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lhqing / mouse_brain_2020

Jupyter notebook repository for reproducing analysis in "DNA Methylation Landscape of the Mouse Brain at Single-Cell Resolution"
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Match between cell IDs #1

Open marvinquiet opened 2 years ago

marvinquiet commented 2 years ago

Thank you for your great work!

I am trying to follow your work to deal with the ALLC files and take the .mcds file as ground truth to guide through my analysis. However, I met the problem with matching cell IDs listed in the .mcds files and the ALLC files uploaded to the GEO.

For example, in the mcds file, the cell is named 3C_M_1015 which I can find the metadata in Supplementary Table 5. However, in ALLC files, one of the names became GSM3767528_allc_171213_CEMBA_mm_P56_P63_3C_MOp_CEMBA171206_3C_1_CEMBA171206_3C_3_A1_AD012_indexed.tsv. I thus wonder if there are any mappings between these two?

Thank you in advance and I look forward to your reply!

Sincerely, Wenjing

johnmoll commented 2 weeks ago

Hi, congrats for your great resource.

Same issue as @marvinquiet here. Is there a mapping from GEO's ALLC filenames to the paper's supplementary material (and mcds files) cell naming? Or cell metadata using GEO's ALLC filenames?