Quickgene 800

Manufactured by Fujifilm

Sourced in Japan

The QuickGene-800 is a DNA/RNA extraction system designed for high-throughput nucleic acid purification. It utilizes a proprietary silica-based membrane technology to efficiently extract DNA and RNA from a variety of sample types. The system is capable of processing up to 96 samples simultaneously, making it suitable for applications requiring rapid and reliable nucleic acid extraction.

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Lab products found in correlation

Taqman 5 exonuclease assay, by Thermo Fisher Scientific (3 mentions) Steponeplus real time pcr system, by Thermo Fisher Scientific (3 mentions) Trizol, by Thermo Fisher Scientific (2 mentions) Luminex multi analyzer profiling system, by Thermo Fisher Scientific (1 mentions) Lab type sso one lambda typing kit, by Thermo Fisher Scientific (1 mentions) Stepone real time pcr system, by Thermo Fisher Scientific (1 mentions) Stepone software v2, by Thermo Fisher Scientific (1 mentions) Taqman snp genotyping allelic discrimination method, by Thermo Fisher Scientific (1 mentions) Quickgene rna cultured cell kit, by Kurabo (1 mentions) Sybr green, by Takara Bio (1 mentions) Revertra ace, by Toyobo (1 mentions) Lightcycler 480, by Roche (1 mentions) Dna extractor wb rapid kit, by Fujifilm (1 mentions) Faststart universal probe master, by Roche (1 mentions) Taqman gene expression assay, by Thermo Fisher Scientific (1 mentions) Quickgene dna whole blood kit, by Fujifilm (1 mentions)

12 protocols using quickgene 800

Genetic Variant Analysis of PTPN22 in Japanese

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Genomic DNA from patients and controls was isolated from whole blood samples using QuickGene-800 assays (Fujifilm, Tokyo, Japan).
We evaluated nine SNPs (rs1217412, rs1217388, rs2476601, rs1217407, rs3765598, rs33996649, rs2488458, rs3789612, and rs2488457) spanning a 58 kb region in the PTPN22 gene. The SNPs were selected from previous reports14 (link)15 (link)19 (link)22 (link) and had minor allele frequencies of >5% according to HapMap Japanese data (http://hapmap.ncbi.nlm.nih.gov/). Genotyping of all SNPs was performed with a TaqMan 5′ exonuclease assay using primers supplied by Applied Biosystems (Foster City, CA, USA). The probe’s fluorescence signals were detected with the StepOne Plus Real-Time PCR System (Applied Biosystems) according to the manufacturer’s instructions.

Umemura T., Joshita S., Yamazaki T., Komatsu M., Katsuyama Y., Yoshizawa K., Tanaka E, & Ota M. (2016). Genetic Association of PTPN22 Polymorphisms with Autoimmune Hepatitis and Primary Biliary Cholangitis in Japan. Scientific Reports, 6, 29770.

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HLA and KIR Genotyping for Immune Interactions

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Genomic DNA from all participants was extracted from whole-blood samples using QuickGene-800 assays (Fujifilm, Tokyo, Japan). We genotyped HLA-A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 as reported previously.²⁴ (link) HLA-A3 and -A11, HLA-Bw4, HLA-B Bw4-80Ile, HLA-B Bw4-80Thr, HLA-C1, and HLA-C2 KIR ligands were assigned based on the amino acid residues of the HLA-A, HLA-B, and HLA-C alleles, as described previously.²⁵ (link)^,²⁶ (link) KIR genotyping was performed using PCR with sequence-specific primers.²⁷ (link) HLA typing was combined with KIR typing to stratify patients according to predicted KIR-ligand interactions and binding affinities. The selected KIR-HLA pairs were KIR2DL1/2DS1-HLA-C2, 2DL2/2DS2-HLA-C1, 3DL1/3DS1-HLA-Bw4, and 3DL2-HLA-A3 and -A11.

Umemura T., Joshita S., Saito H., Yoshizawa K., Norman G.L., Tanaka E, & Ota M. (2019). KIR/HLA genotypes confer susceptibility and progression in patients with autoimmune hepatitis. JHEP Reports, 1(5), 353-360.

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HLA and KIR Genotyping from Whole Blood

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Genomic DNA from patients was isolated from whole blood samples using QuickGene-800 assays (Fujifilm, Tokyo, Japan). HLA-Bw4, HLA-C1, HLA-C2, and KIR genes were typed by using PCR with sequence-specific primers [17 (link), 18 (link)]. The KIR genotype profiles were assigned to the A/A or B/x genotypes as defined previously [19 (link)]. Genotypes for the centromeric (Cen) and telomeric (Tel) parts of the KIR locus were determined based on the presence or absence of B haplotype-defining KIR genes (i.e. A/A, A/B, or B/B) as earlier described in detail [20 (link)].

Saito H., Hirayama A., Umemura T., Joshita S., Mukawa K., Suga T., Tanaka E, & Ota M. (2018). Association between KIR-HLA combination and ulcerative colitis and Crohn’s disease in a Japanese population. PLoS ONE, 13(4), e0195778.

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Genetic Profiling of Autoimmune Hepatitis

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Genomic DNA from patients and controls was isolated from whole blood samples using QuickGene-800 assays (Fujifilm, Tokyo, Japan). HLA typing in AIH patients was carried out using a Luminex multi-analyzer profiling system with a LAB type SSO One Lambda typing kit (One Lambda, Inc. Canoga Park, CA). HLA genotypes were determined by sequence-based typing, as earlier described^{32 (link)}. The rs9277534 SNP in the HLA-DP locus was genotyped using a TaqMan 5′ exonuclease assay (Applied Biosystems, Tokyo, Japan). The polymerase chain reaction (PCR) was performed with the StepOne Plus Real-Time PCR System (Applied Biosystems) following the manufacturer’s instructions. Pairwise linkage disequilibrium patterns between HLA-DPB1 alleles and rs9277534 (A/G) were assessed by the Arlequin program (ver. 3.5.2.2) (http://lgb.unige.ch/arlequin/)^{33 (link)}. The linkage of rs9277534 to HLA-DPB1 was examined in all AIH patients pursuant to a previous report^{23 (link)}.

Yamazaki T., Umemura T., Joshita S., Yoshizawa K., Tanaka E, & Ota M. (2018). A cis-eQTL of HLA-DPB1 Affects Susceptibility to Type 1 Autoimmune Hepatitis. Scientific Reports, 8, 11924.

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Molecular Diagnosis of FOXL2 Mutations

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Blood samples were collected from all the individuals in this family, and genomic DNA was extracted from the leukocytes of peripheral venous blood using Automatic Nucleic Acid Isolation System (QuickGene 800, Fujifilm Life Science, Tokyo, Japan). For mutation analysis, PCR amplification of the genomic fragments encompassing FOXL2 coding regions was performed using overlapping sets of primers [16] . Purified PCR products were sequenced in both directions on an ABI 3730 DNA sequencer (Applied Biosystems PerkinElmer) to confirm the mutations. The mutation was analysed using Finch TV software, and the sequences were compared with the reference from the GenBank database (NM_023067). The mutation nomenclature was based on the Human Genome Variation Society guidelines (http://varnomen.hgvs.org/ recommendations/general/). The possible pathogenicity of the mutation were predicted using SIFT [11] and MutationTaster [17] .

Li F., Chai P., Fan J., Wang X., Lu W., Li J., Ge S., Jia R., Zhang H, & Fan X. (2018). A Novel FOXL2 Mutation Implying Blepharophimosis-Ptosis-Epicanthus Inversus Syndrome Type I. Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology, 45(1).

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Genotyping AGER Gene Variants

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The genomic DNA samples were extracted from the venous blood of all patients using QuickGene800 (FUJI FILM, Tokyo, Japan). Allele discrimination was performed for the rs2070600, rs1800625, and rs2853807 SNPs of the AGER with the StepOne Real-Time PCR System (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions. After thermal cycling, genotype data were automatically acquired and analyzed using sequence detection software (StepOne Software v2.3, Thermo Fisher Scientific).

Kinjo T., Kitaguchi Y., Droma Y., Yasuo M., Wada Y., Ueno F., Ota M, & Hanaoka M. (2020). The Gly82Ser mutation in AGER contributes to pathogenesis of pulmonary fibrosis in combined pulmonary fibrosis and emphysema (CPFE) in Japanese patients. Scientific Reports, 10, 12811.

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Genetic Profiling of KIR-HLA Interactions

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Genomic DNA from patients and controls was isolated from whole blood samples using QuickGene-800 assays (Fujifilm, Tokyo, Japan). HLA-Bw4, -C1, and -C2 genotyping [41 (link)] and KIR genotyping [42 (link)] were performed using PCR with sequence-specific primers. HLA typing was combined with KIR typing to stratify patients according to predicted KIR-ligand interactions and binding affinities. These KIR-HLA pairs were KIR2DL1/2DS1-HLA-C2, 2DL2/3/2DS2-HLA-C1, and 3DL1/3DS1-HLA-Bw4. Genotyping of rs2596542 and rs1051792 in the MICA gene was performed using the TaqMan SNP genotyping allelic discrimination method (Applied Biosystems, Foster City, CA). The rs2596542 has been associated with HCV-induced HCC in a GWAS [22 (link)], and rs1051792 corresponds to a methionine/valine polymorphism at amino acid 129 of MICA, with the methionine allele as a strong binder to NKG2D [43 (link)]. Both SNPs had minor allele frequencies of >5%. All genotyping was blinded to clinical variables.

Saito H., Umemura T., Joshita S., Yamazaki T., Fujimori N., Kimura T., Komatsu M., Matsumoto A., Tanaka E, & Ota M. (2018). KIR2DL2 combined with HLA-C1 confers risk of hepatitis C virus-related hepatocellular carcinoma in younger patients. Oncotarget, 9(28), 19650-19661.

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Developmental expression analysis of Fgf18

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Total RNA of the spinal cord and the diaphragm of C57BL/6 J and Fgf18−/− mice at different embryonic and postnatal days were isolated using Trizol (Thermo Fisher Scientific) or QuickGene RNA cultured cell kit (Kurabo) on QuickGene-800 (FUJIFILM). First strand cDNA was synthesized with ReverTra Ace (Toyobo). cDNA was quantified in triplicates using SYBR Green (Takara) on Light Cycler 480 (Roche). The mRNA levels were normalized for that of Gapdh. Primer sequences are shown in Supplementary Table 1.

Ito K., Ohkawara B., Yagi H., Nakashima H., Tsushima M., Ota K., Konishi H., Masuda A., Imagama S., Kiyama H., Ishiguro N, & Ohno K. (2018). Lack of Fgf18 causes abnormal clustering of motor nerve terminals at the neuromuscular junction with reduced acetylcholine receptor clusters. Scientific Reports, 8, 434.

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Genomic DNA Extraction and Genotyping

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Genomic DNA was extracted from whole blood samples using a DNA Extractor WB-Rapid Kit (Wako, Osaka, Japan) or a Quick Gene DNA Whole Blood Kit (Fujifilm, Tokyo, Japan) with a Quick Gene-800 (Fujifilm) according to the manufacturer's protocol.
The polymorphic regions were amplified with a Taqman SNP genotyping assay with a 7500 Real-Time PCR System using 10 ng genomic DNA in a 20 µL reaction mixture containing 2× FastStart Universal Probe Master (Roche, Mannheim, Germany) and forward and reverse primers, encompassing the polymorphic sites (T/C at rs3749117 and G/C at rs35771982). The primers were predesigned by Taq-Man Gene Expression Assays (Applied Biosystems) (Assay IDs, C_25805618_10 and C_25621628_10, respectively). The amplification protocol consisted of initial denaturation at 95°C for 2 min, followed by 35 cycles of denaturation at 95°C for 30 sec, annealing for 30 sec at the appropriate temperature for the primer pair, extension at 72°C for 30 sec, and final extension at 72°C for 5 min.

Si N.V., Fujioka D., Watanabe K., Watanabe Y., Watanabe K., Nakamura K., Yamaguchi K., Uematsu M, & Kugiyama K. (2016). Phospholipase A2 Receptor Gene Polymorphisms Alter its Functions and Present a Genetic Risk of an Increased Intima-Media Thickness of the Carotid Artery. Journal of Atherosclerosis and Thrombosis, 23(10), 1227-1241.

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Desiccation-based DNA Extraction from Biofilms

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The frozen biofilm suspension and lake water (1 mL) samples were placed in 1.5 mL Eppendorf tubes. The samples were dried in a desiccator under a vacuum for 12 h. The dried biofilm and the lake water residue were used for DNA extraction with QuickGene (QuickGene 800; Fujifilm, Tokyo, Japan) according to the manufacturer's instructions. A negative control without a sample was also prepared from the vacuuming step to check for contamination from the reagents and cross-contamination among the samples.

Kurniawan A, & Yamamoto T. (2019). Accumulation of NH4+ and NO3− inside Biofilms of Natural Microbial Consortia: Implication on Nutrients Seasonal Dynamic in Aquatic Ecosystems. International Journal of Microbiology, 2019, 6473690.

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