3' DGE (3'-digital gene expression) for knockdown analysis

Question

[upendrakumar.devisetty]

Hi all,

I wonder if anyone used the 3'DGE (3'-digital gene expression) approach to measure the knockdown of target genes. I ask this because I have read that 3'end is not a good measure of knockdown. As you can see from this figure 3'end is definitely not preferred for measuring knockdown of target genes

Please let me know your experience using 3' DGE for knockdown or as a general approach for performing differentially gene expression and other downstream analysis and finally arriving at biological conclusions.

Thanks,

Upendra

[ATpoint]

What does this figure show exactly (what is 3' and 5', are these RNA-seq library prep protocols)? Is this qPCR data, or RNA-seq, and if RNA-seq...well, what are the datasets, and how have data been processed?

End-tagged RNA-seq is very common. For most common 10X single-cell RNA-seq technology is based on it, so yes, you can make good research with it. So what is the setup here, is this CRISPR, or shRNAs? Please give some details.