Mixing cDNA samples from Ovation RNA‐Seq System V2 of NuGEN with Nextera Dual Indexes

[seq_uestion]

Hello,

I have a question regarding the compatibility of the "IDT® for Illumina Nextera™ DNA UD Indexes". Illumina says "These index kits are NOT interchangeable with the Nextera DNA or Nextera XT Index Kits".
But, are they compatible with amplified cDNA samples prepared using the Ovation® RNA‐Seq System V2 of NuGEN from RNA?
Our preferred sequence facility (uses HiSeq4000) has strongly recommended the use of duel index adaptors (in specific the Ovation® Ultralow System V2 developed by Illumina) to avoid index hoping, we will like to know if Nextera indexes are also an option,

Best regards

[luc]

Best ask Nugen. Likely Nugen is using the Truseq design for their kits, not Nextera sequences.