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Cannot Access the 5' Data sets from the 10x website for Comparison

Posted By: MatheW, on Jan 10, 2019 at 2:44 AM

Hello,

 

I have been looking through the forums in order to determine which kit to use for my Trasncriptome analysis, I realize that 3' and 5' kit capture different information from the transcripts, I was wondering if there are any comparitive data sets available to look at.

 

I have also gone through one of the previous topics which posed a similar question, but in that post I can only access the 3' data but not the 5' data.

 

https://community.10xgenomics.com/t5/Single-Cell-Forum/use-of-5-kit-for-transcriptome-analysis/m-p/6...

 

When I click on the 5' data I get a 500 error.

 

https://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/vdj_v1_pbmc_5gex 

 

I was wondering if you could please help me out in this regard. Are there any 5' data sets we can access or are there any compartivie data sets available.

 

 

3 Replies

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Re: Cannot Access the 5' Data sets from the 10x website for Comparison

Posted By: agottscho, on Jan 11, 2019 at 10:11 AM

Hi MatheW,

 

This is Andrew with 10x support. As Laura DeMare noted in the thread you linked to, we don't have a direct comparison between 3' and 5' gene expression data currently available, although we do have 3' and 5' gene expression datasets for PBMCs available on the 10x website that you may be interested in exploring. However we have updated the datasets with versions run through the latest versions of Cell Ranger, which is why the 5' link you referred to is broken.

 

Please see this page for a current list of 5' GEX and V(D)J datasets:

https://support.10xgenomics.com/single-cell-vdj/datasets 

 

Here is a 5' GEX dataset from PBMCs: https://support.10xgenomics.com/single-cell-vdj/datasets/2.2.0/vdj_v1_hs_pbmc_5gex 

 

And our 3' datasets are here:

https://support.10xgenomics.com/single-cell-gene-expression/datasets

 

Hope this helps, if you have any follow up questions please open a ticket with support@10xgenomics.com. Thanks!

 

Best, Andrew

 

 

 

Re: Cannot Access the 5' Data sets from the 10x website for Comparison

Posted By: MatheW, on Jan 14, 2019 at 7:10 AM

Thank you very much Andrew for your reply, but sadly I still cannot access the 5' data set page:

https://support.10xgenomics.com/single-cell-vdj/datasets/2.2.0/vdj_v1_hs_pbmc_5gex , I'am still getting Error 500 Cannot Display this page.

 

and

 

this just says coming soon

https://support.10xgenomics.com/single-cell-vdj/datasets 

 

Please help me out.

 

Thanking you

Mathew

Re: Cannot Access the 5' Data sets from the 10x website for Comparison

Posted By: agottscho, on Jan 14, 2019 at 10:22 AM

Hi Mathew,

 

Sorry about that, something strange is happening with those links in this community forum. If I copy and paste the link directly into my browser it works. Can you please try that?

 

Best, Andrew

Solution

Re: Cannot Access the 5' Data sets from the 10x website for Comparison

Posted By: MatheW, on Jan 16, 2019 at 1:06 AM

Thank you very much Andrew it has worked.