TCGA slides not available anymore

Hi All,
It seems to me that TCGA whole slides image website has been down for a month. Anyone knows that it’s a permanent removal or it’s just temporary that we still can wait?
Thinking that someone at TCGA may accidentally remove the files.
When I come to the website, it says: “All slide and diagnostic images from the TCGA program are currently unavailable for download”

Hope anyone knows an alternative backup link?

Thanks so much!
Tuyet

Hi Tuyet,

I wonder the same. I contacted with the GDC User Support and they cannot give any date but they said they will be unavailable for several months.
The slides can be seen in The Cancer Digital Slide Archive of Emory University. But there is no download option over there.
I would be glad to learn any other repository.

Best,
Caner

Is it the GDC group at U Chicago? Why can’t they give you any date and reason?

I do not know their location. It was the official GDC Helpdesk. What they said to me is; “all TCGA slides are currently unavailable at this time for download and for viewing in the portal, and likely will be unavailable for several months.”

It is a little bit concerning that when you do attempt a download the error message you receive is:

Request contains a redacted file(s): …, action not allowed

But I suspect that’s down to them using permissions to disable downloads so that you don’t receive an uglier error.

As far as I can tell, most, if not all, of the TCGA radiology and pathology data is alternatively available through the ISB-CGC Google Cloud Storage mirror. Details here:

You can also explore the data via the ISB-CGC web application:

The web application also has a warning **All tissue slide images from the TCGA program are currently unavailable for viewing.** but I haven’t had any issues viewing or exploring the data.

Thanks Chris,

But these images are not accessible on ISB-CGC Google Cloud Storage! When I tried to download some of these images on Google Cloud Storage, they also yield errors:

gsutil cp gs://gdc-tcga-phs000178-open/9c4b1b5c-b5cf-48f6-bf41-047ceb8c883c/TCGA-CR-7365-01A-01-TS1.811bb2b7-66e3-4694-891b-10b436ec300d.svs .
ServiceException: 401 Anonymous caller does not have storage.objects.get access to the Google Cloud Storage object.

The ISB-CGC web application is viewable, but not downloadable…

Thanks for checking, @Tuyet. I had naively assumed that since the URI lookups were there the data was available. There’s a currently closed issue on one of the ISB-CGC GitHub repositories related to this:

The issue doesn’t provide much detail but does say that access was removed by NCI.

The notification went up on the web application 26 days ago: