Library preparation reagents we use

UD=unique dual (index)

Illumina UD support documents

DNA library prep kits:

• Nextera^TM DNA FLEX library prep kit (Cat.Nr. 20018705), Illumina + adapters: IDT for Illumina DNA/RNA UD Indexes Set A/B/C/D Tagmentation (384 Indexes)  
• Swift 2S ® Turbo DNA library kit (Cat. No. 45024), Swift Biosciences + adapters: IDT for Illumina – TruSeq DNA UD Indexes (96 Indexes) (Cat.Nr. 20022370), Illumina
• TruSeq nano DNA library prep kit (Cat.Nr. 20015965), Illumina + adapters: IDT for Illumina – TruSeq DNA UD Indexes (96 Indexes) (Cat.Nr. 20022370), Illumina
• TruSeq DNA PCR-free library prep kit (Cat.Nr. 20015963), Illumina + adapters: IDT for Illumina – TruSeq DNA UD Indexes (96 Indexes) (Cat.Nr. 20022370), Illumina

• SMARTer® ThruPLEX® DNA-Seq Kit (Cat.Nr.R400676), Takara + adapters: SMARTer® DNA Unique Dual Index Kit - 24U Set A (Cat.Nr. R400665) and SMARTer® DNA Unique Dual Index Kit - 24U Set B (Cat.Nr. R400666), Takara

RNA preps:

• TruSeq® Stranded mRNA Library Prep (96 Samples) (Cat.Nr. 20020595), Illumina + adapters: IDT for Illumina – TruSeq RNA UD Indexes (96 Indexes) (Cat.Nr. 2002237), Illumina

Small (micro) RNA preps:

• NEBNext® Multiplex Small RNA Prep Set for Illumina (1-48) (Cat.Nr. E7560S), New England Biolabs (the kit includes adapters)

• QIAseq miRNA Library Kit (96) (Cat.Nr. 331505) + adapters: QIAseq miRNA NGS 96 Index IL (96)- (Cat.Nr. 331565)

Ribosomal 16S DNA library prep protocol:

• An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Fadrosh DW et. al. Microbiome. 2014 Feb 24;2(1):6. doi: 10.1186/2049-2618-2-6. https://www.ncbi.nlm.nih.gov/pubmed/24558975