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zhangzlab / covid_balf

R script for the covid balf data analysis

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10x chemistry of samples

mxposed opened this issue · comments

commented

Hello,

Could you please confirm which chemistry was used for which samples in the study?

In the methods you say

Single-cell capturing and downstream library constructions were performed using Chromium Single Cell 3g Reagent kits v.2 (10x Genomics; PN-120237, PN-120236 and PN-120262) for HC1 and HC2, kit v.3 (10x Genomics; PN-1000075, PN-1000073 and PN-120262) for HC3 and Chromium Single Cell V(D)J Reagent kits (10x Genomics; PN-1000006, PN-1000014, PN-1000020, PN-1000005) for all patients with COVID-19

which I interpret like this:
2 healthy control samples were prepared with 10x 3' V2
1 healthy control sample was prepared with 10x 3' V3
all COVID-19 samples were prepare with 10x 5'

However, on GEO this information is lacking, and all samples are reported as 10x 5': https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4475048

I would be very grateful for clarification and maybe updated materials! Thank you

commented

You are right. The description in GEO is not accurate, and please follow the information provided in the original paper. Will revise the description in GEO later, thanks!

commented

Thank you for the quick reply!