Illumina Single Cell RNA Indexes

Do not use quality trimming or adapter trimming when converting BCL files into FASTQ files. When using a sample sheet, make sure that no adapter reads are listed under Adapter, Adapter Read 1, or Adapter Read 2.

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

Refer to Index 2 (i5) Orientation for more information on how to enter i5 bases on the sample sheet in forward or reverse complement orientation.

Index Name	i7 Bases in Adapter	i7 Bases for Sample Sheet	i5 Bases in Adapter	i5 Bases for Sample Sheet in Forward Orientation	i5 Bases for Sample Sheet in Reverse Complement Orientation
SCUDP0001	CGCTCAGTTC	GAACTGAGCG	TCGTGGAGCG	TCGTGGAGCG	CGCTCCACGA
SCUDP0002	TATCTGACCT	AGGTCAGATA	CTACAAGATA	CTACAAGATA	TATCTTGTAG
SCUDP0003V3	TCGGATGTCG	CGACATCCGA	TACGTTCATT	TACGTTCATT	AATGAACGTA
SCUDP0004	CTTATGGAAT	ATTCCATAAG	TGCCTGGTGG	TGCCTGGTGG	CCACCAGGCA
SCUDP0005V3	TCCTATTGTG	CACAATAGGA	TCCATCCGAG	TCCATCCGAG	CTCGGATGGA
SCUDP0006	GCGCGATGTT	AACATCGCGC	GTCCACTTGT	GTCCACTTGT	ACAAGTGGAC
SCUDP0007	AGAGCACTAG	CTAGTGCTCT	TGGAACAGTA	TGGAACAGTA	TACTGTTCCA
SCUDP0008	TGCCTTGATC	GATCAAGGCA	CCTTGTTAAT	CCTTGTTAAT	ATTAACAAGG
SCUDP0009	CTACTCAGTC	GACTGAGTAG	GTTGATAGTG	GTTGATAGTG	CACTATCAAC
SCUDP0010	TCGTCTGACT	AGTCAGACGA	ACCAGCGACA	ACCAGCGACA	TGTCGCTGGT
SCUDP0011	GAACATACGG	CCGTATGTTC	CATACACTGT	CATACACTGT	ACAGTGTATG
SCUDP0012	CCTATGACTC	GAGTCATAGG	GTGTGGCGCT	GTGTGGCGCT	AGCGCCACAC
SCUDP0013	TAATGGCAAG	CTTGCCATTA	ATCACGAAGG	ATCACGAAGG	CCTTCGTGAT
SCUDP0014	GTGCCGCTTC	GAAGCGGCAC	CGGCTCTACT	CGGCTCTACT	AGTAGAGCCG
SCUDP0015	CGGCAATGGA	TCCATTGCCG	GAATGCACGA	GAATGCACGA	TCGTGCATTC
SCUDP0016	GCCGTAACCG	CGGTTACGGC	AAGACTATAG	AAGACTATAG	CTATAGTCTT
SCUDP0017	AACCATTCTC	GAGAATGGTT	TCGGCAGCAA	TCGGCAGCAA	TTGCTGCCGA
SCUDP0018	GGTTGCCTCT	AGAGGCAACC	CTAATGATGG	CTAATGATGG	CCATCATTAG
SCUDP0019	CTAATGATGG	CCATCATTAG	GGTTGCCTCT	GGTTGCCTCT	AGAGGCAACC
SCUDP0020	TCGGCCTATC	GATAGGCCGA	CGCACATGGC	CGCACATGGC	GCCATGTGCG
SCUDP0021	AGTCAACCAT	ATGGTTGACT	GGCCTGTCCT	GGCCTGTCCT	AGGACAGGCC
SCUDP0022	GAGCGCAATA	TATTGCGCTC	CTGTGTTAGG	CTGTGTTAGG	CCTAACACAG
SCUDP0023	AACAAGGCGT	ACGCCTTGTT	TAAGGAACGT	TAAGGAACGT	ACGTTCCTTA
SCUDP0024	GTATGTAGAA	TTCTACATAC	CTAACTGTAA	CTAACTGTAA	TTACAGTTAG
SCUDP0025	TTCTATGGTT	AACCATAGAA	GGCGAGATGG	GGCGAGATGG	CCATCTCGCC
SCUDP0026	CCTCGCAACC	GGTTGCGAGG	AATAGAGCAA	AATAGAGCAA	TTGCTCTATT
SCUDP0027	TGGATGCTTA	TAAGCATCCA	TCAATCCATT	TCAATCCATT	AATGGATTGA
SCUDP0028	ATGTCGTGGT	ACCACGACAT	TCGTATGCGG	TCGTATGCGG	CCGCATACGA
SCUDP0029	AGAGTGCGGC	GCCGCACTCT	TCCGACCTCG	TCCGACCTCG	CGAGGTCGGA
SCUDP0030	TGCCTGGTGG	CCACCAGGCA	CTTATGGAAT	CTTATGGAAT	ATTCCATAAG
SCUDP0031	TGCGTGTCAC	GTGACACGCA	GCTTACGGAC	GCTTACGGAC	GTCCGTAAGC
SCUDP0032	CATACACTGT	ACAGTGTATG	GAACATACGG	GAACATACGG	CCGTATGTTC
SCUDP0033	CGTATAATCA	TGATTATACG	GTCGATTACA	GTCGATTACA	TGTAATCGAC
SCUDP0034	TACGCGGCTG	CAGCCGCGTA	ACTAGCCGTG	ACTAGCCGTG	CACGGCTAGT
SCUDP0035	GCGAGTTACC	GGTAACTCGC	AAGTTGGTGA	AAGTTGGTGA	TCACCAACTT
SCUDP0036	TACGGCCGGT	ACCGGCCGTA	TGGCAATATT	TGGCAATATT	AATATTGCCA
SCUDP0037	GTCGATTACA	TGTAATCGAC	GATCACCGCG	GATCACCGCG	CGCGGTGATC
SCUDP0038	CTGTCTGCAC	GTGCAGACAG	TACCATCCGT	TACCATCCGT	ACGGATGGTA
SCUDP0039	CAGCCGATTG	CAATCGGCTG	GCTGTAGGAA	GCTGTAGGAA	TTCCTACAGC
SCUDP0040	TGACTACATA	TATGTAGTCA	CGCACTAATG	CGCACTAATG	CATTAGTGCG
SCUDP0041	ATTGCCGAGT	ACTCGGCAAT	GACAACTGAA	GACAACTGAA	TTCAGTTGTC
SCUDP0042	GCCATTAGAC	GTCTAATGGC	AGTGGTCAGG	AGTGGTCAGG	CCTGACCACT
SCUDP0043	GGCGAGATGG	CCATCTCGCC	TTCTATGGTT	TTCTATGGTT	AACCATAGAA
SCUDP0044	TGGCTCGCAG	CTGCGAGCCA	AATCCGGCCA	AATCCGGCCA	TGGCCGGATT
SCUDP0045	TAGAATAACG	CGTTATTCTA	CCATAAGGTT	CCATAAGGTT	AACCTTATGG
SCUDP0046V3	TCCATGTTGC	GCAACATGGA	CTTGTCTTAA	CTTGTCTTAA	TTAAGACAAG
SCUDP0047	TATCCAGGAC	GTCCTGGATA	CGGTGGCGAA	CGGTGGCGAA	TTCGCCACCG
SCUDP0048	AGTGCCACTG	CAGTGGCACT	TAACAATAGG	TAACAATAGG	CCTATTGTTA
SCUDP0049	GTGCAACACT	AGTGTTGCAC	CTGGTACACG	CTGGTACACG	CGTGTACCAG
SCUDP0050	ACATGGTGTC	GACACCATGT	TCAACGTGTA	TCAACGTGTA	TACACGTTGA
SCUDP0051	GACAGACAGG	CCTGTCTGTC	ACTGTTGTGA	ACTGTTGTGA	TCACAACAGT
SCUDP0052	TCTTACATCA	TGATGTAAGA	GTGCGTCCTT	GTGCGTCCTT	AAGGACGCAC
SCUDP0053V3	TACCGAACTA	TAGTTCGGTA	CCATGTGTAG	CCATGTGTAG	CTACACATGG
SCUDP0054V3	GTAGTAATAG	CTATTACTAC	GAGTCTCTCC	GAGTCTCTCC	GGAGAGACTC
SCUDP0055V3	GGTTATGCTA	TAGCATAACC	GCTATGCGCA	GCTATGCGCA	TGCGCATAGC
SCUDP0056V3	ACAATAGAGT	ACTCTATTGT	ATCGCATATG	ATCGCATATG	CATATGCGAT
SCUDP0057	TTAGGATAGA	TCTATCCTAA	CGTCGACTGG	CGTCGACTGG	CCAGTCGACG
SCUDP0058	CCGAAGCGAG	CTCGCTTCGG	TACTAGTCAA	TACTAGTCAA	TTGACTAGTA
SCUDP0059	GGACCAACAG	CTGTTGGTCC	ATAGACCGTT	ATAGACCGTT	AACGGTCTAT
SCUDP0060	TTCCAGGTAA	TTACCTGGAA	ACAGTTCCAG	ACAGTTCCAG	CTGGAACTGT
SCUDP0061	TGATTAGCCA	TGGCTAATCA	AGGCATGTAG	AGGCATGTAG	CTACATGCCT
SCUDP0062	TAACAGTGTT	AACACTGTTA	GCAAGTCTCA	GCAAGTCTCA	TGAGACTTGC
SCUDP0063	ACCGCGCAAT	ATTGCGCGGT	TTGGCTCCGC	TTGGCTCCGC	GCGGAGCCAA
SCUDP0064	GTTCGCGCCA	TGGCGCGAAC	AACTGATACT	AACTGATACT	AGTATCAGTT
SCUDP0065	AGACACATTA	TAATGTGTCT	GTAAGGCATA	GTAAGGCATA	TATGCCTTAC
SCUDP0066	GCGTTGGTAT	ATACCAACGC	AATTGCTGCG	AATTGCTGCG	CGCAGCAATT
SCUDP0067	AGCACATCCT	AGGATGTGCT	TTACAATTCC	TTACAATTCC	GGAATTGTAA
SCUDP0068	TTGTTCCGTG	CACGGAACAA	AACCTAGCAC	AACCTAGCAC	GTGCTAGGTT
SCUDP0069V3	AAGGCCTTGG	CCAAGGCCTT	TCGAAGTACT	TCGAAGTACT	AGTACTTCGA
SCUDP0070V3	TGTGGAGTAA	TTACTCCACA	GACACCGATG	GACACCGATG	CATCGGTGTC
SCUDP0071V3	CACTTCTACT	AGTAGAAGTG	CTAGCGTCGA	CTAGCGTCGA	TCGACGCTAG
SCUDP0072V3	TGGACTCGTA	TACGAGTCCA	TAGCGAAGCA	TAGCGAAGCA	TGCTTCGCTA
SCUDP0073V3	TATCATGAGA	TCTCATGATA	AACACGTGGA	AACACGTGGA	TCCACGTGTT
SCUDP0074V3	CTTGGCCTCG	CGAGGCCAAG	GTGTTACCGG	GTGTTACCGG	CCGGTAACAC
SCUDP0075V3	GTCTCGTGAA	TTCACGAGAC	AGATTGTTAC	AGATTGTTAC	GTAACAATCT
SCUDP0076V3	CCATCCACGC	GCGTGGATGG	TTGACCAATG	TTGACCAATG	CATTGGTCAA
SCUDP0077	GGATACCAGA	TCTGGTATCC	CGTTGCTTAC	CGTTGCTTAC	GTAAGCAACG
SCUDP0078	CGCACTAATG	CATTAGTGCG	TGACTACATA	TGACTACATA	TATGTAGTCA
SCUDP0079	TCCTGACCGT	ACGGTCAGGA	CGGCCTCGTT	CGGCCTCGTT	AACGAGGCCG
SCUDP0080	CTGGCTTGCC	GGCAAGCCAG	CAAGCATCCG	CAAGCATCCG	CGGATGCTTG
SCUDP0081	ACCAGCGACA	TGTCGCTGGT	TCGTCTGACT	TCGTCTGACT	AGTCAGACGA
SCUDP0082	TTGTAACGGT	ACCGTTACAA	CTCATAGCGA	CTCATAGCGA	TCGCTATGAG
SCUDP0083	GTAAGGCATA	TATGCCTTAC	AGACACATTA	AGACACATTA	TAATGTGTCT
SCUDP0084V3	TAGATCCAGT	ACTGGATCTA	TCGCCGCTAG	TCGCCGCTAG	CTAGCGGCGA
SCUDP0085	TTAGGTACCA	TGGTACCTAA	CATGAGTACT	CATGAGTACT	AGTACTCATG
SCUDP0086	GGAATTCCAA	TTGGAATTCC	ACGTCAATAC	ACGTCAATAC	GTATTGACGT
SCUDP0087	CATGTAGAGG	CCTCTACATG	GATACCTCCT	GATACCTCCT	AGGAGGTATC
SCUDP0088	TACACGCTCC	GGAGCGTGTA	ATCCGTAAGT	ATCCGTAAGT	ACTTACGGAT
SCUDP0089	GCTTACGGAC	GTCCGTAAGC	CGTGTATCTT	CGTGTATCTT	AAGATACACG
SCUDP0090	CGCTTGAAGT	ACTTCAAGCG	GAACCATGAA	GAACCATGAA	TTCATGGTTC
SCUDP0091	CGCCTTCTGA	TCAGAAGGCG	GGCCATCATA	GGCCATCATA	TATGATGGCC
SCUDP0092	ATACCAACGC	GCGTTGGTAT	ACATACTTCC	ACATACTTCC	GGAAGTATGT
SCUDP0093	CTGGATATGT	ACATATCCAG	TATGTGCAAT	TATGTGCAAT	ATTGCACATA
SCUDP0094	CAATCTATGA	TCATAGATTG	GATTAAGGTG	GATTAAGGTG	CACCTTAATC
SCUDP0095	GGTGGAATAC	GTATTCCACC	ATGTAGACAA	ATGTAGACAA	TTGTCTACAT
SCUDP0096	TGGACGGAGG	CCTCCGTCCA	CACATCGGTG	CACATCGGTG	CACCGATGTG

Illumina Single Cell UDI Mix Strip

Well	Index Name	i7 Bases in Adapter	i7 Bases for Sample Sheet	i5 Bases in Adapter	i5 Bases for Sample Sheet in Forward Orientation	i5 Bases for Sample Sheet in Reverse Complement Orientation
Mix 1	SCUDP0017	AACCATTCTC	GAGAATGGTT	TCGGCAGCAA	TCGGCAGCAA	TTGCTGCCGA
Mix 2	SCUDP0018	GGTTGCCTCT	AGAGGCAACC	CTAATGATGG	CTAATGATGG	CCATCATTAG
Mix 3	SCUDP0019	CTAATGATGG	CCATCATTAG	GGTTGCCTCT	GGTTGCCTCT	AGAGGCAACC
Mix 4	SCUDP0020	TCGGCCTATC	GATAGGCCGA	CGCACATGGC	CGCACATGGC	GCCATGTGCG
Mix 5	SCUDP0021	AGTCAACCAT	ATGGTTGACT	GGCCTGTCCT	GGCCTGTCCT	AGGACAGGCC
Mix 6	SCUDP0022	GAGCGCAATA	TATTGCGCTC	CTGTGTTAGG	CTGTGTTAGG	CCTAACACAG
Mix 7	SCUDP0023	AACAAGGCGT	ACGCCTTGTT	TAAGGAACGT	TAAGGAACGT	ACGTTCCTTA
Mix 8	SCUDP0024	GTATGTAGAA	TTCTACATAC	CTAACTGTAA	CTAACTGTAA	TTACAGTTAG