text: user1708: In "RNA velocity of single cells", La Manno et al. look at ratios between spliced and unspliced mRNA as a way of estimating the velocity of a cell through transcriptome space.
  In checking for a universal steady-state spliced-unspliced ratio, they write "We found that the steady-state behaviour of most genes across a wide range of cell types was consistent with a single fixed [ratio between spliced and unspliced] (Extended Data Fig. 3a–c). However, 11% of genes showed distinct slopes in different subsets of tissues (Extended Data Fig. 3d, e), suggesting tissue-specific alternative splicing (Extended Data Fig. 3f) or degradation rates." 
  Tissue-specific alternative splicing or degradation rates certainly could account for these patterns, but how do La Manno et al. rule out that some tissues are simply not in a steady state? The figure they cite (screenshotted below) uses data from the Tabula Muris adult mouse cell encyclopedia. In an adult mouse, not all cells would not be expected to be in steady state -- for example, T-cell progenitors from the thymus and epithelial cells in many organs undergo continual replenishment. 
  
  
  
  user77: If cells aren't in a steady state then one wouldn't expect to see the results in (e), where there are two slopes. One would instead expect to see results more like Plekha3 in panel (c), where there's more variability around the the steady state line (or perhaps no steady state line at all).
  
  user1708: In addition to Devon Ryan's data-driven answer, I've found a clue in the text. La Manno et al have not used the full Tabula Muris: the figure legend indicates that they used only terminally differentiated cells. 
  
original_text: 1708: <p>In <a href="https://www.nature.com/articles/s41586-018-0414-6#Fig7" rel="nofollow noreferrer">"RNA velocity of single cells"</a>, La Manno et al. look at ratios between spliced and unspliced mRNA as a way of estimating the velocity of a cell through transcriptome space.</p>
  
  <p>In checking for a universal steady-state spliced-unspliced ratio, they write "We found that the steady-state behaviour of most genes across a wide range of cell types was consistent with a single fixed [ratio between spliced and unspliced] (Extended Data Fig. 3a–c). However, 11% of genes showed distinct slopes in different subsets of tissues (Extended Data Fig. 3d, e), suggesting tissue-specific alternative splicing (Extended Data Fig. 3f) or degradation rates." </p>
  
  <p>Tissue-specific alternative splicing or degradation rates certainly could account for these patterns, but how do La Manno et al. rule out that some tissues are simply not in a steady state? The figure they cite (screenshotted below) uses data from the Tabula Muris adult mouse cell encyclopedia. In an adult mouse, not all cells would not be expected to be in steady state -- for example, T-cell progenitors from the thymus and epithelial cells in many organs undergo continual replenishment. </p>
  
  <p><a href="https://i.stack.imgur.com/HwLew.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/HwLew.jpg" alt="enter image description here"></a>
  <a href="https://i.stack.imgur.com/JCsxu.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/JCsxu.png" alt="enter image description here"></a></p>
   77: <p>If cells aren't in a steady state then one wouldn't expect to see the results in (e), where there are two slopes. One would instead expect to see results more like Plekha3 in panel (c), where there's more variability around the the steady state line (or perhaps no steady state line at all).</p>
   1708: <p>In addition to Devon Ryan's data-driven answer, I've found a clue in the text. La Manno et al have not used the full Tabula Muris: the figure legend indicates that they used only terminally differentiated cells. </p>
  