Illumina UD Indexes

The following tables depict plate layouts and pooling strategies for Illumina UD Indexes, which are designed for dual indexing.

Pooling strategies differ based on the type of chemistry used. Refer to [XLEAP-SBS Chemistry] Two-Plex Through Eight-Plex Pooling Strategies for instruments using XLEAP-SBS chemistry.

These indexes include Illumina DNA/RNA UD Indexes, Tagmentation and Illumina RNA UD Indexes, Ligation.

 

1

2

3

4

5

6

7

8

9

10

11

12

A

UDP0001

UDP0009

UDP0017

UDP0025

UDP0033

UDP0041

UDP0049

UDP0057

UDP0065

UDP0073V3

UDP0081

UDP0089

B

UDP0002

UDP0010

UDP0018

UDP0026

UDP0034

UDP0042

UDP0050

UDP0058

UDP0066

UDP0074V3

UDP0082

UDP0090

C

UDP0003V3

UDP0011

UDP0019

UDP0027

UDP0035

UDP0043

UDP0051

UDP0059

UDP0067

UDP0075V3

UDP0083

UDP0091

D

UDP0004

UDP0012

UDP0020

UDP0028

UDP0036

UDP0044

UDP0052

UDP0060

UDP0068

UDP0076V3

UDP0084V3

UDP0092

E

UDP0005V3

UDP0013

UDP0021

UDP0029

UDP0037

UDP0045

UDP0053V3

UDP0061

UDP0069V3

UDP0077

UDP0085

UDP0093

F

UDP0006

UDP0014

UDP0022

UDP0030

UDP0038

UDP0046V3

UDP0054V3

UDP0062

UDP0070V3

UDP0078

UDP0086

UDP0094

G

UDP0007

UDP0015

UDP0023

UDP0031

UDP0039

UDP0047

UDP0055V3

UDP0063

UDP0071V3

UDP0079

UDP0087

UDP0095

H

UDP0008

UDP0016

UDP0024

UDP0032

UDP0040

UDP0048

UDP0056V3

UDP0064

UDP0072V3

UDP0080

UDP0088

UDP0096
 

1

2

3

4

5

6

7

8

9

10

11

12

A

UDP0097

UDP0105

UDP0113

UDP0121

UDP0129

UDP0137

UDP0145V3

UDP0153

UDP0161

UDP0169

UDP0177

UDP0185

B

UDP0098

UDP0106

UDP0114

UDP0122

UDP0130

UDP0138

UDP0146V3

UDP0154

UDP0162

UDP0170

UDP0178

UDP0186

C

UDP0099

UDP0107

UDP0115

UDP0123

UDP0131

UDP0139

UDP0147V3

UDP0155V3

UDP0163

UDP0171

UDP0179V3

UDP0187

D

UDP0100

UDP0108

UDP0116

UDP0124

UDP0132

UDP0140

UDP0148V3

UDP0156

UDP0164

UDP0172

UDP0180

UDP0188

E

UDP0101

UDP0109

UDP0117

UDP0125

UDP0133

UDP0141

UDP0149

UDP0157

UDP0165

UDP0173

UDP0181

UDP0189

F

UDP0102V3

UDP0110

UDP0118

UDP0126

UDP0134

UDP0142

UDP0150

UDP0158

UDP0166

UDP0174

UDP0182

UDP0190

G

UDP0103

UDP0111

UDP0119

UDP0127

UDP0135

UDP0143

UDP0151

UDP0159

UDP0167

UDP0175

UDP0183

UDP0191

H

UDP0104

UDP0112

UDP0120

UDP0128

UDP0136

UDP0144

UDP0152

UDP0160

UDP0168

UDP0176

UDP0184

UDP0192
 

1

2

3

4

5

6

7

8

9

10

11

12

A

UDP0193V3

UDP0201

UDP0209

UDP0217

UDP0225

UDP0233

UDP0241

UDP0249

UDP0257

UDP0265V3

UDP0273

UDP0281

B

UDP0194V3

UDP0202

UDP0210

UDP0218V3

UDP0226

UDP0234

UDP0242V3

UDP0250

UDP0258V2

UDP0266V3

UDP0274

UDP0282

C

UDP0195V3

UDP0203

UDP0211

UDP0219

UDP0227V3

UDP0235

UDP0243

UDP0251

UDP0259

UDP0267V3

UDP0275

UDP0283

D

UDP0196V3

UDP0204

UDP0212

UDP0220

UDP0228

UDP0236

UDP0244V3

UDP0252V2

UDP0260

UDP0268V3

UDP0276

UDP0284

E

UDP0197

UDP0205

UDP0213

UDP0221V3

UDP0229

UDP0237

UDP0245

UDP0253

UDP0261

UDP0269

UDP0277

UDP0285V3

F

UDP0198

UDP0206

UDP0214

UDP0222V3

UDP0230

UDP0238

UDP0246

UDP0254

UDP0262

UDP0270

UDP0278

UDP0286V3

G

UDP0199

UDP0207

UDP0215

UDP0223V3

UDP0231

UDP0239

UDP0247

UDP0255

UDP0263

UDP0271

UDP0279

UDP0287V3

H

UDP0200

UDP0208

UDP0216

UDP0224V3

UDP0232

UDP0240

UDP0248

UDP0256V3

UDP0264

UDP0272

UDP0280

UDP0288V3
 

1

2

3

4

5

6

7

8

9

10

11

12

A

UDP0289V2

UDP0297

UDP0305

UDP0313

UDP0321V3

UDP0329

UDP0337

UDP0345

UDP0353

UDP0361

UDP0369V3

UDP0377

B

UDP0290V2

UDP0298V3

UDP0306

UDP0314

UDP0322

UDP0330

UDP0338

UDP0346

UDP0354

UDP0362

UDP0370V3

UDP0378

C

UDP0291V2

UDP0299

UDP0307

UDP0315

UDP0323

UDP0331

UDP0339

UDP0347

UDP0355

UDP0363

UDP0371V3

UDP0379

D

UDP0292

UDP0300

UDP0308

UDP0316

UDP0324

UDP0332

UDP0340

UDP0348

UDP0356

UDP0364

UDP0372V3

UDP0380

E

UDP0293

UDP0301V2

UDP0309

UDP0317

UDP0325

UDP0333

UDP0341

UDP0349

UDP0357

UDP0365

UDP0373

UDP0381

F

UDP0294

UDP0302

UDP0310

UDP0318

UDP0326

UDP0334

UDP0342

UDP0350

UDP0358

UDP0366

UDP0374

UDP0382

G

UDP0295

UDP0303

UDP0311

UDP0319

UDP0327

UDP0335

UDP0343

UDP0351

UDP0359

UDP0367

UDP0375

UDP0383

H

UDP0296

UDP0304

UDP0312

UDP0320

UDP0328

UDP0336

UDP0344

UDP0352

UDP0360

UDP0368

UDP0376

UDP0384

Two-plex through eight-plex pooling strategies are only recommended for Illumina UD Indexes Set A and Set B. Illumina UD Indexes Set C and Set D are not designed for low-plexity pooling.

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 Set A and Set B

Combinations Set C and Set D

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.

Not Recommended

Orange

3

The first three or last three wells in a column:

• A–C
• F–H

Rows D and E are not used.

Not Recommended

Gray

4

The first four or last four wells in a column:

• A–D
• E–H

Not Recommended

Purple

5

The first five or last five wells in a column:

• A–E
• D–H

Not Recommended

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.

Not Recommended

Green

7

The first seven or last seven wells in a column:

• A–G
• B–H

Not Recommended

Pink

8

The entire column.

Not Recommended

Teal

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

Two-plex through eight-plex pooling strategies are only recommended for Illumina UD Indexes Set A and Set B. Illumina UD Indexes Set C and Set D are not designed for low-plexity pooling.

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

Plexity

Combinations Set A

Combinations Set B

Combinations Set C and Set D

2
• C6, D11
• C6, H10
• E4, A11
• F1, H12
• F3, G11
• H7, E10
• B9, D11
• D11, A12
• D11, B12
• F3, D11
• G3, C10
• G3, D11
• H5, G9
• H7, B10
• H8, D11
• C8, D11

Not Recommended

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
• F8, G8, H8
• E9, G9, H9
• B10, C10, D10
• C10, D10, E10
• A12, C12, E12
• A12, C12, F12
• B12, F12, H12
• A11, C11, D11

Not Recommended

The following figures display four-plex through eight-plex index pooling recommendations by column for Plates A and B. Numbers represent plate columns, and letters represent the rows to be paired within each column. For example, Plate A, column 2, rows ABCD represent indexes UDP0009, UDP0010, UDP0011, and UDP0012.

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

Illumina UD Plate A Indexes

Illumina UD Plate B Indexes

Nine-plex pooling strategies are only recommended for Illumina UD Indexes Set A and Set B. Illumina UD Indexes Set C and Set D are not designed for low-plexity pooling.

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.