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Ampliseq cd indexes

Manufactured by Illumina
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The AmpliSeq CD Indexes are a set of barcoding indexes designed for use with Illumina's AmpliSeq technology. They enable the multiplexing of samples to increase throughput and efficiency in targeted sequencing workflows.

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Lab products found in correlation

Tapestation 4200, by Agilent Technologies (1 mentions) High sensitivity d1000 screentape assay, by Agilent Technologies (1 mentions) Miseq system, by Illumina (1 mentions) Qubit 3.0 fluorometer, by Thermo Fisher Scientific (1 mentions) Truseq dual index sequencing primers, by Illumina (1 mentions) Ampliseq custom dna panel, by Illumina (1 mentions) Qubit dsdna hs assay, by Thermo Fisher Scientific (1 mentions) Truseq custom amplicon low input kit, by Illumina (1 mentions) Miseq reagent micro kit v2, by Illumina (1 mentions) Miseq sequencing platform, by Illumina (1 mentions) Basespace application, by Illumina (1 mentions)

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AmpliSeq CD Indexes Set A (2 citations)

2 protocols using ampliseq cd indexes

1

UCP1 Genetic Variant Analysis in MetS

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High quality DNA was selected for NGS sequencing. We performed targeted panel sequencing to identify genetic variants within the UCP1 gene for MetS patients and controls. To build amplicon sequencing libraries for the coding region of the UCP1 gene, we used TruSeq Custom Amplicon Low Input Kit (Illumina, San Diego, CA, USA) with TruSeq Dual Index Sequencing Primers (Illumina, San Diego, CA, USA). For 3′UTR and 5′UTR regions of the UCP1 gene, we used AmpliSeq Illumina Custom DNA Panel (Illumina, San Diego, CA, USA) with AmpliSeq CD Indexes (Illumina, San Diego, CA, USA). The quality and quantity of the purified libraries was assessed by Qubit 3.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) using Qubit dsDNA HS Assay (ThermoFisher Scientific, Waltham, MA, USA) and TapeStation 4200 (Agilent Technologies, Santa Clara, CA, USA) using High Sensitivity D1000 ScreenTape Assay (Agilent Technologies, Santa Clara, CA, USA). Only high-quality libraries were sequenced on the MiSeq System (Illumina, San Diego, CA, USA) using the V2 Illumina Sequencing Kit 500 (Illumina, San Diego, CA, USA).
Andrzejczak A., Witkowicz A., Kujawa D., Skrypnik D., Szulińska M., Bogdański P., Łaczmański Ł, & Karabon L. (2023). NGS Sequencing Reveals New UCP1 Gene Variants Potentially Associated with MetS and/or T2DM Risk in the Polish Population—A Preliminary Study. Genes, 14(4), 789.
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2

Targeted Cancer Gene Sequencing

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Samples with sufficient material and negative for our targeted testing protocol had their DNA constructed into DNA-sequencing libraries using the Illumina Ampliseq Comprehensive DNA Focus Panel Kit (Illumina, San Diego, CA), following the manufacturer’s guidelines utilizing the Illumina Library PLUS Kit (Illumina, San Diego, CA). Sequencing adapters were ligated to the fragments to allow for amplification DNA followed by a quality control validation step to ensure proper adapter ligation. Samples were next hybridized to Ampliseq CD indexes (Illumina, San Diego, CA) used to enrich for 52 cancer-associated genes outlined in the manufacturer’s documentation prior to amplification. Paired-end DNA-sequencing was performed using the Illumina MiSeq sequencing platform and the MiSeq Reagent Micro Kit V2 (Illumina, San Diego, CA). Raw sequencing data was converted to the fastq format and analyzed using the BaseSpace application (Illumina, San Diego, CA), with DNA-Seq Alignment V. 1.0.0. Variant calling was completed in BaseSpace using the Isaac Variant Caller.
Ryall S., Zapotocky M., Fukuoka K., Nobre L., Guerreiro-Stucklin A., Bennett J., Siddaway R., Li C., Pajovic S., Arnoldo A., Kowalski P.E., Johnson M., Sheth J., Lassaletta A., Tatevossian R.G., Orisme W., Qaddoumi I., Surrey L.F., Li M.M., Waanders A.J., Gilheeney S., Rosenblum M., Bale T., Tsang D.S., Laperriere N., Kulkarni A., Ibrahim G.M., Drake J., Dirks P., Taylor M.D., Rutka J.T., Laughlin S., Shroff M., Shago M., Hazrati L.N., D’Arcy C., Ramaswamy V., Bartels U., Huang A., Bouffet E., Karajannis M.A., Santi M., Ellison D.W., Tabori U, & Hawkins C. (2020). Integrated molecular and clinical analysis of 1,000 pediatric low-grade gliomas. Cancer cell, 37(4), 569-583.e5.
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