Some questions about Figure1

[CYGRY]

Dear Dr. J. Regner, Hi! This article has great inspiration for our research. We are very interested in this article! Therefore, currently I am trying to reproduce the content of the article. But I encountered some difficulties in reproducing the chart in Figure 1, mainly due to the annotation of cell types, and it seems that I cannot obtain the RDS file of the reference dataset. At the same time, I am trying to use this tutorial [https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html] to complete the same work as you, but it seems that I cannot achieve the same results. Similarly, in order to obtain Figure 1B&C, which code should I use in sequence? I am eager to receive your reply, thank you very much!

Chunyu

[RegnerM2015]

Hi Chunyu,

Thanks for reaching out.

But I encountered some difficulties in reproducing the chart in Figure 1, mainly due to the annotation of cell types, and it seems that I cannot obtain the RDS file of the reference dataset.

Can you clarify what you mean by the reference dataset? Do you mean the seurat object and ArchR project object used to generate the UMAPs in Figure 1? Or are you referring to the reference scRNA-seq dataset used to annotate cell types in each individual scRNA-seq dataset via SingleR?

At the same time, I am trying to use this tutorial [https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html] to complete the same work as you, but it seems that I cannot achieve the same results.

Depending on your responses to the above, I think there are a number of factors that could affect your ability to exactly reproduce the content of Figure 1. These include differences in computational environment, random seeds, etc.

Similarly, in order to obtain Figure 1B&C, which code should I use in sequence?

The following code was used to generate the UMAP plots in Figure 1B-C: https://github.com/RegnerM2015/scENDO_scOVAR_2020/blob/fb5937d144cae97753db978f2d031c484c6126df/Figure_1/Figure_1.R#L6-L271

[CYGRY]

Dear Dr. J. Regner, Thanks a lot for your reply. The reference dataset I mentioned in my question comes from this part of the article:

I have only seen the definition method of ovarian cancer cells in this article, which is of great reference significance for us. So my question may mainly focus on using singleR to define cell types. Best wishes Chunyu

[RegnerM2015]

Datasets for Patients 1-5 were annotated based on a reference scRNA-seq dataset from the human endometrium (Wang et al., 2020). Datasets for Patients 6-11 were annotated based on a reference scRNA-seq dataset from a human ovarian tumor (sample ID: HTAPP-624-SMP-3212) (Slyper et al., 2020).

The reference scRNA-seq dataset (two files) used to annotate Patients 1-5, can be found here:

https://www.dropbox.com/scl/fi/5tt0qa82elu8ie5j2ismc/GSE111976_ct_endo_10x.rds?rlkey=sqec2z4f7ahjeli4p2q500qac&dl=0

https://www.dropbox.com/scl/fi/y5v2pbkepy2cx9n8aneoi/GSE111976_summary_10x_day_donor_ctype.csv?rlkey=583q1zg6n8hv1rbmyjzuq4u8i&dl=0

The reference scRNA-seq dataset used to annotate Patients 6-11, can be found here:

https://www.dropbox.com/scl/fi/ocgq84ze32mv92j0jncsl/HTAPP_ovarian_reference.rds?rlkey=gy4usa9xqg1g7n1vvis4t2lu1&dl=0

The following code below shows how the HTAPP_ovarian_reference was used to annotate cell types within each individual sample:

https://github.com/RegnerM2015/scENDO_scOVAR_2020/blob/fb5937d144cae97753db978f2d031c484c6126df/scRNA-seq%20Processing%20Scripts/Individual_Samples/Patient8_scRNA-seq.R#L1438-L1475

Does this help answer your question?

[CYGRY]

Dear Dr. J. Regner, Thank you very much for your reply and the provided annotation dataset file, which can completely help me solve the problem! Thank you again for your careful and timely response! Best wishes Chunyu

[RegnerM2015]

Happy to help! I will close the issue now.