Question about stateFate_inVitro_clone_matrix.mtx.gz in lineage tracing data

[yutongo]

Hello!

Thank you for the amazing data resources.

I have a question about stateFate_inVitro_clone_matrix.mtx.gz:
It seems like the columns only include cells from day6. Does it mean the matrix only has the clonal membership of day6 cells from day2/4 (not include the clonal membership of day4 cells from day2)?

I am trying to reproduce Fig5.A (Clonal fate probability of cells belonging to the neutrophil/monocyte trajectory). But I notice that the day2 cells belonging to the neutrophil/monocyte trajectory have clones end with other cell types such as Baso.

Did I misunderstand the clonal membership matrix?

Appreciate your help!

[calebweinreb]

stateFate_inVitro_clone_matrix.mtx.gz contains a sparse matrix with 130887 rows and 5864 columns. The columns correspond to clones (which may be contained within one or multiple timepoints). The rows correspond to cells. The cells are in the same order as in the stateFate_inVitro_metadata.txt.gz file and include all the cells from all 3 time points.

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On Mon, Jul 18, 2022 at 2:20 PM yutong ***@***.***> wrote: Hello! Thank you for the amazing data resources. I have a question about stateFate_inVitro_clone_matrix.mtx.gz: It seems like the columns only includes cells from day6. Does it mean the matrix only have the clonal membership of day6 cells from day2/4 (not include the clonal membership of day4 cells from day2)? I am trying to reproduce Fig5.A (Clonal fate probability of cells belonging to the neutrophil/monocyte trajectory). But I notice that the day2 cells belonging to the neutrophil/monocyte trajectory have clones end with other cell types such as Baso. Did I misunderstand the clonal membership matrix? Appreciate your help! — Reply to this email directly, view it on GitHub <#11>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABO45MXQODZZ7RO7GQIC6CLVUWN6JANCNFSM535FGFMA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[yutongo]

Got it.
Thank you for the prompt response!