MasahiroNakano-hub
commented
1 year ago Thanks for contacting me.
the "clinical_diagnosis_age_sex_annotation.txt" file does not seem to have information on which SLE cases are active or inactive
You are right. We have not made disease activity information publicly available in NBDC. For further details, please contact the lead contact in the current paper (doi: 10.1016/j.cell.2022.07.021).
as "Phase" is always set to "2", even for controls
Our annotation file in NBDC (ID: JGAS000486) was prepared so that it has the same columns with the annotation file in our flagship paper (ID: E-GEAD-397), which included Phase 1 and 2 samples. Regarding the detail of the "Phase", please refer to the flagship paper (doi: 10.1016/j.cell.2021.03.056). Since the current SLE manuscript included only Phase 2 samples, this "Phase" column in the annotation file is correct.
We also cannot find the files you seem to use in your codes, such as "211109_COI_SLEinc_andHC_27subsets_cond.txt".
This file is the metadata which includes celltype, case/control, age and sex information. You can utilize "clinical_diagnosis_age_sex_annotation.txt" file in NBDC instead.
mpluz
Hello, Very interesting paper! My group has been able to obtain access to your gene expression data from NBDC (ID: JGAS000486). Unfortunately, the "clinical_diagnosis_age_sex_annotation.txt" file does not seem to have information on which SLE cases are active or inactive, as "Phase" is always set to "2", even for controls. We also cannot find the files you seem to use in your codes, such as "211109_COI_SLEinc_andHC_27subsets_cond.txt". If it's a case of us having somehow misunderstood information on one of the files, I am very sorry and would really appreciate it if you could explain what we are missing. If not and indeed the information wasn't shared, is it possible for you to send us the file that distinguishes which SLE cases are active and inactive? You can contact me via e-mail if you prefer, my address is m.luz@campus.fct.unl.pt. Thank you in advance!