Amplicon Sequencing of SS3

The SS3 locus is a commonly used integration locus in E. coli engineering (Bassalo 2016). Here we validated the wildtype locus (containing the gRNA target sequence) using primers

 

Primer Name	Sequence
SS3_forward	GGC GGT GCA CAG CAA CAC G
SS3_reverse	CCG GTG ATA CAG CTT CAA TTC CAA CC

This amplifies a short product about 250 bp long.

Result when submitted to our Linear Amplicon service: https://seqresults.angstrominno.com/orders/AI-1272

The IGV plot shows the sequencing coverage of this amplicon product. About 15-20 bp at the ends of the amplicon are cleaved when using the rapid barcoding tagmentation process. However, we can still validate that the locus has the intended engineering. 

https://igv.angstrominno.com/?sessionURL=/data/AI-1272_1_SS3_locus/session.json# (make sure to log in first to SeqResults)

Here is a view of the reference aligned with the sequencing result:

https://seqresults.angstrominno.com/orders/AI-1272/alignment-tool