Bladder terms

[olgabot]

Hello! We performed single-cell RNA-seq on ~100k cells and annotated them with the Cell Ontology as part of the Tabula Muris project (paper: https://www.biorxiv.org/content/early/2018/03/29/237446). With the help of @akershner and @bkiss, there were some terms we felt could be added to more clearly describe the cells of the bladder (https://github.com/czbiohub/tabula-muris/issues/183). Here they are below, including references. Please let me know if we can provide anything else! Warmest, Olga

Bladder mesenchymal cell is_a bladder cell

• Lilly MA, Kulkulka NA, Firmiss PR, Ross MJ, Flum AS, Santos GBD, et al. (2015) The Murine Bladder Supports a Population of Stromal Sca-1+/CD34+/lin- Mesenchymal Stem Cells. PLoS ONE 10(11): e0141437.

Basal bladder epithelial cell is_a bladder urothelial cell

• Hedgehog/Wnt feedback supports regenerative proliferation of epithelial stem cells in bladder Kunyoo Shin, John Lee, Nini Guo, James Kim, Agnes Lim, Lishu Qu, Indira U. Mysorekar & Philip A. Beachy Nature volume 472, pages 110–114 (07 April 2011)
• KRT14 marks a subpopulation of bladder basal cells with pivotal role in regeneration and tumorigenesis. Papafotiou G, Paraskevopoulou V, Vasilaki E, Kanaki Z, Paschalidis N, Klinakis A. Nat Commun. 2016 Jun 20;7:11914
• Retinoid signaling in progenitors controls specification and regeneration of the urothelium. Gandhi D, Molotkov A, Batourina E, Schneider K, Dan H, Reiley M, Laufer E, Metzger D, Liang F, Liao Y, Sun TT, Aronow B, Rosen R, Mauney J, Adam R, Rosselot C, Van Batavia J, McMahon A, McMahon J, Guo JJ, Mendelsohn C.

Luminal bladder epithelial cellis_a bladder urothelial cell

• Retinoid signaling in progenitors controls specification and regeneration of the urothelium. Gandhi D, Molotkov A, Batourina E, Schneider K, Dan H, Reiley M, Laufer E, Metzger D, Liang F, Liao Y, Sun TT, Aronow B, Rosen R, Mauney J, Adam R, Rosselot C, Van Batavia J, McMahon A, McMahon J, Guo JJ, Mendelsohn C.

[olgabot]

Hello! Checking in here. Is there anything else we need to provide to add this ontology?

[akershner]

Hi Olga,

I am happy to help, but I a little confused as to what you are asking. Could you be a bit more specific?

Thanks, Aaron

On Fri, Oct 26, 2018 at 9:59 AM Olga Botvinnik notifications@github.com wrote:

Hello! Checking in here. Is there anything else we need to provide to add this ontology?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/obophenotype/cell-ontology/issues/522#issuecomment-433475618, or mute the thread https://github.com/notifications/unsubscribe-auth/AimFTUSDuH9NHHKuhRzNglbxG4CFUy0wks5uoz93gaJpZM4Wyoe4 .

[dosumis]

Adding 'bladder mesenchymal cell'

Is it correct to make this part of the submucosa of urinary bladder or of the lamina propria of urinary bladder ?

Or could it be either, in which case I could just define as 'mesenchymal cell' that 'part of' some 'wall of urinary bladder' (?)

(see https://github.com/obophenotype/uberon/issues/1482)

[paolaroncaglia]

@dosumis tagging you due to your previous comment. I can't see those bladder cell terms in CL. Let me know if they're still needed, happy to help.