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use of 5' kit for transcriptome analysis

Posted By: NG, on Dec 18, 2017 at 2:47 AM

 

Hello,

 

Is the performance of the 5' kit equivalent to the 3' kit for transcriptome analysis?

In particular, are transcripts captured as efficiently by the added cytosines as with their polyA tail?

It would be nice to be able to do 5' tag counting with the Chromium as well, but only with the data is as good.

Thanks

 

 

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Re: use of 5' kit for transcriptome analysis

Posted By: laura, on Dec 19, 2017 at 4:57 PM

The 5' and 3' gene expression kits capture different information from the transcript, although both amplify full-length cDNA using a polyd(T) and switch oligo primers. In the Single Cell 3' assay, the polyd(T) oligo sequence is on the gel bead and the switch oligo is provided in the master mix, while in the Single Cell 5' gene expression assay, the switch oligo is on the gel bead and the polyd(T) is provided in the master mix.

 

The 3' and 5' assays provide comparable sensitivity in terms of genes and UMIs captured per cell. We don't have a direct comparison between 3' and 5' gene expression data currently available, although we have 3' and 5' gene expression datasets for PBMCs available on the 10x website that you may be interested in exploring:

https://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/pbmc8k

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

 

The Single Cell 3' solution is recommended for general gene expression applications, as 3' is the gold standard and the better understood approach in the scientific community.

 

Re: use of 5' kit for transcriptome analysis

Posted By: hirokomatsui, on Mar 11, 2019 at 10:22 AM

I'm interested in to see the difference between 3' and 5' assays. The one of the links to the data is expired:

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

 

Do you have any suggestion about the data?

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Re: use of 5' kit for transcriptome analysis

Posted By: shauna-10x, on Mar 12, 2019 at 8:22 AM

Hi,

 

Apologies for the expired link.  You can explore all of our 5' gene expression datasets here: https://support.10xgenomics.com/single-cell-vdj/datasets

 

Please let us know if you have any additional questions.

 

Best,

Shauna

Re: use of 5' kit for transcriptome analysis

Posted By: mswift, on Oct 25, 2019 at 10:19 AM

Hi, 

 

I'm curious if a direct comparison has been made yet? By that I mean processing the same sample in parallel using both 5' chemistry and 3' chemistry

 

Thanks, 

 

Michael