Illumina Single Cell Unique Dual Indexes (96 Indexes, 96 Samples)

Illumina Single Cell 3' RNA Prep libraries require a minimum of 1% PhiX to be added to the loaded library pools. It is recommended to increase PhiX to a minimum of 2% with the NovaSeq X Series.

The Illumina Single Cell Prep UDI Mix Strip uses the same set of indexes as the Illumina Single Cell Unique Dual Indexes plate. Do not use the plate and mix strip together.

Plate Layout
 

1

2

3

4

5

6

7

8

9

10

11

12

A

SCUDP0001

SCUDP0009

SCUDP0017

SCUDP0025

SCUDP0033

SCUDP0041

SCUDP0049

SCUDP0057

SCUDP0065

SCUDP0073V3

SCUDP0081

SCUDP0089

B

SCUDP0002

SCUDP0010

SCUDP0018

SCUDP0026

SCUDP0034

SCUDP0042

SCUDP0050

SCUDP0058

SCUDP0066

SCUDP0074V3

SCUDP0082

SCUDP0090

C

SCUDP0003V3

SCUDP0011

SCUDP0019

SCUDP0027

SCUDP0035

SCUDP0043

SCUDP0051

SCUDP0059

SCUDP0067

SCUDP0075V3

SCUDP0083

SCUDP0091

D

SCUDP0004

SCUDP0012

SCUDP0020

SCUDP0028

SCUDP0036

SCUDP0044

SCUDP0052

SCUDP0060

SCUDP0068

SCUDP0076V3

SCUDP0084V3

SCUDP0092

E

SCUDP0005V3

SCUDP0013

SCUDP0021

SCUDP0029

SCUDP0037

SCUDP0045

SCUDP0053V3

SCUDP0061

SCUDP0069V3

SCUDP0077

SCUDP0085

SCUDP0093

F

SCUDP0006

SCUDP0014

SCUDP0022

SCUDP0030

SCUDP0038

SCUDP0046V3

SCUDP0054V3

SCUDP0062

SCUDP0070V3

SCUDP0078

SCUDP0086

SCUDP0094

G

SCUDP0007

SCUDP0015

SCUDP0023

SCUDP0031

SCUDP0039

SCUDP0047

SCUDP0055V3

SCUDP0063

SCUDP0071V3

SCUDP0079

SCUDP0087

SCUDP0095

H

SCUDP0008

SCUDP0016

SCUDP0024

SCUDP0032

SCUDP0040

SCUDP0048

SCUDP0056V3

SCUDP0064

SCUDP0072V3

SCUDP0080

SCUDP0088

SCUDP0096

The following table shows index adapters (wells) that can be combined in a two-plex through eight-plex pool, while the color-coded figure illustrates each combination.

Pool any plexity ≥ 2 from the top or bottom of a column. Do not pool across a row.

Plexity

Combinations in 96 UD Plate

Color in Figure

2

The first two or last two wells in a column:

• A and B
• G and H

Rows C–F are not used.

Orange

3

The first three or last three wells in a column:

• A–C
• F–H

Rows D and E are not used.

Gray

4

The first four or last four wells in a column:

• A–D
• E–H

Purple

5

The first five or last five wells in a column:

• A–E
• D–H

Blue

6

[Option 1] The first six or last six wells in a column:

• A–F
• C–H

[Option 2] The first two wells (A and B) or last two wells (G and H) in one column, and any four wells in an adjacent column.

Green

7

The first seven or last seven wells in a column:

• A–G
• B–H

Pink

8

The entire column.

Teal

This section applies to any instruments using XLEAP-SBS Chemistry.

The following table shows index adapters (wells) that can be combined in a two-plex or three-plex pool.

Plexity

Combinations in 96 UD Plate

2
• C6, D11
• C6, H10
• E4, A11
• F1, H12
• F3, G11
• H7, E10

3
• A3, C3, D3
• E3, G3, H3
• B4, C4, D4
• F8, G8, H8
• B11, C11, G11
• B11, F11, G11
• A12, G12, H12
• E12, G12, H12
• D12, G12, H12

The following figures display four-plex through eight-plex index pooling recommendations by column. Numbers represent plate columns, and letters represent the rows to be paired within each column. For example, column 2, rows ABCD represent indexes SCUDP0009, SCUDP0010, SCUDP0011, and SCUDP0012.

The orange wells in the following color-coded figures are not recommended for use.

Illumina Single Cell Unique Dual Indexes (96 indexes, 96 samples)

Use index adapters from any wells that optimize color balance in a sequencing run, for example:

• A1–H1 and A2
• A4–D4 and A5–E5
• A7–F7 and A8–C8
• A10–C10, A11–C11, and A12–C12

The following figure depicts all four examples.