Cat. # | Size | Qty. | Price |
---|---|---|---|
47538S | 1 Kit (96 assays) |
|
$ 630 |
Product Includes | Volume (with Count) | Storage Temp | |||
---|---|---|---|---|---|
Adaptor for Illumina Systems | 1 x 960 µl | -20°C | |||
USER Enzyme | 1 x 288 µl | -20°C | |||
Index Primer Orange Tube Caps | 1 x 24 ea | RT | |||
Index Primer White Tube Caps | 1 x 16 ea | RT | |||
Index 501 Primer for Illumina Systems | 1 x 60 µl | -20°C | |||
Index 502 Primer for Illumina Systems | 1 x 60 µl | -20°C | |||
Index 503 Primer for Illumina Systems | 1 x 60 µl | -20°C | |||
Index 504 Primer for Illumina Systems | 1 x 60 µl | -20°C | |||
Index 505 Primer for Illumina Systems | 1 x 60 µl | -20°C | |||
Index 506 Primer for Illumina Systems | 1 x 60 µl | -20°C | |||
Index 507 Primer for Illumina Systems | 1 x 60 µl | -20°C | |||
Index 508 Primer for Illumina Systems | 1 x 60 µl | -20°C | |||
Index 701 Primer for Illumina Systems | 1 x 40 µl | -20°C | |||
Index 702 Primer for Illumina Systems | 1 x 40 µl | -20°C | |||
Index 703 Primer for Illumina Systems | 1 x 40 µl | -20°C | |||
Index 704 Primer for Illumina Systems | 1 x 40 µl | -20°C | |||
Index 705 Primer for Illumina Systems | 1 x 40 µl | -20°C | |||
Index 706 Primer for Illumina Systems | 1 x 40 µl | -20°C | |||
Index 707 Primer for Illumina Systems | 1 x 40 µl | -20°C | |||
Index 708 Primer for Illumina Systems | 1 x 40 µl | -20°C | |||
Index 709 Primer for Illumina Systems | 1 x 40 µl | -20°C | |||
Index 710 Primer for Illumina Systems | 1 x 40 µl | -20°C | |||
Index 711 Primer for Illumina Systems | 1 x 40 µl | -20°C | |||
Index 712 Primer for Illumina Systems | 1 x 40 µl | -20°C |
Product Information
Upon receipt, #54631 and #70942 tube caps should be removed from the kit box and stored at room temperature. Store remaining components at -20ºC. This product is stable for 12 months if stored properly.
Next generation sequencing (NG-seq) is a high throughput method that can be used downstream of chromatin immunoprecipitation (ChIP) and Cleavage Under Targets and Release Using Nuclease (CUT&RUN) assays to identify and quantify target DNA enrichment across the entire genome. Multiplex Oligos for Illumina Systems (Dual Index Primers) (ChIP-seq, CUT&RUN) contains adaptors and primers that are ideally suited for multiplex sample preparation for NG-seq on the Illumina Systems platform (Illumina, Inc.). This kit can be used to generate up to 96 distinct, barcoded ChIP-seq or CUT&RUN DNA libraries that can be combined into a single sequencing reaction.
Each kit component must pass rigorous quality control standards, and for each new lot the entire set of reagents is functionally validated together by construction and sequencing of indexed libraries on the Illumina Systems sequencing platform.
This product provides enough reagents to support up to 96 DNA sequencing libraries, and must be used in combination with DNA Library Prep Kit for Illumina Systems (ChIP-seq, CUT&RUN) #56795.
Compatible Assay kits:
CUT&RUN Assay Kit #86652
SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) #9003
SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) #9005
SimpleChIP® Plus Sonication Chromatin IP Kit #56383
ChIP-seq DNA Library Prep Kit for Illumina Systems (ChIP-seq, CUT&RUN) #56795
Non-Compatible SimpleChIP® kits:
SimpleChIP® Enzymatic Chromatin IP Kit (Agarose Beads) #9002
SimpleChIP® Plus Enzymatic Chromatin IP Kit (Agarose Beads) #9004
Note: Agarose beads are blocked with sonicated salmon sperm DNA, which will contaminate DNA library preps and NG-seq.
Required Reagents:
Reagents Included:
Reagents Not Included:
The dual index primer strategy utilizes two 8 base indices within each primer. Index 7 primers contain indices that are adjacent to the P7 sequence while index 5 primers contain indices that are adjacent to the P5 sequence. Dual indexing is enabled by adding a unique index to both ends of a sample to be sequenced. Up to 96 different samples can be uniquely indexed by combining each of the 12 index 7 primers with each of the 8 index 5 primers.
Illumina Systems NG-seq platforms use a red laser/LED to sequence A/C and a green laser/LED to sequence G/T. For each cycle, both the red and the green channel need to be read to ensure proper image registration (i.e. A or C must be present in each cycle, and G or T must be present in each cycle). If this color balance is not maintained, sequencing the index read could fail. Please check the sequences of each index to be used to ensure that you will have signal in both the red and green channels for every cycle. See example below:
Index 7 Primers for Illumina Systems | Index 5 Primers for Illumina Systems | ||
Index 701 Primer for Illumina Systems |
ATTACTCG |
Index 503 Primer for Illumina Systems |
CCTATCCT |
Index 702 Primer for Illumina Systems |
TCCGGAGA |
Index 504 Primer for Illumina Systems |
GGCTCTGA |
Index 703 Primer for Illumina Systems |
CGCTCATT |
Index 505 Primer for Illumina Systems |
AGGCGAAG |
Index 704 Primer for Illumina Systems |
GAGATTCC |
Index 506 Primer for Illumina Systems |
TAATCTTA |
✔✔✔✔✔✔✔✔ | ✔✔✔✔✔✔✔✔ |
Index 7 Primers for Illumina Systems | Index 5 Primers for Illumina Systems | |||
Index 701 Primer for Illumina Systems |
ATTACTCG |
Index 502 Primer for Illumina Systems |
ATAGAGGC |
|
Index 702 Primer for Illumina Systems |
TCCGGAGA |
Index 504 Primer for Illumina Systems |
GGCTCTGA |
|
Index 703 Primer for Illumina Systems |
CGCTCATT |
Index 506 Primer for Illumina Systems |
TAATCTTA |
|
Index 704 Primer for Illumina Systems |
GAGATTCC |
Index 508 Primer for Illumina Systems |
GTACTGAC |
|
✔✔✔✔✔✔✔✔ | ✔✔✘✔✔✘✔✘ |
The following table lists some (but not all) valid index combinations that can be sequenced together:
Plex | Index 7 primers for Illumina Systems | Index 5 Primers for Illumina Systems |
2 | Index 701 and Index 702 Index 703 and Index 704 Index 705 and Index 706 Index 707 and Index 708 Index 709 and Index 710 Index 711 and Index 712 |
Any Index 5 Primer |
3 | Index 701, Index 702 and Index 703 Index 703, Index 704 and Index 705 Index 705, Index 706 and Index 707 Index 707, Index 708 and Index 709 Index 709, Index 710 and Index 711 |
Any Index 5 Primer |
4 | Index 701, Index 702, Index 703 and Index 704 Index 703, Index 704, Index 705 and Index 706 Index 705, Index 706, Index 707 and Index 708 Index 707, Index 708, Index 709 and Index 710 Index 709, Index 710, Index 711 and Index 712 |
Any Index 5 Primer |
5-12 | Any valid Index 7 4-plex combination with any other i7 Primers (as needed) | Any Index 5 Primer |
> 12 |
Any valid Index 7 4-plex combination with any other i7 primer (as needed) | Index 501, Index 502 and any other Index 5 primer (as needed) Index 503, Index 504 and any other Index 5 primer (as needed) Index 505, Index 506 and any other Index 5 primer (as needed) Index 507, Index 508 and any other Index 5 primer (as needed) |
Some other valid combinations are listed below. Choose a valid set of Index 7 primers and a valid set of Index 5 primers. Use each Index 7 primer with each i5 primer to form desired number of primer pairs for PCR amplification of desired number of libraries.
Pool of 12 samples | (1) A set of 4 Index 7 primers * A set of 3 Index 5 primers (2) A set of 3 Index 7 primers * A set of 4 Index 5 primers (3) A set of 6 Index 7 primers * A set of 2 Index 5 primers (4) A set of 12 Index 7 primers * A set of 1 Index 5 primers |
Pool of 26 samples | (1) A set of 6 Index 7 primers * A set of 4 Index 5 primers Plus any of the Index 7 primers with any other two Index 5 primers (besides the set of 4) (2) A set of 6 Index 7 primers * A set of 5 Index 5 primers Use 26 of the 30 primer pairs to amplify 26 libraries |
Each Index 5 Primer for Illumina Systems is provided in volume of 60 µl.
Index 501 Primer for Illumina Systems | 5´-AATGATACGGCGACCACCGAGATCTACACTATAGCCTA- CACTCTTTCCCTACACGACGCTCTTCCGATC-s-T-3´ |
TATAGCCT |
Index 502 Primer for Illumina Systems | 5´-AATGATACGGCGACCACCGAGATCTACACATAGAGGCA- CACTCTTTCCCTACACGACGCTCTTCCGATC-s-T-3´ |
ATAGAGGC |
Index 503 Primer for Illumina Systems | 5´-AATGATACGGCGACCACCGAGATCTACACCCTATCCTA- CACTCTTTCCCTACACGACGCTCTTCCGATC-s-T-3´ |
CCTATCCT |
Index 504 Primer for Illumina Systems | 5´-AATGATACGGCGACCACCGAGATCTACACGGCTCTGAA- CACTCTTTCCCTACACGACGCTCTTCCGATC-s-T-3´ |
GGCTCTGA |
Index 505 Primer for Illumina Systems | 5´-AATGATACGGCGACCACCGAGATCTACACAGGCGAAGA- CACTCTTTCCCTACACGACGCTCTTCCGATC-s-T-3´ |
AGGCGAAG |
Index 506 Primer for Illumina Systems | 5´-AATGATACGGCGACCACCGAGATCTACACTAATCTTAA- CACTCTTTCCCTACACGACGCTCTTCCGATC-s-T-3´ |
TAATCTTA |
Index 507 Primer for Illumina Systems | 5´-AATGATACGGCGACCACCGAGATCTACACCAGGACGTA- CACTCTTTCCCTACACGACGCTCTTCCGATC-s-T-3´ |
CAGGACGT |
Index 508 Primer for Illumina Systems | 5´-AATGATACGGCGACCACCGAGATCTACACGTACTGACA- CACTCTTTCCCTACACGACGCTCTTCCGATC-s-T-3´ |
GTACTGAC |
Where -s- indicates phosphorothioate bond.
Each Index 7 Primer for Illumina Systems is provided in a volume of 40 µl.
Index 701 Primer for Illumina Systems | 5´-CAAGCAGAAGACGGCATACGAGATCGAGTAATGTGACTG- GAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´ |
ATTACTCG |
Index 702 Primer for Illumina Systems | 5´-CAAGCAGAAGACGGCATACGAGATTCTCCGGAGTGACTG- GAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´ |
TCCGGAGA |
Index 703 Primer for Illumina Systems | 5´-CAAGCAGAAGACGGCATACGAGATAATGAGCGGTGACTG- GAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´ |
CGCTCATT |
Index 704 Primer for Illumina Systems | 5´-CAAGCAGAAGACGGCATACGAGATGGAATCTCGTGACTG- GAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´ |
GAGATTCC |
Index 705 Primer for Illumina Systems | 5´-CAAGCAGAAGACGGCATACGAGATTTCTGAATGTGACTG- GAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´ |
ATTCAGAA |
Index 706 Primer for Illumina Systems | 5´-CAAGCAGAAGACGGCATACGAGATACGAATTCGTGACTG- GAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´ |
GAATTCGT |
Index 707 Primer for Illumina Systems | 5´-CAAGCAGAAGACGGCATACGAGATAGCTTCAGGTGACTG- GAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´ |
CTGAAGCT |
Index 708 Primer for Illumina Systems | 5´-CAAGCAGAAGACGGCATACGAGATGCGCATTAGTGACTG- GAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´ |
TAATGCGC |
Index 709 Primer for Illumina Systems | 5´-CAAGCAGAAGACGGCATACGAGATCATAGCCGGTGACTG- GAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´ |
CGGCTATG |
Index 710 Primer for Illumina Systems | 5´-CAAGCAGAAGACGGCATACGAGATTTCGCGGAGTGACTG- GAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´ |
TCCGCGAA |
Index 711 Primer for Illumina Systems | 5´-CAAGCAGAAGACGGCATACGAGATGCGCGAGAGTGACTG- GAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´ |
TCTCGCGC |
Index 712 Primer for Illumina Systems | 5´-CAAGCAGAAGACGGCATACGAGATCTATCGCTGTGACTG- GAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´ |
AGCGATAG |
Where -s- indicates phosphorothioate bond.
The components in the Multiplex Oligos for Illumina Systems (Dual Index Primers) (ChIP-seq, CUT&RUN) #47538 are individually validated by the functional testing listed below and must pass rigorous quality control standards. Furthermore, each set of components is functionally validated together by construction and sequencing of indexed libraries on the Illumina Systems sequencing platform.
5´-/5Phos/GAT CGG AAG AGC ACA CGT CTG AAC TCC AGT C/ideoxyU/A CAC TCT TTC CCT ACA CGA CGC TCT TCC GAT C-s-T-3´
Quality Control Assays
Supplied in: 50 mM KCl, 5 mM NaCl, 10 mM Tris-HCl (pH 7.4 @ 25°C), 0.1 mM EDTA, 1 mM DTT, 175 µg/ml BSA, and 50% Glycerol
Quality Control Assays
Quality Control Assays
posted November 2017
revised March 2023
protocol id: 1625
Protocol Id: 1625
Next generation sequencing (NG-seq) is a high throughput method that can be used downstream of chromatin immunoprecipitation (ChIP) and Cleavage Under Targets and Release Using Nuclease (CUT&RUN) assays to identify and quantify target DNA enrichment across the entire genome. Multiplex Oligos for Illumina® (Dual Index Primers) (ChIP-seq, CUT&RUN) contains adaptors and primers that are ideally suited for multiplex sample preparation for NG-seq on the Illumina® platform (Illumina, Inc.). This kit can be used to generate up to 96 distinct, barcoded ChIP-seq or CUT&RUN DNA libraries that can be combined into a single sequencing reaction.
Each kit component must pass rigorous quality control standards, and for each new lot the entire set of reagents is functionally validated together by construction and sequencing of indexed libraries on the Illumina® sequencing platform.
This product provides enough reagents to support up to 96 DNA sequencing libraries, and must be used in combination with DNA Library Prep Kit for Illumina® (ChIP-seq, CUT&RUN) #56795.
Compatible Assay kits:
SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) #9003
SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) #9005
SimpleChIP® Plus Sonication Chromatin IP Kit #56383
ChIP-seq DNA Library Prep Kit for Illumina® (ChIP-seq, CUT&RUN) #56795
CUT&RUN Assay Kit #86652
Non-Compatible SimpleChIP® kits:
SimpleChIP® Enzymatic Chromatin IP Kit (Agarose Beads) #9002
SimpleChIP® Plus Enzymatic Chromatin IP Kit (Agarose Beads) #9004
Note: Agarose beads are blocked with sonicated salmon sperm DNA, which will contaminate DNA library preps and NG-seq.
Required Reagents:
Reagents Included:
Reagents Not Included:
The dual index primer strategy utilizes two 8 base indices within each primer. Index 7 primers contain indices that are adjacent to the P7 sequence while index 5 primers contain indices that are adjacent to the P5 sequence. Dual indexing is enabled by adding a unique index to both ends of a sample to be sequenced. Up to 96 different samples can be uniquely indexed by combining each of the 12 index 7 primers with each of the 8 index 5 primers.
Illumina® NG-seq platforms use a red laser/LED to sequence A/C and a green laser/LED to sequence G/T. For each cycle, both the red and the green channel need to be read to ensure proper image registration (i.e. A or C must be present in each cycle, and G or T must be present in each cycle). If this color balance is not maintained, sequencing the index read could fail. Please check the sequences of each index to be used to ensure that you will have signal in both the red and green channels for every cycle. See example below:
The following table lists some (but not all) valid index combinations that can be sequenced together:
Some other valid combinations are listed below. Choose a valid set of Index 7 primers and a valid set of Index 5 primers. Use each Index 7 primer with each i5 primer to form desired number of primer pairs for PCR amplification of desired number of libraries.
Each Index 5 Primer for Illumina® is provided in volume of 60 µl.
Where -s- indicates phosphorothioate bond.
Each Index 7 Primer for Illumina® is provided in a volume of 40 µl.
Where -s- indicates phosphorothioate bond.
The components in the Multiplex Oligos for Illumina® (Dual Index Primers) (ChIP-seq, CUT&RUN) #47538 are individually validated by the functional testing listed below and must pass rigorous quality control standards. Furthermore, each set of components is functionally validated together by construction and sequencing of indexed libraries on the Illumina® sequencing platform.
5´-/5Phos/GAT CGG AAG AGC ACA CGT CTG AAC TCC AGT C/ideoxyU/A CAC TCT TTC CCT ACA CGA CGC TCT TCC GAT C-s-T-3´
Quality Control Assays
Supplied in: 50 mM KCl, 5 mM NaCl, 10 mM Tris-HCl (pH 7.4 @ 25°C), 0.1 mM EDTA, 1 mM DTT, 175 µg/ml BSA, and 50% Glycerol
Quality Control Assays
Quality Control Assays
posted November 2017
revised April 2022
protocol id: 1625
Protocol Id: 2805
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