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One of the original reviewers as well as myself confirm that the revision has been appropriately done.
[# PeerJ Staff Note - this decision was reviewed and approved by Jun Chen, a PeerJ Section Editor covering this Section #]
I have no comment.
I have no comment.
I have no comment.
Authors change the points of reviewers, and this article is acceptable for this journal.
Your manuscript has been reviewed by two experts in the field. As you can see from their comments below, both of them appreciate the value of this work but raise several minor points for further improvement. Particularly, it seems important to add more details in the Materials and Methods section. Please read the comments carefully and revise the manuscript accordingly.
[# PeerJ Staff Note: Please ensure that all review comments are addressed in a rebuttal letter and any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate. It is a common mistake to address reviewer questions in the rebuttal letter but not in the revised manuscript. If a reviewer raised a question then your readers will probably have the same question so you should ensure that the manuscript can stand alone without the rebuttal letter. Directions on how to prepare a rebuttal letter can be found at: https://peerj.com/benefits/academic-rebuttal-letters/ #]
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The author reports here that ASPS resembles a mesenchymal stromal progenitor at the mRNA level. The study is well illustrated and documented, and the conclusions are certainly supported by the data presented. However, some parts of the manuscript need revision, before it can be accepted for publication.
#1 Materials and methods are too short and not sufficient to understand.
In Table 1, the author has listed the top 50 transcripts overexpressed in the ASPS-1 cell line relative to the average. Is it an appropriate analysis method to use the average value of completely different samples? A bias exists in the number of cell lines. The number of Ewing sarcoma cell lines is 22; on the other hand, the number of DDLS cell lines is only 2. The average value reflects the majority of data (Ewing sarcoma gene expression value). The author has to better compare with ASPS-1 individually for each cell line type.
#2 In Figure 1A, cell lines from the same tumor are grouped into separate clusters. For example, fibrosarcoma and osteosarcoma cell lines are classified into various clusters. The author should check the bootstrap value to confirm the reliability of the branches of the phylogenetic tree. The author may also attempt nonhierarchical clustering, such as PCA.
#3 In Figure 3, the letters are too small and the graph is complicated. The unit of the vertical axis of the graph is not listed.
This study investigated the many genes expression levels in ASPS compared to other sarcoma cells, normal tissues etc. They showed ASPS transcriptome resembles that of mesenchymal stromal progenitor. Therefore, their study based on the data from gene expressions, I thought that it had a certain level of reliability.
Experimental design had no problem. I thought they should do the experiments such as RNAi for comparison between the gene expressions of ASPL-TFE3 knockdown and not. But they commented about the point in the Conclusions. ASPS sarcoma cells have chromosomal translocation of ASPL-TFE3, so, in the cells, various changes could be occurred. So, it is very interesting that they investigate the changes of gene expressions based of RNAi experiments (ASPL-TFE3 knockdown).
Their findings had a certain level of reliability.
There are several points that need minor changes as followings;
・In line 53, ASPSCR should be changed to ASPSCR1.
・In line 309, ASPL-TFE should be change to ASPL-TFE3.
・Author should use the unified abbreviation such as MSC in line293-302.
・In Figure2, Table1, 2, author should correct the spelling of “fifty”.
I thought this study is acceptable for this journal. ASPS sarcoma cells have chromosomal translocation of ASPL-TFE3, so, in the cells, various changes could be occurred. So, it is very interesting that they investigate the changes of gene expressions based of RNAi experiments (ASPL-TFE3 knockdown).
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