Answers.Body: <p><strong>Answer:</strong>
  There are no methods that exist for investigating transcript data inside a cell without destroying the cell. Separating RNA from cells requires essentially destroying the cells and using a <a href="https://en.wikipedia.org/wiki/Trizol" rel="nofollow noreferrer">chemical cocktail</a> to split its constituent components.</p>
  
  <p><strong>Alternative 1:</strong> One option is to investigate extracellular transcripts of living cells is to centrifuge cells in culture and isolating RNA from the growth media supernatant <a href="https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471143030.cb0322s30%4010.1002/%28ISSN%291934-2616.SubcellularFractionationandIsolationofOrganelles" rel="nofollow noreferrer">[1]</a>. Cell-free DNA and cell-free RNA are hot topics in contemporary biology and bioinformatics as a potential source for disease biomarkers. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5133845/" rel="nofollow noreferrer">[2]</a></p>
  
  <p><strong>Alternative 2:</strong> Another option to monitor a transcript from a living cell is to use a transgenic construct with a reporter molecule like <a href="https://en.wikipedia.org/wiki/Luciferase" rel="nofollow noreferrer">luciferase</a> or a <a href="https://en.wikipedia.org/wiki/Green_fluorescent_protein" rel="nofollow noreferrer">fluorescent protein</a> to produce light or become fluorescent when a promotor is activated [<a href="https://pubs.rsc.org/en/content/articlelanding/2016/cs/c6cs00296j/unauth#!divAbstract" rel="nofollow noreferrer">3</a>, <a href="https://www.sciencedirect.com/science/article/pii/S0958166907000043" rel="nofollow noreferrer">4</a>]. This does not directly measure transcript quantity but answers a similar question: how does transcription change in a living cell?</p>
  
  <p>Sources:</p>
  
  <p><a href="https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471143030.cb0322s30%4010.1002/%28ISSN%291934-2616.SubcellularFractionationandIsolationofOrganelles" rel="nofollow noreferrer">[1] Théry, C., Amigorena, S., Raposo, G., &amp; Clayton, A. (2006). Isolation and characterization of exosomes from cell culture supernatants and biological fluids. Current protocols in cell biology, 30(1), 3-22.</a></p>
  
  <p><a href="https://www.mdpi.com/1422-0067/17/11/1845" rel="nofollow noreferrer">[2] Yu, X. M., Wu, Y. C., Liu, X., Huang, X. C., Hou, X. X., Wang, J. L., ... &amp; Ling, Z. Q. (2016). Cell-Free RNA content in peripheral blood as potential biomarkers for detecting circulating tumor cells in non-small cell lung carcinoma. International journal of molecular sciences, 17(11), 1845.</a></p>
  
  <p><a href="https://pubs.rsc.org/en/content/articlelanding/2016/cs/c6cs00296j/unauth#!divAbstract" rel="nofollow noreferrer">[3] Kaskova, Z. M., Tsarkova, A. S., &amp; Yampolsky, I. V. (2016). 1001 lights: luciferins, luciferases, their mechanisms of action and applications in chemical analysis, biology and medicine. Chemical Society Reviews, 45(21), 6048-6077.</a></p>
  
  <p><a href="https://www.sciencedirect.com/science/article/pii/S0958166907000043" rel="nofollow noreferrer">[4] Rao, J., Dragulescu-Andrasi, A., &amp; Yao, H. (2007). Fluorescence imaging in vivo: recent advances. Current opinion in biotechnology, 18(1), 17-25.</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-05T03:30:22.010Z
Answers.LastActivityDate: 2018-12-05T04:24:08.397Z
Answers.LastEditDate: 2018-12-05T04:24:08.397Z
Answers.UserDisplayName: conchoecia
Body: <p>Do any methods exist (or are in the process of development) for investigating transcript data without lysing the cells, i.e, destroying the sample?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-05T08:06:02.700Z
Comments.Text: You may find this review useful: https://www.cell.com/molecular-cell/pdf/S1097-2765(18)30591-4.pdf
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-05T13:46:29.853Z
Comments.Text: I'm not sure this question is about bioinformatics, because there isn't any method that is able to produce the data the way you ask. Or if it would exists it doesn't ask about any tool or method analysing/processing it
Comments.UserDisplayName: llrs
Tags: <rna-seq><transcriptome><rna>
Title: Real time transcript profiles
ThreadText: # Real time transcript profiles
  
  (Asked by: username_0 on 2018-12-05)
  
  Do any methods exist (or are in the process of development) for investigating transcript data without lysing the cells, i.e, destroying the sample?
  
  **Tags:** rna-seq, transcriptome, rna
  
  > **Comments:**
  > **username_1**: You may find this review useful: https://www.cell.com/molecular-cell/pdf/S1097-2765(18)30591-4.pdf  
  > **username_2**: I'm not sure this question is about bioinformatics, because there isn't any method that is able to produce the data the way you ask. Or if it would exists it doesn't ask about any tool or method analysing/processing it  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2018-12-05. Score: 3
  
  **Answer:**
  There are no methods that exist for investigating transcript data inside a cell without destroying the cell. Separating RNA from cells requires essentially destroying the cells and using a [chemical cocktail](https://en.wikipedia.org/wiki/Trizol) to split its constituent components.
  
  **Alternative 1:** One option is to investigate extracellular transcripts of living cells is to centrifuge cells in culture and isolating RNA from the growth media supernatant [[1]](https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471143030.cb0322s30%4010.1002/%28ISSN%291934-2616.SubcellularFractionationandIsolationofOrganelles). Cell-free DNA and cell-free RNA are hot topics in contemporary biology and bioinformatics as a potential source for disease biomarkers. [[2]](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5133845/)
  
  **Alternative 2:** Another option to monitor a transcript from a living cell is to use a transgenic construct with a reporter molecule like [luciferase](https://en.wikipedia.org/wiki/Luciferase) or a [fluorescent protein](https://en.wikipedia.org/wiki/Green_fluorescent_protein) to produce light or become fluorescent when a promotor is activated [[3](https://pubs.rsc.org/en/content/articlelanding/2016/cs/c6cs00296j/unauth#!divAbstract), [4](https://www.sciencedirect.com/science/article/pii/S0958166907000043)]. This does not directly measure transcript quantity but answers a similar question: how does transcription change in a living cell?
  
  Sources:
  
  [[1] Théry, C., Amigorena, S., Raposo, G., & Clayton, A. (2006). Isolation and characterization of exosomes from cell culture supernatants and biological fluids. Current protocols in cell biology, 30(1), 3-22.](https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471143030.cb0322s30%4010.1002/%28ISSN%291934-2616.SubcellularFractionationandIsolationofOrganelles)
  
  [[2] Yu, X. M., Wu, Y. C., Liu, X., Huang, X. C., Hou, X. X., Wang, J. L., ... & Ling, Z. Q. (2016). Cell-Free RNA content in peripheral blood as potential biomarkers for detecting circulating tumor cells in non-small cell lung carcinoma. International journal of molecular sciences, 17(11), 1845.](https://www.mdpi.com/1422-0067/17/11/1845)
  
  [[3] Kaskova, Z. M., Tsarkova, A. S., & Yampolsky, I. V. (2016). 1001 lights: luciferins, luciferases, their mechanisms of action and applications in chemical analysis, biology and medicine. Chemical Society Reviews, 45(21), 6048-6077.](https://pubs.rsc.org/en/content/articlelanding/2016/cs/c6cs00296j/unauth#!divAbstract)
  
  [[4] Rao, J., Dragulescu-Andrasi, A., & Yao, H. (2007). Fluorescence imaging in vivo: recent advances. Current opinion in biotechnology, 18(1), 17-25.](https://www.sciencedirect.com/science/article/pii/S0958166907000043)
  
  
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