Cell type annotations

[xliu38]

Dear authors

I recently came across the publication "Epigenetic regulation during cancer transitions across 11 tumor types" and was impressed by the massive scale analysis you have performed.

I understand that you performed cell type analysis based on curated lists of marker genes and validated with inferCNV. I was wondering, if the result of this (i.e., cell type annotation) was available to download somewhere?

Thanks in advance,
Xueying

[nvterekhanova]

Hello Xueying,

We have cell type annotation for GEO samples (tumor GBM and ccRCC samples) available as a supplementary files here:
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE240822 .

As for all other samples, we are now working on uploading L4 data into HTAN DCC that will also include cell type information. Once available, we will list the links on the main page, stay tuned.

Nadezhda

[xliu38]

Hi Nadezhda,

Thank you for the update. Looking forward to it!

[VKonstantakos]

Hello,

Thanks a lot for this useful resource!
Is there any update regarding the cell type annotations for the remaining samples?

Thank you in advance,
Vasilis

[nvterekhanova]

Hi Vasilis,

The data we submitted will be probably included in the next data release by HTAN DCC. The expected date of the next release is around mid February. We will update the main page with the information as soon as it's released.

Nadezhda

[aurelieGabriel]

Dear authors,
Thank you for making this valuable dataset available.
I noticed that there was indeed a release on February 9th but the release refers to another dataset. I was wondering if you have any updates about the HTAN release related to the WULST dataset?
Thank you in advance for your help.
Best regards,
Aurélie

[nvterekhanova]

Hi Aurelie,

WUSTL datasets were included in the next HTAN release and they are now available via HTAN DCC.

Nadezhda

[aurelieGabriel]

Hi Nadezhda,
This is great news, thank you for the update.
Best wishes,
Aurélie

[xliu38]

Hi Nadezhda,

Thank you for the update and new release of data! I checked on the level 4 data and it seems that some L3 data do not have a matching L4 version, e.g. most of the Pancreatobiliary-type carcinoma datasets. Is this correct, or I'm missing something here?

Xueying

[nvterekhanova]

Hi Xueying,

It looks like most “Pancreatobiliary-type” samples are single cell RNA-seq samples from this other paper: https://www.nature.com/articles/s41588-022-01157-1, and they were not used in this study. To obtain PDAC samples used here, you can filter files by the “Organ” > “Pancreas”, and after this filtering there should be many PDAC L4 files.

Nadezhda

[VKonstantakos]

Hello Nadezhda,

Thank you again for this useful resource and the helpful responses.

I noticed that some Biospecimens have two annotation files (i.e., two filenames can correspond to the same specimen). Is there a reason behind that and are there differences between these files?

An example of such a case can be seen here:

Thanks in advance!

Vasilis

[nvterekhanova]

Hi Vasilis,

This can be because some of the samples were used in more than one project/publication. And in that case, they could have different L4 files, because processing and annotation may have some differences between those projects. The L4 files from the pancan-ATAC publication will have the cancer type id at the beginning of their “Filename”, for example “BRCA_” in the sample filename shown above.

Nadezhda