Updates are available New version dated 2016-03-09

Current Referee Status

Referee status: Indexed

Article Reports

Referee Report: https://doi.org/10.5256/f1000research.8245.r12053, Gary Loughran, School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland, 02 Feb 2016, version 1, indexed

Referee Comment: <b>Catr&iacute;ona Dowling</b>; <i>Posted: 05 Feb 2016</i>; We thank the reviewer for the suggestion.The sequences of the primers and probes we used in our assays are pre-designed and are the proprietary of Life Technologies who are unable to release this information to us. However, as stated within the MIQE guidelines, it is acceptable to use the unique assay ID for each TaqMan assay in place of the primer and probe sequences. We are grateful to the reviewer for the suggestion to include such information and we will include a table which displays assay ID, exon boundary and amplicon size for all reference genes.The agarose gels that we ran were non-denaturing gels. We will add this in to the text and to avoid any confusion.

Referee Report: https://doi.org/10.5256/f1000research.8245.r12476, Verónica Ayllón Cases, Gene Regulation, Stem Cells and Development Group, Department of Genomic Oncology, Centre for Genomics and Oncological Research (Genyo), Pfizer-University of Granada-Regional Government of Andalusia, Granada, Spain, 24 Feb 2016, version 1, indexed

Referee Comment: <b>Catr&iacute;ona Dowling</b>; <i>Posted: 01 Mar 2016</i>; We thank the reviewer for the suggestions. We have adjusted the manuscript accordingly and we agree that it is better presented now.The values given on the datasets corresponds to three independent experiments i.e three biological replicates. We have now written a note within each dataset to clear any ambiguity.We are grateful to the reviewer for making the observation on Figure 2C. We have now updated the figure and removed the area between 1 and -1. We have also changed the layout in our graphs to ensure the gene names don’t overlap with the bars.We agree with the reviewer, using a Bioanalyzer is the preferable method for looking at RNA integrity and purity. Unfortunately, it is not possible for us to complement our data with a Bioanalyzer analysis as we don’t have access to this piece of equipment. We used non-denaturing agarose gels and a nanospectrometer for our work.&nbsp; There are many Universities that do not have access to a Bioanalyzer and for this reason we wanted to offer this alternative approach to encourage all researchers to carry out integrity and purity tests in the absence of such equipment.

Referee Comment: <b>Catr&iacute;ona Dowling</b>; <i>Posted: 05 Mar 2016</i>; We thank the reviewer for the suggestions. We have adjusted the manuscript accordingly and we agree that it is better presented now.The values given on the datasets corresponds to three independent experiments i.e three biological replicates. We have now written a note within each dataset to clear any ambiguity.We are grateful to the reviewer for making the observation on Figure 2C. We have now updated the figure and removed the area between 1 and -1. We have also changed the layout in our graphs to ensure the gene names don’t overlap with the bars.We agree with the reviewer, using a Bioanalyzer is the preferable method for looking at RNA integrity and purity. Unfortunately, it is not possible for us to complement our data with a Bioanalyzer analysis as we don’t have access to this piece of equipment.We used non-denaturing agarose gels and a nanospectrometer for our work. There are many Universities that do not have access to a Bioanalyzer and for this reason we wanted to offer this alternative approach to encourage all researchers to carry out integrity and purity tests in the absence of such equipment.

Grant Information: This work was supported by grants received from the Irish Cancer Society Grant CRS12DOW (to CD), the Mid-Western Cancer Foundation and funding from Science Foundation Ireland grant 13/CDA/2228 (to PK).

Copyright: This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Data associated with the article are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication).