The following is in response to a query from Dr. Lucy Cherbas on the identity of the cultured cell line used in Böttcher et al., NAR   42:203 , e89. and Esslinger et al., RNA Biol.  10:1042 .
Unfortunately, I cannot say much about the detailed origin of our lab-stock of S2-cells. They were handed to me by a colleague while I was a Post-Doc in Phil Zamore's lab. At the Time, Gyorgy Hutvagener (a fellow Post-Doc) had them in culture and I really don't know exactly where he got them from. Thus, I cannot help much with this.
When I started my own lab here in Munich in 2006, I wanted to get a defined source of S2-cells to work with. We tried the ones that are sold by Invitrogen, but found out that they are rather refractory to RNAi by dsRNA soaking (see our publication Shah et al., BBA 2008 http://www.ncbi.nlm.nih.gov/pubmed/18634912). Furthermore, around that time the word spread that many of the S2-stocks are persistently infected with viruses (e.g. FHV); ours was not, so we decided to stick with it. 
To have a defined starting point, we subjected these cells to two rounds of cloning and the internal code-name for our starting cells is "S2-B2" (referring to the final clone B2). Thus, you could change the isolate name from "unspecified" to "S2-B2", but I don't think that this will make much of a difference for the other users. A gene expression profile for our cells was published in this paper:
http://www.ncbi.nlm.nih.gov/pubmed/23669073 (but this is still with Affymetrix-arrays so probably difficult to use with the current RNA-seq data)
The good news is that method from the paper you have mentioned in your email really does not depend on any particular cell line. Transient transfection of a cas9 expression plasmid is almost as efficient as using the stable cas9 cell line, and I think for those who want to use a defined and comparable background that is the way to go.