Dna 5k rna charge variant assay labchip

Manufactured by PerkinElmer

The DNA 5K/RNA/Charge Variant Assay LabChip is a microfluidic-based system designed to perform automated analysis of DNA, RNA, and charge variants. The device utilizes electrophoretic separation of biomolecules and fluorescence detection to provide quantitative data on size, concentration, and charge properties.

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Lab products found in correlation

Labchip gxii touch ht, by PerkinElmer (2 mentions) Hiseq platform, by Illumina (1 mentions) Truseq stranded mrna kit, by Illumina (1 mentions) Superscript 4 reverse transcriptase, by Thermo Fisher Scientific (1 mentions) Cbot 2 system, by Illumina (1 mentions) Trizol reagent, by Thermo Fisher Scientific (1 mentions)

2 protocols using dna 5k rna charge variant assay labchip

RNA-seq Library Preparation and Sequencing

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The integrity and concentration of the extracted RNA was assessed on the LabChip GXII Touch HT using the RNA Assay and the DNA 5K/RNA/Charge Variant Assay LabChip (PerkinElmer). Sequencing mRNA libraries were constructed from 500 ng of total RNA using the Illumina TruSeqStranded mRNA kit (Illumina). cDNA was synthesized using Superscript IV Reverse Transcriptase (Thermo Fisher) and amplified for 15 cycles after ligating with TruSeq RNA Combinatorial Dual-Index adapters. Clonal amplification and cluster generation was performed using Illumina’s cBot 2 System. Sequencing libraries were run on Illumina HiSeq platforms using 75 bp (93% of samples) or 150 bp (7% of samples) paired-end reads at the Clinical Genomics Laboratory, Sidra Medicine. We targeted a coverage of 20 M reads per sample. Obtained coverage was 18.4 M (s.d. 4.7 M).

Roelands J., Kuppen P.J., Ahmed E.I., Mall R., Masoodi T., Singh P., Monaco G., Raynaud C., de Miranda N.F., Ferraro L., Carneiro-Lobo T.C., Syed N., Rawat A., Awad A., Decock J., Mifsud W., Miller L.D., Sherif S., Mohamed M.G., Rinchai D., Van den Eynde M., Sayaman R.W., Ziv E., Bertucci F., Petkar M.A., Lorenz S., Mathew L.S., Wang K., Murugesan S., Chaussabel D., Vahrmeijer A.L., Wang E., Ceccarelli A., Fakhro K.A., Zoppoli G., Ballestrero A., Tollenaar R.A., Marincola F.M., Galon J., Khodor S.A., Ceccarelli M., Hendrickx W, & Bedognetti D. (2023). An integrated tumor, immune and microbiome atlas of colon cancer. Nature Medicine, 29(5), 1273-1286.

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Exon Skipping Analysis of Muscle Biopsy

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Cryosectioned tissue sections from muscle biopsy samples were treatment-blinded and samples homogenized in TRIzol reagent (Thermo Fisher Scientific, Waltham, MA) to isolate total RNA. RNA quality was evaluated using a DNA 5K/RNA/Charge Variant Assay LabChip and LabChip GXII Touch HT (PerkinElmer, Inc., Waltham, MA). A detailed description of the methodology used for exon skipping analysis, including patient genotypes, is shown in table e-1 and percentage of exon 53 skipping in figure e-1 (https://doi.org/10.5061/dryad.g003051).

Frank D.E., Schnell F.J., Akana C., El-Husayni S.H., Desjardins C.A., Morgan J., Charleston J.S., Sardone V., Domingos J., Dickson G., Straub V., Guglieri M., Mercuri E., Servais L, & Muntoni F. (2020). Increased dystrophin production with golodirsen in patients with Duchenne muscular dystrophy. Neurology, 94(21), e2270-e2282.

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