What is each sample?

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3.7 years ago

pomodoro_sinensis ▴ 110

Hello,

I am trying to wrap my head around this GSE entry:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE124395

This is a scRNA-seq study, using the technology m-CelSeq 2. As far as I understand, in this technology you sort cells into 384-well plates and then you sequence each cell in each well. Following this logic, each GSM entry should be the results of a single cell. However, there are only 319 GSMs, and the paper states that they sequenced 10,000 cells. What is, then, each sample in this dataset?

Thanks!!

scRNA-seq • 719 views

ADD COMMENT • link 3.7 years ago by pomodoro_sinensis ▴ 110

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Have you written the author to ask? His email address is listed on the record entry. There are also some data structures there in the submission, a matrix of cells and counts, an R Data structure, and a "Supplemetary file contains cellds and one of the 192 unique cellbarcode associated with the cellid." Have you tried sifting through any of these? Some of those GSMs could be mixtures of cells (some of the IDs resemble different plate IDs).

ADD REPLY • link 3.7 years ago by seidel 11k

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