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FredHutch / Galeano-Nino-Bullman-Intratumoral-Microbiota_2022

Analysis code used in Galeano Nino et al., Impact of Intratumoral Microbiota on Spatial and Cellular Heterogeneity in human cancer. 2022
MIT License
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Sample name in `headneck_gex_16s_mix_dedup.csv` #17

Closed tmaruy closed 11 months ago

tmaruy commented 11 months ago

Dear Hanrui, @hanruiw

I am trying to reanalyze INVADEseq data of OSCC samples for my project. I tried to use bacterial UMI count in headneck_gex_16s_mix_dedup.csv but could not understand correspondence between samples and barcodes.

By parsing the barcode names (e.g., sample_9218_T_AAAGTAGGTACCGGCT-1), I found the following seven prefixes. I suppose these prefixes represent seven donors in the paper (from OSCC_11 to OSCC_17) but could not find correspondence.

prefix | number of barcodes   -- | -- sample_9218_T | 267 sample_9236_T | 1215   sample_9237_T | 1051 sample_9347 | 163 sample_9398 | 2688 sample_BM319435 | 307 sample_BM320030 | 4976

Could you give us the information? Or could you upload Seurat object you used in your manuscript? It would be super helpful to reuse your data.

Thank you so much, tmaruy

hanruiw commented 11 months ago

Dear tmaruy,

Thank you very much for your interest in our paper titled "Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer". For questions regarding sample IDs, could you please contact Dr. Jorge Luis Galeano Niño at jgaleano[at]fredhutch.org? Please feel free to reopen this issue if you have any other questions!

Thank you, Hanrui

tmaruy commented 10 months ago

Could you share the Seurat object?

hanruiw commented 10 months ago

Hi, the expression matrix is not uploaded, so the best way to obtain the Seurat object is to process the raw fastq files. Please let me know if you have any questions!

tmaruy commented 10 months ago

Okay. I tried to contact Dr. Galeano Nino two weeks ago but no response. Would it be okay to ask him from your side?

hanruiw commented 8 months ago

Hi Tmaruy, Sorry for delayed response, we updated the bacteria count matrix csv file with OSCC IDs, please let us know if you need anything else! Best regards, Hanrui