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theislab / singlecell_proteomics

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Consultation on data issues #6

Open YuzhiSun opened 5 months ago

YuzhiSun commented 5 months ago

Dear Sabrina, @SabrinaRichter Thanks for your research and your contribution to the single-cell proteomic data. I am very interested in the data mentioned in your article. I am a PhD student and I would like to simply obtain the mass spectrometry-measured single-cell proteomic data mentioned in your article for my research. I am not particularly interested in comparing with other methods, so I just want to obtain the data that you have measured, which can be directly used for downstream analysis of single-cell proteomics, such as data in matrix format: cell-protein matrix.

SabrinaRichter commented 5 months ago

Hi @YuzhiSun,

you can find the data here https://www.ebi.ac.uk/pride/archive/projects/PXD024043 in DIANN1.8_SingleCells_CellCycle.7z. The file 20210919_DIANN_SingleCellOutput.pg_matrix_cellcyclepred.tsv should be the one you want to work with.

YuzhiSun commented 5 months ago

Hi @SabrinaRichter , Thank you very much for your guidance. I have another question: are the row indices in this file protein IDs or gene IDs? It seems to me that they are gene IDs. Do I need to manually map them to proteins or how should I proceed?