Peer Review History
| Original SubmissionApril 15, 2025 |
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-->PONE-D-25-19046-->-->Single nucleus RNA sequencing of the cerebral cortex from genetically diverse inbred mouse strains reveals differences in pericyte and endothelial cell composition-->-->PLOS ONE Dear Dr. Zylka, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. If you think you can address all the reviewers' points, you are welcome to submit a revised version. Importantly, your revised manuscript will be sent out for re-review. Please note that if changes do not meet editorial expectations, your manuscript will be rejected. Please submit your revised manuscript in Jun 28 2025 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org . When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript:-->
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Kind regards, Anju Vasudevan, PhD Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and 2. To comply with PLOS ONE submissions requirements, in your Methods section, please provide additional information regarding the experiments involving animals and ensure you have included details on (1) methods of sacrifice, and (2) efforts to alleviate suffering. 3. Thank you for stating the following financial disclosure: “J.P. is supported by grants from the National Institute of Child Health and Human Development (NICHD; T32HD040127). Microscopy was performed at the UNC Neuroscience Microscopy Core (RRID:SCR_019060), supported, in part, by funding from the NIH-NINDS (P30 NS045892) and the NIH-NICHD (P50 HD103573). M.J.Z. is supported by grants from the NINDS, NIMH, and NIEHS (R01NS109304, R01MH120229, R35ES028366).” Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 4. Thank you for stating the following in the Acknowledgments Section of your manuscript: “We thank Zylka lab members for technical assistance. J.P. is supported by grants from the National Institute of Child Health and Human Development (NICHD; T32HD040127). Microscopy was performed at the UNC Neuroscience Microscopy Core (RRID: SCR_019060), supported, in part, by funding from the NIH-NINDS (P30 NS045892) and the NIH-NICHD (P50 HD103573). M.J.Z. is supported by grants from the NINDS, NIMH, and NIEHS (R01NS109304, R01MH120229, R35ES028366).” We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: “J.P. is supported by grants from the National Institute of Child Health and Human Development (NICHD; T32HD040127). Microscopy was performed at the UNC Neuroscience Microscopy Core (RRID:SCR_019060), supported, in part, by funding from the NIH-NINDS (P30 NS045892) and the NIH-NICHD (P50 HD103573). M.J.Z. is supported by grants from the NINDS, NIMH, and NIEHS (R01NS109304, R01MH120229, R35ES028366).” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 5. In the online submission form, you indicated that “Additional data supporting the findings of this study are available from the corresponding author upon reasonable request.” All PLOS journals now require all data underlying the findings described in their manuscript to be freely available to other researchers, either 1. In a public repository, 2. Within the manuscript itself, or 3. Uploaded as supplementary information. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If your data cannot be made publicly available for ethical or legal reasons (e.g., public availability would compromise patient privacy), please explain your reasons on resubmission and your exemption request will be escalated for approval. 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: Partly Reviewer #2: Yes ********** -->2. Has the statistical analysis been performed appropriately and rigorously? --> Reviewer #1: Yes Reviewer #2: Yes ********** -->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 ********** -->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 ********** -->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: The authors utilized snRNA-seq of a variety of different inbred mouse strains to investigate cell population differences. This is an important line of research to investigate, especially in regards to the variance observed across numerous different mouse strains. However, the author's dataset is under-analyzed with no form of gene expression analysis outside of cell type identification. Also, it is unclear how the authors could differentiate between CD13 and PECAM-1 positive nuclei at the magnification provided, with no representative images showing the differences across different strains. Thirdly, the conclusions that the authors have drawn are presumptuous and without sufficient data to support. Overall, this manuscript requires further work to aid the author's interpretations before suitable for publication. Please see specific comments below. Introduction - Authors should mention relevant examples of recorded phenotypic differences between inbred mouse strains Results - Fig.4: Authors should show representative images for 4 strains being compared in figure. - From the images shown in Fig.4, it is unclear how authors could differentiate between pericyte and endothelial nuclei due to the overlap of CD13 and PECAM-1 staining. Clearer images should be provided in supplement to support their analysis. - The authors should analyze gene expression changes across strains to identify potential pathways that have been dysregulated by differing population numbers. - Supplemental Fig.4: Differences in neuronal subtype population sizes are identified but authors should confirm by FISH or IHC, as they have attempted to do with the pericytes and endothelial cells. Discussion - Overly speculative without authors providing substantial evidence from their results. For example, authors identify neurovascular issues are associated with Alzheimer’s disease using Yang et al., 2022 and that their dataset expressed pericyte markers more closely aligned with T-pericytes. Yet, the authors did not present gene expression data outside of cell-type identification. Reviewer #2: The authors surveyed the cortical cellular composition of 14 Collaborative Cross mice and further validated the differences in pericyte and endothelial cells using IHC. This information is critical to understand the potential cellular mechanism behind phenotype diversity found in this population of mice. Some outstanding questions remain to be addressed: What is the selection criteria of the 14 strains of CC. Are there particular neural trait of interest that the authors are looking into within this population of mice? Why the excitatory and inhibitory neurons being the most conserved cell population across strains? Is it because they comprise the large majority of the cells and tolerant to any small changes if there's any? Lack of control/reference strain. The authors mentioned the commonly used laboratory inbred mice in the neuroscience studies like B6J and 129. So it is important to know where do reference strains like B6J and 129 fall in the cell composition spectrum of principal/neuronal subtypes among the phenotyped CC? Can they take advantage of existing single nucleus seq data of B6J and compare to other CC strains? Have any neuronal/behavioral phenotypes that have been identified in any of the CC009, CC025, CC046, CC045 that can be explained by the differential cellular composition? Please cite and discuss other brain/vascular related phenotypic diversity that have been published in CC or their founder strains that pertain to the scope of this study: PMID: 34321020, PMID: 36275853, and PMID: 38185315. ********** -->6. 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 ********** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/ . PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org . Please note that Supporting Information files do not need this step. |
| Revision 1 |
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<p>Single nucleus RNA sequencing of the cerebral cortex from genetically diverse inbred mouse strains reveals differences in pericyte and endothelial cell composition PONE-D-25-19046R1 Dear Dr. Zylka, 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. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Anju Vasudevan, Ph.D Academic Editor PLOS ONE 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 #2: All comments have been addressed ********** -->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 #2: Yes ********** -->3. Has the statistical analysis been performed appropriately and rigorously? --> Reviewer #2: Yes ********** -->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 #2: Yes ********** -->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 #2: Yes ********** -->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 #2: All concerns have been addressed. Comparison to reference C57BL6J or 129 is highly recommended, or at least discussed. ********** -->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 #2: No ********** |
| Formally Accepted |
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PONE-D-25-19046R1 PLOS ONE Dear Dr. Zylka, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Anju Vasudevan Academic Editor PLOS ONE |
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