Peer Review History
| Original SubmissionOctober 3, 2025 |
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Dear Dr. Manuel, Please submit your revised manuscript by Dec 27 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.. 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.. 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.. 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.
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Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.... We look forward to receiving your revised manuscript. Kind regards, Annie Angers, Ph.D. 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. 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We therefore suggest that you provide this information now, though we will not hold up the peer review process if you are unable. 7. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. 8. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. Additional Editor Comments: Thank you for submitting this very interesting study. All reviewers praise the work done and consider your study highly valuable. However, they raise some concerns that need to be addressed before publication. Specifically, it is emphasized that the transcriptomics findings should be validated in vivo, and that it should be demonstrated whether the cell count, read depth, reads per cell, and gene representation are sufficient to provide the statistical power needed to detect differences in these populations, if such differences exist. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? Reviewer #1: Partly Reviewer #2: Partly Reviewer #3: No ********** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: No ********** 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.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 Reviewer #3: No ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ********** Reviewer #1: General Comments This manuscript by Manuel et al. presents a valuable investigation into the functional differentiation of three inhibitory efferent neuron subtypes (REN, ROLE, and RELL) in the zebrafish lateral line. The authors employ a dual strategy, combining single-cell transcriptomics with an anatomical analysis of neuromast innervation patterns. The study is well-designed, addressing a clear and important question in sensory neurobiology. The finding that these morphologically distinct neuron subtypes are remarkably similar at both the molecular and anatomical levels is a significant contribution, highlighting that functional specificity may arise from upstream inputs rather than intrinsic cellular properties. The technically challenging approach of manually collecting visually-identified single neurons is commendable, as it ensures exceptional sample purity for sequencing. The manuscript is well-written, and the conclusions are generally drawn with appropriate caution. The work is potentially suitable for publication in PLOS ONE, provided the major concerns outlined below are addressed. Major Comments Requirement for In Vivo Validation of Key Genes: The primary weakness of this study is the lack of validation for its novel transcriptomic findings. It is essential to perform in vivo validation via methods such as HCR-FISH for the most critical discoveries, including the expression of GABA-related genes (gad1b, gad2), as well as key differentially expressed genes (DEGs) and membrane potential-related genes that suggest subtle differences between subtypes. This validation is critical for substantiating the study's conclusions. If this is not feasible, the authors must clearly state that these findings are hypotheses generated from the transcriptomic data, not established facts. Minor Comments aRNA Amplification Bias: While necessary for such low-input samples, the two rounds of aRNA amplification are known to introduce potential bias. A brief acknowledgment of this limitation in the Methods or Discussion would enhance the study's transparency. Interpretation of Anatomical Differences: The authors conclude that the neuron subtypes are molecularly similar, yet they report a significant anatomical difference (fewer synaptic boutons for RELL neurons). The manuscript would be strengthened if the authors added a discussion on how this subtle structural difference might arise despite the transcriptomic similarity and what its potential functional implications might be. Reviewer #2: This study aims to investigate the differences of the three Inhibitory efferent neurons, REN, ROLE, and RELLby single-cell RNA sequencing in 5 dpf zebrafish larvae. The work is conceptually interesting and presents a potentially valuable hypothesis. However, in its current form, the manuscript is a little simple and lacks the methodological rigor for publication. The study is primarily descriptive of sequencing results, and the results are not adequately supported by quantitative or histological stains. My comments are as follows: 1. In the abstract, the author emphasizes that no strong molecular evidence for functional differences is found between the three types of inhibitory efferent neurons, and genes related to membrane potentials were equally expressed across REN, ROLE, and RELL cells. I think this description is inaccurate. The ScRNA Seq results showed that there are significantly different expressed genes in Figure 6. 2. Different maturity levels may lead to different phenotypes. In this study, the authors only chose the 5 dpf time point for RNA sequencing. Why? The author should add the RNA sequencing data at a late stage. 3. This study uses whole-cell scRNA-seq; however, for cells with long protrusions, such as neurons, which are prone to the loss of cytoplasmic mRNA, snRNA-seq is often more robust. Why was snRNA-seq not chosen? Could the differences between these two sequencing methods affect the conclusions? 4. In this study, the authors investigate the differences of the three inhibitory efferent neurons, REN, ROLE, and RELL, only by ScRNA-Seq. It’s not enough. The authors must add the Immunohistochemistry or in situ hybridization experiments to further confirm the results of scRNA-Seq in Figure 2- 6. 5. In Figure 6, the authors should add the Electrophysiological experiment to check the scRNA-seq results. 6. In Figure 7 (The author mistakenly wrote it as Figure 6), the authors explored whether the efferent neurons displayed unique anatomical innervation of neuromasts by confocal imaging. However, only diagrams are displayed in this study. The representative pictures should be added. 7. The cell numbers should be added in Figure 3A. 8. The full term should be provided when an abbreviation is used for the first time. Reviewer #3: This manuscript uses single cell RNA sequencing to characterize gene expression and possible gene expression differences in the efferent inhibitory neurons REN, ROLE, and RELL that innervate the zebrafish neuromast sensory organs in the lateral line. Understanding how these neurons differentiate and differentially innervate the neuromasts is an important goal. The authors use a single-cell extraction technique to physically remove the individual neurons identified by shape from the hindbrain. Using a single cell RNA seq technique developed for patch clamp extraction of cytoplasm from neurons, they sequenced the RNAs of each cell and characterized gene expression differences. Upon PCA clustering, the different neuron types displayed no significant clustering, suggesting that they largely had the same gene expression profiles. The authors conclusions are that these neurons were identified as inhibitory cholinergic by neurotransmitter phenotype, but no other significant gene expression differences existed to explain their different innervation patterns and morphologies. Very few cells in each class were analyzed, only 4-16 cells for each class. Furthermore, there is no indication of read depth, number of reads for each cell, and number of genes in the genome represented by the technique. This small cell number and potentially small read and gene representation number cause concern for the statistical power to detect changes in gene expression, especially if the differences are subtle which is to be expected of similar neuron classes. There is no indication of statistical power or resolution to detect expression differences based upon these low cell numbers and possibly low read counts. Lack of statistical power could explain the lack of gene expression differences detected between the classes. This undermines the statistical power and rigor of the conclusions about gene expression differences. If there is a published example of low cell numbers like this detecting significant differences between neurons, it should be discussed. Without the data regarding read counts and statistical power, these results do not support the conclusions of the authors that no significant differences exist. Other comments: The authors say they use the “top 2000 genes”, but representation of 100 genes was the cut-off. Please explain. Some DEGs are identified, but the authors say they are not important. This needs to be explained. Was a GO term analysis on these genes conducted on these genes? Why do the authors dismiss them? Using percentages as indications of number of cells expressing a gene is problematic, given the small cell number. Maybe percentage ranges could be used instead. The patch clamp RNA seq method is a non-standard way to do RNA seq, basically first making a full-length cDNA, and then conducting in vitro transcription to produce RNAs that are then sequenced. I understand that the technique prevents bias of PCR amplification, but use of this technique needs to be justified in analysis of differential gene expression in scRNA seq. The characterization of gene classes in these neurons is fine, but is still plagued by low cell numbers and read counts. A table showing cell number, counts for each cell, and gene representation for each cell would help. along with a discussion of statistical power to detect gene expression differences with these low cell numbers. ********** what does this mean?). If published, this will include your full peer review and any attached files.). If published, this will include your full peer review and any attached files.). If published, this will include your full peer review and any attached files.). 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 For information about this choice, including consent withdrawal, please see our For information about this choice, including consent withdrawal, please see our For information about this choice, including consent withdrawal, please see our Privacy Policy..--> Reviewer #1: No Reviewer #2: No Reviewer #3: 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.] To ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation. NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications. |
| Revision 1 |
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SINGLE-CELL ANALYSIS OF INHIBITORY EFFERENT NEURONS OF THE ZEBRAFISH LATERAL LINE PONE-D-25-53779R1 Dear Dr. Manuel, 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. For questions related to billing, please contact and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact billing support.... 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, Annie Angers, Ph.D. Academic Editor PLOS One Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author Reviewer #1: All comments have been addressed Reviewer #2: All comments have been addressed Reviewer #3: All comments have been addressed ********** 2. Is the manuscript technically sound, and do the data support the conclusions??> Reviewer #1: Yes Reviewer #2: Partly Reviewer #3: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: 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.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 Reviewer #3: Yes ********** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ********** Reviewer #1: (No Response) Reviewer #2: Most of the authors’ responses are satisfactory to me. Although the authors have provided some explanation for my comments 4 and 5, I still believe that, to further strengthen the persuasiveness of the manuscript, additional histological or functional validation is needed. Reviewer #3: (No Response) ********** what does this mean?). If published, this will include your full peer review and any attached files.). If published, this will include your full peer review and any attached files.). If published, this will include your full peer review and any attached files.). 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 For information about this choice, including consent withdrawal, please see our For information about this choice, including consent withdrawal, please see our For information about this choice, including consent withdrawal, please see our Privacy Policy..--> Reviewer #1: No Reviewer #2: No Reviewer #3: No ********** |
| Formally Accepted |
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PONE-D-25-53779R1 PLOS One Dear Dr. Manuel, 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. Annie Angers Academic Editor PLOS One |
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