ONE for re-evaluation.

This reviewer sees the improvement and rather appreciates their efforts in their revision. My original concerns have been solved.

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: No

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