Bead types in Illumina library preparation kits

Illumina library preparation kits use various bead types for different functions. While these beads often look similar, it is important to use the correct beads when called for because they have different properties and functions. All beads should be:

• Brought to room temperature before use (for approximately 30 minutes).

• Pulse-vortexed for 1 full minute to ensure homogenous resuspension.

• Stored at the appropriate temperature when not in use. Storage requirements for each bead type can be found in the library preparation reference guide.

The tables below list bead types by function and provide additional information about each bead type.

DNA Purification

Bead Name	Used in	Function	Additional information
AMPure XP beads	Numerous Illumina library preparation kits	Beads are used for DNA purification and/or size selection of DNA fragments based on the ratio of beads:sample.	AMPure XP beads are purchased separately for use with Illumina library prep kits.
Refer to the Equipment and Consumables section of the appropriate Reference Guide or Product Documentation for the recommended Beckman Coulter catalog number.
SPB	Numerous Illumina library preparation kits	Beads are used for DNA purification and/or size selection of DNA fragments based on the ratio of beads:sample.	Are functionally similar to AMPure XP beads.
(Sample Purification Beads)
IPB	Numerous Illumina library preparation kits	Beads are used for DNA purification and/or size selection of DNA fragments based on the ratio of beads:sample.	This bead is stored at room temperature.
(Illumina Purification Beads)
IPB2	Illumina Single Cell 3' RNA	Beads are used for DNA purification and/or size selection of DNA fragments based on the ratio of beads:sample.	This bead is stored at 4°C.
(Illumina Purification Beads 2)

RNA Isolation and Purification

Bead Name	Used in	Function	Additional information
RPB	TruSeq Stranded mRNA	Beads isolate mRNA by capturing polyadenylated RNAs.
(RNA Purification Beads)
RPBX	Illumina Stranded mRNA Prep, Ligation	Beads isolate mRNA by capturing polyadenylated RNAs.
(RNA Purification Beads)
RRB	TruSeq Stranded Total RNA	Beads remove rRNA by binding rRNA removal probes bound to rRNA.
(rRNA Removal Beads)
RNAClean XP Beads	TruSeq Stranded Total RNA	Beads are used to purify RNA through binding. In TruSeq Stranded Total RNA, these beads clean up the remaining RNA after rRNA is removed.	RNAClean XP beads are purchased separately from Beckman Coulter Genomics.
Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus

Tagmentation

Bead Name	Used in	Function	Additional information
BLT	Illumina DNA Prep, (M) Tagmentation (formerly Nextera DNA Flex)	Transposomes bound to beads fragment and tag (tagment) DNA input.	BLT is not interchangeable with eBLT, BLT-PF, or eBLTL.
(Bead-Linked Transposomes)
eBLT	Illumina DNA Prep with Enrichment (S) Tagmentation (formerly Nextera Flex for Enrichment), Illumina Microbial Amplicon Prep (IMAP), IMAP-Flu	Transposomes bound to beads fragment and tag (tagment) DNA input for subsequent enrichment.	eBLT is not interchangeable with BLT, BLT-PF, or eBLTL.
(Enrichment Bead-Linked Transposomes)
BLT-PF	Illumina DNA PCR-Free Prep, Tagmentation	Transposomes bound to beads fragment and tag (tagment) DNA input for Illumina DNA PCR-Free workflow.	BLT-PF are not used in the TruSeq PCR Free library prep kit, where fragmentation is achieved with Covaris shearing.
(Bead-Linked Transposomes PCR-Free)
BLT-PF is not interchangeable with BLT, eBLT, or eBLTL.
	This bead is stored at -20°C.
eBLTL	Illumina RNA Prep with Enrichment (L) Tagmentation	Transposomes bound to beads fragment and tag (tagment) cDNA for the Illumina RNA Prep with Enrichment Tagmentation workflow.	eBLTL is not interchangeable with BLT, eBLT, or BLT-PF.
(Bead-Linked Transposomes for Enrichment)
This bead is stored at -20°C.
TDE1	Illumina Tagment DNA TDE1 Enzyme and Buffer kits	Free-floating transposomes fragment and tag (tagment) cDNA	Contains the Tagment DNA Enzyme (TDE1) and the Tagment DNA (TD) buffer previously included in the discontinued Nextera DNA library preparation kits.
(Tagment DNA Enzyme)
These reagents are used for numerous applications, such as ATAC-Seq and other custom protocols developed by Illumina customers.

Enrichment

Bead Name	Used in	Function	Additional information
SMB	Numerous Illumina library preparation kits	Streptavidin bound to magnetic beads pulls down biotinylated capture probes.	Beads are not interchangeable with streptavidin beads from third-party vendors.
(Streptavidin Magnetic Beads)
SMB3	Numerous Illumina library preparation kits	Streptavidin bound to magnetic beads pulls down biotinylated capture probes.
(Streptavidin Magnetic Beads 3)	Improved reagent stability over SMB, but no changes to reagent performance or function.
SMB4	Numerous Illumina library preparation kits	Streptavidin bound to magnetic beads pulls down biotinylated capture probes.	Lighter in color than SMB3, but no changes to reagent performance or function.
(Streptavidin Magnetic Beads 4)

Normalization

Bead Name	Used in	Function	Additional information
LNB1	Numerous Illumina library preparation kits	Library normalization: a fixed volume of beads is added to each sample, beads bind and saturate with library fragments, excess library is washed away, and normalized library is eluted from the beads.	Eluted libraries are single-stranded DNA.
(Library Normalization Beads 1)
LNB3	Newer Illumina library preparation kits	Library normalization: a fixed volume of beads is added to each sample, beads bind and saturate with library fragments, excess library is washed away, and normalized library is eluted from the beads.	Eluted libraries are single-stranded DNA.
(Library Normalization Beads 3)
Equalizer Beads	AmpliSeq for Illumina library preparation kits	Library normalization: Equalizer Capture reagent is added to final libraries and washed Equalizer Beads are added to the sample. After library fragments are captured by the beads, the beads are washed, and normalized library is eluted from the beads.	Eluted libraries are double-stranded DNA.
AmpliSeq for Illumina Equalizer reagents are not compatible with other library types.

For any feedback or questions regarding this article (Illumina Knowledge Article #3342), contact Illumina Technical Support [email protected].