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cameliaquek / singlecell_spatial_multiomics

Data integration across different modalities
GNU General Public License v3.0
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Data integration output #2

Open cameliaquek opened 2 years ago

cameliaquek commented 2 years ago

Hi Aditya @adyprat

Thanks very much for sending the CSV files. I am wondering if it will be feasible to edit the script and integrate only scRNAseq and CODEX only? We want to map those UMAP clusters generated from scRNAseq data to spatial. The CITEseq markers seem not to resolve the issue and missed important phenotypes such as gamma delta T cells, fibroblast, Tregs etc.

Please see below Figure 2 for MIA11 patient (CODEX ID: P1 (MIA11 PRE), P2 (MIA11 PROG) and P3 (MIA11 EDT)). We require the last figure 2H from your side to show some or each of the phenotypes as detailed in Figure 2A UMAP at a spatial level. One of the hypothesis we are testing is that the peritumoural Tregs (outside the tumour) expressing TGF-beta is influencing the growth of fibroblast and thus prevent activated Tem cells from entering. You can see from Figure 2B, using scRNAseq data, the proportion of Fibroblast is high and as well as Tregs at the first timepoint. This tumour seems to have potential T cell activity but somehow not responding to the drug.

I am not sure if I have missed your ShinyApp as your initial layout of your ShinyApp is very useful for us to put into Figure 2H.

In addition, the CODEX ID on the first column is really useful. We also require the Cell ID from the single-cell data so that we can grab those cells and delve into the mechanism and gene expression profiles.

I look forward to your next reply. Thanks so much.

Cheers Cam

SingleCellRNA-CODEX_figs_v1_fig2

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adyprat commented 2 years ago

Can we both meet sometime briefly this week regarding this? Does 9am your time tomorrow work(Wed morning Sydney time) ? image

cameliaquek commented 2 years ago

I can do or 4.30 am - 5.30 am or 5-6am tomorrow. Does that suits your schedule ?

Thank you.

Regards, Cam

On 15 Feb 2022, at 14:41, adyprat @.***> wrote:  Can we both meet sometime briefly this week regarding this? Does 9am your time tomorrow work(Wed morning Sydney time) ?

— Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you authored the thread.

cameliaquek commented 2 years ago

Hi Aditya

I can do 5am today which is 6pm at your side. Let me know if this work for you.

Regards, Cam

On 15 Feb 2022, at 16:39, Camelia Quek @.***> wrote:  I can do or 4.30 am - 5.30 am or 5-6am tomorrow. Does that suits your schedule ?

Thank you.

Regards, Cam

On 15 Feb 2022, at 14:41, adyprat @.***> wrote:  Can we both meet sometime briefly this week regarding this? Does 9am your time tomorrow work(Wed morning Sydney time) ?

— Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you authored the thread.

adyprat commented 2 years ago

Hey; I'm on EST, not sure why that screen-cap had London time, haha.