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Autopure ls system

Manufactured by Qiagen
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Sourced in Germany, Spain, United States

The Autopure LS system is a DNA extraction and purification instrument designed for automated high-throughput processing of biological samples. It utilizes magnetic bead-based technology to efficiently extract and purify DNA from a variety of sample types.

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Lab products found in correlation

Qiaamp 96 dna blood kit, by Qiagen (3 mentions) Affymetrix axiom exome genotyping array, by Thermo Fisher Scientific (3 mentions) Puregene chemistry, by Qiagen (3 mentions) Taqman snp genotyping assay, by Thermo Fisher Scientific (2 mentions) Massarray typer v4, by Agena (2 mentions) Iplex gold chemistry, by Agena (2 mentions) Massarray system, by Agena (2 mentions) Elution buffer, by Qiagen (2 mentions) Picogreen, by Thermo Fisher Scientific (2 mentions) Dneasy tissue kit, by Qiagen (2 mentions) Qiaamp dna blood midi kit, by Qiagen (2 mentions) Anaprep, by BioChain (2 mentions) Viia7 real time pcr machine, by Thermo Fisher Scientific (1 mentions) Iscan reader, by Illumina (1 mentions) Ez dna methylation gold kit, by Zymo Research (1 mentions) Humanmethylation450 beadchip, by Illumina (1 mentions) Illustra genomiphi v2 dna amplification kit, by GE Healthcare (1 mentions) Bn 2 system, by Siemens (1 mentions) Taqman assay, by Thermo Fisher Scientific (1 mentions) Big dye terminator abi prism kit, by Thermo Fisher Scientific (1 mentions)

20 protocols using autopure ls system

1

Automated Saliva DNA Extraction

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Saliva samples were stored at room temperature and batched for DNA extraction. We performed automated DNA isolation using Autopure LS system (Qiagen) and Puregene chemistry (Gentra Systems) according to the manufacturer’s protocols. DNA yield was quantified using 1:10 diluted DNA performed in triplicate by quantitative real-time PCR using absolute quantification on an ABI 7900 Prism real-time instrument and extracted DNA was aliquoted and stored at -20°C until genotyping.
Marcotte E.L., Pankratz N., Amatruda J.F., Frazier A.L., Krailo M., Davies S., Starr J.R., Lau C.C., Roesler M., Langer E., Hallstrom C., Hooten A.J, & Poynter J.N. (2017). Variants in BAK1, SPRY4, and GAB2 are associated with pediatric germ cell tumors: a report from the Children’s Oncology Group. Genes, chromosomes & cancer, 56(7), 548-558.
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2

Idiopathic Scoliosis Family Study

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A three-generation family (Fig 1) with a high burden of idiopathic scoliosis participated in the study. All participating family members (n = 15) were blood-sampled and radiographed. All but one (I:II) were examined by a spine surgeon; however this individual had no scoliosis on radiographs. Individuals with a curve angle of 10 degrees or more, as measured by the Cobb method [14 ], were diagnosed with scoliosis. No one had any signs of a non-idiopathic scoliosis and all had an onset in adolescence, i.e. after the age of ten years (S1 Table). DNA was extracted from blood either by a salt precipitation method on the Autopure LS system (Qiagen, Hilden, Germany) or the QIAamp 96 DNA blood kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
Einarsdottir E., Grauers A., Wang J., Jiao H., Escher S.A., Danielsson A., Simony A., Andersen M., Christensen S.B., Åkesson K., Kou I., Khanshour A.M., Ohlin A., Wise C., Ikegawa S., Kere J, & Gerdhem P. (2017). CELSR2 is a candidate susceptibility gene in idiopathic scoliosis. PLoS ONE, 12(12), e0189591.
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3

IRGM SNP Genotyping by TaqMan Assays

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DNA was extracted from blood using the Autopure LS system (Qiagen) and IRGM SNPs were genotyped using fluorescence-based allelic TaqMan SNP Genotyping Assays (Applied Biosystems, Life Technologies, Grand Island, NY). TaqMan SNP Genotyping Assays were used, as follows: rs10065172, Assay ID C__30593568_10; rs13361189, Assay ID C__31986315_10; and rs9637876, custom assay. Polymerase chain reactions were performed using 30 ng of genomic DNA isolated from whole blood in a 10ul reaction volume using an Applied Biosystems ViiA-7 Real time PCR machine.
Ajayi T., Rai P., Shi M., Gabor K.A., Karmaus P.W., Meacham J.M., Katen K., Madenspacher J.H., Schurman S.H, & Fessler M.B. (2023). Race-specific association of an IRGM risk allele with cytokine expression in human subjects. Scientific Reports, 13, 12911.
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4

Genotyping and Quality Control Procedures

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Genotyping and quality control procedures have also been described elsewhere(Velez Edwards et al., 2014 (link)). Briefly, DNA samples were isolated from whole blood using the Autopure LS system (QIAGEN Inc., Valencia, CA). We genotyped DNA from the 492 participants using the custom Affymetrix Axiom Exome Genotyping Array (Affymetrix Inc., Santa Clara, CA). The genomic DNA samples were processed according to standard Affymetrix procedures for processing of the assay and genotype calling was performed using the Affymetrix Power Tools software (APT, Affymetrix Inc., Santa Clara, CA).
Hellwege J.N., Russell S.B., Williams S., Edwards T.L, & Velez Edwards D.R. (2018). Gene-based evaluation of low frequency variation and genetically predicted gene expression impacting risk of keloid formation. Annals of human genetics, 82(4), 206-215.
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5

Genetic Profiling of Osteoporosis Risk

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We recruited AIS subjects from six hospitals in Sweden and one in Denmark as with previously described inclusion criteria22 (link)–25 (link). We recruited control subjects from the Osteoporosis Prospective Risk Assessment cohort and PEAK-25 cohort26 (link),27 (link). Dual-energy X-ray absorptiometry (DXA) scan was performed in both cohorts and subjects with any sign of scoliosis on DXA were excluded. We extracted genomic DNA from blood or saliva using the QIAamp 96 DNA Blood Kit and Autopure LS system (Qiagen, Hilden, Germany). We used iPLEX Gold chemistry and MassARRAY system (Agena Bioscience, CA, USA) for genotyping. Two persons checked genotype calls using the MassARRAY Typer v4.0 Software (Agena Bioscience).
Ogura Y., Takeda K., Kou I., Khanshour A., Grauers A., Zhou H., Liu G., Fan Y.H., Zhou T., Wu Z., Takahashi Y., Matsumoto M., Einarsdottir E., Kere J., Huang D., Qiu G., Xu L., Qiu Y., Wise C.A., Song Y.Q., Wu N., Su P., Gerdhem P., Watanabe K, & Ikegawa S. (2018). An international meta-analysis confirms the association of BNC2 with adolescent idiopathic scoliosis. Scientific Reports, 8, 4730.
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6

Genetic Polymorphisms and Pollution Response

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Blood samples were collected from 2,996 EPR participants for whom health data were available, and total genomic DNA was isolated using Qiagen’s Autopure LS system. DNA was genotyped for four genes in the TLR4 pathway. Samples were genotyped using Illumina multiplexing and/or TaqMan SNP Genotyping Assays (Applied Biosystems): rs8177374, TIRAP; rs4986791, TLR4; rs2569190, CD14; and rs1800629, TNFa. Our analyses defined and used individuals with one (heterozygous) or both (homozygous minor) copies of the minor allele as carriers of the SNP. Individuals with both major alleles are WT. Based on genotyping results, subjects were divided into three responder-types:

Hyper-responders: [carriers of CD14 and TNFa minor SNPs] and [WT for TLR4 and TIRAP SNPs];

Hypo-responders: [carriers of TLR4 and/or TIRAP minor SNPs] and [WT for CD14 and TNFa SNPs];

Neither-responders: All others.

Hyper- and hypo-responders were anticipated to have over- and under-reactive responses to air pollution exposure, respectively. Neither-responders were expected to have intermediate responses to pollution.
Schurman S.H., Bravo M.A., Innes C.L., Jackson WB I.I., McGrath J.A., Miranda M.L, & Garantziotis S. (2018). Toll-like Receptor 4 Pathway Polymorphisms Interact with Pollution to Influence Asthma Diagnosis and Severity. Scientific Reports, 8, 12713.
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7

Affymetrix Exome Genotyping Array Protocol

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All DNA samples were isolated from whole blood using the Autopure LS system (QIAGEN Inc., Valencia, CA). Genomic DNA was quantitated via an ND-8000 spectrophotometer and DNA quality was evaluated via gel electrophoresis. We genotyped DNA from the 272 participants using the custom Affymetrix Axiom Exome Genotyping Array (Affymetrix Inc., Santa Clara, CA). The genomic DNA samples were processed according to standard Affymetrix procedures for processing of the assay. The data were processed for genotype calling using the Affymetrix Power Tools software (APT, Affymetrix Inc., Santa Clara, CA).
Hellwege J.N., Velez Edwards D.R., Acra S., Chen K., Buchowski M.S, & Edwards T.L. (2017). Association of gene coding variation and resting metabolic rate in a multi-ethnic sample of children and adults. BMC obesity, 4, 12.
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8

Automated DNA Extraction from Blood

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To extract the genomic DNA, the whole peripheral blood samples were processed with an Autopure LS system (Qiagen, Germany) for automated nucleotide purification following the manufacturer’s instructions. We omitted the RNase treatment, measured the concentration of the double-stranded DNA with PicoGreen (Life Technologies, Carlsbad, CA), and adjusted the concentration of the DNA to 200 ng/μL in Elution Buffer (Qiagen, Germany).
Motoike I.N., Matsumoto M., Danjoh I., Katsuoka F., Kojima K., Nariai N., Sato Y., Yamaguchi-Kabata Y., Ito S., Kudo H., Nishijima I., Nishikawa S., Pan X., Saito R., Saito S., Saito T., Shirota M., Tsuda K., Yokozawa J., Igarashi K., Minegishi N., Tanabe O., Fuse N., Nagasaki M., Kinoshita K., Yasuda J, & Yamamoto M. (2014). Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population. BMC Genomics, 15(1), 673.
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9

DNA Methylation Analysis of Whole Blood

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DNA was isolated from whole blood using the AutoPure LS system (Qiagen, Inc.), and then bisulfite-converted using the EZ DNA Methylation Gold kit (Zymo, Irvine, CA). To quantify DNA methylation at each site, we used beta values, as determined with the HumanMethylation450 BeadChip (Illumina, Inc.), which targets over 485,000 CpG sites at single-nucleotide resolution, and the iScan Reader (Illumina, Inc.). The ChAMP program (Morris et al., 2014 (link)) in BioConductor was used to initially process the data, using the default import settings. These included removal of methylation probes with a detection p-value less than 0.01, a beadcount less than three, and on the X or Y chromosome. To adjust for the two distinct Infinium assays that are simultaneously measured on this microarray (Infinium I and Infinium II), we used the champ.norm command with BMIQ normalization (Teschendorff et al., 2013 (link)). The BMIQ-normalized data was used for all statistical analysis. Methylation sites with nearby SNPs (as defined by Illumina, dbSNP137, version 2) with a minor allele frequency greater than 0.05 in any population were not included in our results.
Howard T.D., Hsu F.C., Chen H., Quandt S.A., Talton J.W., Summers P, & Arcury T.A. (2016). Changes in DNA Methylation over the growing season differ between North Carolina farmworkers and non-farmworkers. International archives of occupational and environmental health, 89(7), 1103-1110.
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10

Genome-wide genotyping of blood and fibroblast DNA

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All DNA samples were isolated from whole blood or from fibroblasts using the Autopure LS system (QIAGEN Inc., Valencia, CA).
Genomic DNA was quantitated via an ND-8000 spectrophotometer and DNA quality was evaluated via gel electrophoresis. We genotyped DNA from the 494 participants using the custom Affymetrix Axiom Exome Genotyping Array (Affymetrix Inc., Santa Clara, CA). The genomic DNA samples were processed according to standard Affymetrix procedures for processing of the assay. The data were processed for genotype calling using the Affymetrix Power Tools software (APT, Affymetrix Inc., Santa Clara, CA).
Velez Edwards D.R., Tsosie K., Williams S.M., Edwards T.L, & Russell S.B. (2014). Admixture mapping identifies a locus at 15q21.2-22.3 associated with keloid formation in African Americans. Human genetics, 133(12), 1513-1523.
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