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HeleneKretzmer / EpigeneticRegulators_MouseGastrulation

Epigenetic regulator function through mouse gastrulation
GNU General Public License v3.0
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GSE122187 cell barcodes / annotations #2

Open miktrinh opened 3 years ago

miktrinh commented 3 years ago

Hello!

Thank you so much for the fascinating work here! I'm interested in looking into the WT scRNA-seq mouse gastrulation data, which I understood is deposited under GSE122187, and the corresponding annotation of the 42 cell states is provided in Supplementary Table 2 in Grosswendt et al. 2020. If this is correct, I have 2 questions:

  1. For the WT E7.5, there are 2 datasets provided in GSE122187. Is the annotation specifically provided for GSE122187_WT_E7.5_1 or GSE122187_WT_E7.5_2?
  2. When matching the annotations to the raw count matrix data, I noticed that not all BC provided in the annotation table can be found in the CellRanger count_matrix (or in the barcodes.tsv file) for corresponding time point. I'm not sure if I just haven't got the correct datasets etc. or if it's supposed to be this way?

Apologies in advance if any of this comes from my ignorance! Thank you so much for your help with this!

skelviper commented 3 years ago

Hello! Same question , is this due to quality control in your experiments?

Thank you for your time~