Supplementary Table Export

[lahuuki]

order may change depending on cross ref

• [x] Table S1. Demographics of donors included in the study. (stabl_demo)
• [x] Table S2. Summary of DEGs for ANOVA model at broad and fine resolution. (stabl_deg_anova)
• [x] Table S3. Summary of DEGs for enrichment model at broad and fine resolution. (stabl_deg_enrich)
• [x] Table S4. Summary of DEGs for pairwise model at broad and fine resolution. (stabl_deg_pair)
• [x] Table S5. Summary of DEGs across Ant, Mid, Post positions for gray matter. (stabl_deg_postion)
• [x] Table S9. LR pairs from LIANA @boyiguo1 (stable_liana)
• [x] Table S10. Summary of ligand-receptor pairs associated with SCZ genetic risk association. Melissa (stable_lr_scz)

[lahuuki]

• [ ] Table S7. snRNA-seq annotation (stabl_sn_anno)
• [ ] Table S8. snRNA-seq Marker gene stats @Nick-Eagles (stabl_sn_marker)

[Nick-Eagles]

Some updates from my end:

• It looks like we already have Table S1, with columns Brain Num, DateDxt'd, Race, Sex, Age, RIN, PMI, and PrimaryDx. Do we want any more info?
• For the marker gene stats, do we want broad and layer-level results in the same table? Should we just provide the top 25 markers per cell type? Otherwise, I have this table nearly prepared

[lahuuki]

I marked Table S1 done. I would say both since they were used for deconvolution

[boyiguo1]

Is there any space to add another supplementary table? Kristen has suggested adding some LR pairs identified from LIANA. Is that cool?

[Nick-Eagles]

I added the marker stats supplementary table in stabl_marker_stats in the OneDrive. @lahuuki could you handle the column descriptions (in the excel sheet on OneDrive)? I wasn't sure about the meaning of everything output from get_mean_ratio2, though I started with the columns I felt I could handle.

[boyiguo1]

FYI, I created another folder for Melissa's Table S10 (moving from stabl_demo to stabl_lr_scz on OneDrive)

[lcolladotor]

@lahuuki @Nick-Eagles I'm done with my tables (Tables S1 through S5). Dunno if you are done with yours. If you are, we can close this issue then.

[lcolladotor]

@boyiguo1 can you help clarify why there's another Table S10 in the stabl_demo directory on OneDrive? Thanks! Just trying to avoid any confusion. Maybe your OneDrive changes haven't been synched yet?

[boyiguo1]

@lcolladotor I believe Melissa originally put the file Table S10 in stabl_demo. I moved that to a new folder stabl_lr_scz (matched with cross-ref), which didn't sync to the cloud. But now it should be good.

[lcolladotor]

Thanks Boyi!

I wanted to make sure we had the right file =)