Editing BioMicroCenter:News2017+ (section)

=== APRIL 2017 ===
We have used the sunsetting of the [[BioMicroCenter:Neoprep|Illumina Neoprep]] as an opportunity to re-evaluate all of our library prep methodologies with an eye on significantly reducing library preparation costs. We’re now ready to roll out hand preparation for these methods as well as some of our automation to help smooth the transition. We plan to bring in scientists from the different manufacturers we’ve been looking at through our Technology Seminar Series to answer any questions you may have. For all of the methods, we will have a single sample price as well as a batch price that will be significantly cheaper per sample. Below are the RNAseq methods that are already locked in.
{|border="1"
 |Method / Kit	
 |Per sample ||Per 24 ||Per 96 / 384
 |-
 |polyA RNA (>50ng):<BR>Kapa Hyperprep	
 |$150 	||$2,000 (est)	||NA
 |-
 |3’Digital Gene Expression	
 |NA ||$1,200 ||$4,000
 |-
 |Ribosomal Depletion (human/mouse):<BR>Kapa RiboGone 	
 |$225	|| TBD || TBD
 |-	
 |Ribosomal Depletion (other):<BR>Illumina Ribozero + Kapa Hyperprep	
 |$250	|| TBD	|| NA
 |-
 |Low input polyA:<BR>Clontech SMARTseq v4	
 |$300 || $1,600 || $2,500 / $5,000
 |-
 |Low input ribosomal depletion (human/mouse) <BR> Clontech ZapR kit	
 |$200	|| TBD || TBD
|} 
Please note that we do not consider this problem ‘solved’ and we are continuing to work on adapting new protocols with the aim of lowering cost while maintaining quality. We also are not yet complete with the process of getting everything listed in iLabs which will happen over the next couple weeks. The Neoprep will be shut down on July 31.<BR><BR>

A second area we continue to address is data storage.  With recent expansions to the systems, we are able to significantly lower our data storage costs for next year. Active storage will now be $200/TB/y while archival storage (read only) will be at $100/TB/y.<BR><BR>

Finally, many of you may have heard about a recent issue of “index switchng” or “pad swapping” on Illumina sequencers from a bioRxiv preprint from Stanford or social media (http://biorxiv.org/content/early/2017/04/09/125724). We have been well aware of this issue for many years and that it is endemic in all Illumina sequencers (we called it “barcode swapping” in house). Fortunately for us, the non-patterned flowcells (such as MiSeq, NextSeq and HiSeq2000) have a significantly lower issue with this than the newer instruments. Even so, the low level of index switching we have observed (~0.1% of reads for most runs) is a primary reason we have resisted mixing libraries from different labs on single sequencing lanes. If you have any questions/concerns about this instrument ‘feature’, we are happy to discuss it with you. Our hope is the new emphasis on this issue for the patterned flowcells will result in improved methodologies that further lower the likelihood of barcode swaps.