Condition column in the meta.data

[pallavisurana1]

Hi , I am a little unclear as to what 'nan' means in the Condition column of meta.data in the integrated HLCA dataset. Cells set to "nan" come from donors without lung condition. Does this mean they are not healthy or healthy?

If I want only the healthy cells I could ignore the "nan" or unknowns right?

[LisaSikkema]

Hi @PallaviSurana1,

Are you looking at the HLCA core or the extended HLCA? This is a column we forgot to clean up but that will be corrected in the updated/cleaned up HLCA which should be online soon!

[pallavisurana1]

Hi @LisaSikkema

I am looking at the extended HLCA. So should I consider only healthy if I want healthy lung tissues and remove "nan" right?

[LisaSikkema]

To be sure, yes. I think they might all be healthy but not sure.

[LisaSikkema]

If you tell me which datasets they come from I can tell you if they're healthy or not :)

[pallavisurana1]

This is for the condition = "nan" I am interested in

study	Number of cells
Banovich_Kropski_2020	96516
Barbry_Leroy_2020	23988
Jain_Misharin_2021	0
Krasnow_2020	0
Lafyatis_Rojas_2019	10708
Meyer_2019	21602
Misharin_2021	27414
Misharin_Budinger_2018	26912
Nawijn_2021	0
Seibold_2020	28364
Teichmann_Meyer_2019	11667

[LisaSikkema]

So in Supplementary Table 1 from the bioRxiv you can see which datasets contained which kind of lung conditions https://www.biorxiv.org/content/10.1101/2022.03.10.483747v1.supplementary-material

Banovich_Kropski and Misharin_Budinger contain both healthy and disease (the disease samples might be correctly annotated, you can check). The others are healthy (in the case of Krasnow from tumor-adjacent "healthy" tissue)

[pallavisurana1]

Thanks. I will remove those studies and analyze them.