Help choosing library prep for illumina

[N311V]

Hi All,

We have a large RNA-seq experiment planned (320 samples) for which I've been tasked with library prep. The amount and quality of RNA per sample should not be a problem as use of inbred lines affords me virtually unlimited biological material to extract from. Sequencing will likely occur on an illumina 3000/4000 or NextSeq500.

Above all, cost is a major factor in deciding which library prep kit to use. I wouldn't call myself a molecular geneticist but I have some lab experience therefore ease-of-use also matters.

Sorry if I haven't provided enough detail and thanks in advance for any responses I get.

[kerplunk412]

The NEXTflex Rapid Directional RNA-Seq Kit from Bioo Scientific would be a good fit for you. The bundles we offer make RNA-Seq very cost-effective. Other lower-cost options include NEB and Kapa. As a disclaimer, I work for Bioo Scientific.

[james hadfield]

We've got excellent differential gene expression results with Illumina TruSeq stranded mRNA-seq and 10-20M single-end 50bp reads. We're seeing an issue with index number D703 but you can double check with Illumina if this is fixed before starting or simly make 2 48plex pools using the last 48 indexes and run four lanes of each.
Illumina's cost is competetive. For us it is very reliable and includes everything you need.

[N311V]

We've got excellent differential gene expression results with Illumina TruSeq stranded mRNA-seq

Hi James,

Thanks for your advice.

For past experiments I've been involved in library prep was outsourced and that's the kit they used too. The results were also very good. However, cost wise I found TruSeq to be quite expensive. I only compared it to NEBnext and that was about 12 months ago so prices may have changed. I'd better take a second look.

Also, Kapa are currently offering buy 2 kits get 1 free, which is an appealing discount. Anyone had experience with KAPA Stranded mRNA-Seq Kit, with KAPA mRNA Capture Beads?

https://www.kapabiosystems.com/product-applications/products/next-generation-sequencing-2/rna-library-preparation-2/kapa-stranded-mrna-seq-kits/