Notes: The authors purified ctDNA from 1ml plasma using the Maxwell® RSC ccfDNA Plasma Kit with the Maxwell® RSC Instrument. Cell line mismatch repair deficiency was confirmed by the MSI Analysis System, Version 1.2. Cell line authentication was performed using the Cell ID™ and GenePrint® 10 Systems. DNA from cultured and treated cells were purified with the Wizard® SV and SV 96 Genomic DNA Purification Systems. Cetuximab-treated cells were measured for viability with the CellTiter-Glo® Luminescent Cell Viability Assay. (4777)

Notes: The authors extracted genomic DNA from bacteria using the Wizard® Genomic DNA Purification Kit and quantified using the QuantiFluor® dsDNA System. The DNA was made into libraries and sequenced with an Illumina HiSeq 2000. (4805)

Notes: The authors extracted bacterial DNA from 3ml LB broth using the Wizard® Genomic 4 DNA Purification Kit and quantified with the QuantiFluor® dsDNA System prior to sequencing on an Illumina HiSeq 2000. (4796)

Notes: The authors identified a bacterial strain that can use the toxin 3-nitropropionic acid (3NPA) as its sole carbon and nitrogen sources and cloned the genes that encode the enzymes responsible for the initial steps in the 3NPA degradation pathway. The Pseudomonas library used to clone these genes was created using genomic DNA isolated using the Wizard^® SV Genomic DNA Purification System. Closely related genes were amplified from other bacterial species for phylogenetic analysis. PCRs were performed using the GoTaq^® Hot Start Polymerase. (4164)

Notes: These authors studied the formation of centrioles in Drosophila spermatids. Genomic DNA was extracted from whole flies using the Wizard^® SV Genomic DNA Purification System. The DNA was then subjected to PCR, purified and sequenced. RNA was purified from whole flies using the SV Total RNA Isolation System. After RNA extraction, the samples were used in RT-PCR. (4064)

Notes: This study examined the genotype-phenotype correlation of the two major UGT isoforms, UGT1A1 and UGT1A6, involved in resveratrol metabolism. Genomic DNA was isolated from 30mg human liver tissue samples (normal and metastatic) using the Wizard^® SV Genomic DNA Purification System. The purified DNA was eluted with 65°C water and 200–400ng of eluted DNA was used in a PCR-RFLP UGT1A6 genotyping assay. Amplification was carried out using PCR Master Mix in a final volume of 50µl, and the amplimers digested with appropriate restriction enzymes. (4018)

Notes: This study examined the effects of folic acid supplementation on the offspring of pregnant rats fed a protein-restricted diet. Genomic DNA was extracted from rat adipose tissue using the Wizard^® SV Genomic DNA Purification System. The purified DNA was then incubated with methylation-sensitive restriction enzymes and then used in real-time PCR. (4066)

Notes: In this paper, the role of the KAE1/osgep/ygjD gene family, a universally conserved gene set without an assigned function, was investigated in yeast and Caenorhabditis elegans. Genomic DNA was isolated from Saccharomyces cerevisiae using the Wizard^® SV Genomic DNA Purification System. This purified DNA was then used in PCR. (4065)

Notes: The authors were interested in testing platinum (Pt) anticancer drugs that do not bind to DNA to see how they worked in cisplatin- and carboplatin-resistant cells. The human ovarian cancer cells, A2780 and A2780/C30, were seeded in T75 cm² flasks with 1.0 × 10⁷ cells. After 24 hours, the cells were treated with 0, 10, 20, 30 and 50µM Pt compounds for 24 hours. Medium was removed, the cells washed, trypsinized and centrifuged. Genomic DNA was isolated using the Wizard^® SV Genomic DNA Purification System and quantitated using absorbance at 260nm. This DNA was using in DNA-Pt binding assessment. (4019)

Notes: To examine radiation-bystander responses in neonatal mouse cerebellum, heterozygous radiosensitive Patched-1 (Ptch1) mice were exposed to either whole body (WB) x-rays or shielded head/rest of body (SH) irradiation. Genomic DNA was isolated from tumors and normal tissue using the Wizard^® SV Genomic DNA Purification System. Loss of heterozygosity was tested using PCR and sequencing of exon 23 of the Ptch1 gene. (3940)

Notes: To sequence the mitochondrial genome one of the most widespread and common collembolan species of Antarctica, springtail Cryptopygus antarcticus. Specimens were collected from Killingbeck I during a 2002 polar expedition and frozen in liquid nitrogen. The Wizard^® SV Genomic Purification System was used to extract total DNA from the samples and the complete mitochondrial genome was amplified twice, first with universal primers and sequenced, and then using long PCR with specific primers. The long PCR products were mechanically sheared, blunt end repaired and purified using the Wizard^® SV Gel and PCR Clean-Up System. The fragments were then cloned, transformed and sequenced. (3976)

Notes: To study how chemotherapy affects hair follicles (HF), the researchers microdissected and cultured human anagen VI scalp follicles and treated the cells with 4-Hydroperoxycyclophosphamide (4-HC) at similar concentrations to those received during therapy. After incubation for 24 hours with 30µmol/L of 4-HC, the HFs were homogenized and genomic DNA was purified using the Wizard^® SV Genomic DNA Purification System. To determine if the treatment induced the mitochondrial common DNA deletion, the isolated DNA was subjected to real-time PCR. Further examination of gene expression was performed by isolating total RNA from two HF samples, reverse transcribing 3µg of the RNA using 15U of AMV Reverse Transcriptase and 0.025 µg/µl random primers, and amplifying seven human genes in a TaqMan^® Assay. (3746)

Notes: The authors explored the possibility of a domain-based level of gene expression regulation for chromosomes by integrating the green fluorescent protein (GFP) reporter in 90 different locations in cultured human cells. This integration was accomplished by infecting human embryonic kidney cells (HEK293) with a lentiviral construct carrying the GFP gene under the control of the ubiquitously expressed human phosphoglycerate kinase (PGK), sorting GFP-positive cells by FACS and selecting clones for expansion. Genomic DNA was isolated from the various clones using the Wizard^® SV Genomic DNA Purification System and analyzed by PCR or restriction digested for Southern blotting. (3743)

Notes: To examine gross changes in DNA content, genomic DNA was isolated from chicken retinospheroid cultures treated with diazinon, an organophosphate pesticide. DNA purified with the Wizard^® SV Genomic DNA Purification System was used to determine changes in total DNA content after pesticide exposure. (3586)

Notes: To examine how exposure to leptin in utero affects hepatic gene expression and epigenetic status in adulthood, pregnant Wistar rats were fed a standard diet or 30% undernutrition. The three-day-old pups were exposed to saline or leptin for 10 days, weaned and either fed a standard or high-fat diet. On day 170, the rats were sacrificed and tissues snap frozen. Five micrograms of genomic DNA was isolated from rat liver using the Wizard^® SV Genomic DNA Purification System. Then 25ng of the purified DNA was digested with methylation-sensitive restriction enzymes, and the glucocorticoid receptor (GR) and peroxisome proliferator-activated receptor alpha (PPARα) fragments were amplified by real-time PCR. (3744)

Notes: To identify the infectious organism present in human skin biopsy samples, genomic DNA was isolated using the Wizard^® SV Genomic DNA Purification System. Two microliters of purified DNA was amplified and then sequenced for determination of fungal species. (3745)

Notes: The authors examined the effectiveness of a monoclonal antibody treatment to human tumor-derived cells implanted under the kidney capsule of male athymic mice. These tumors were recovered from mouse kidney and the total genomic DNA isolated using the Wizard^® SV Genomic DNA Purification System. The human tumor DNA was quantified using a TaqMan^® qPCR method. (3748)

Notes: In this study, genomic DNA was extracted from 99 frozen thymic epithelial tumor samples using the Wizard^® SV Genomic DNA Purification System. Purified DNA was used in TaqMan SNP genotyping assays for 13 epidermal growth factor receptor (EGFR) gene mutations. (3585)

Notes: To study sarcolemmal ATP-sensitive K+ (KATP) channels, transgenic mice were generated that express SUR2A, the proposed regulatory protein of the complex. Genomic DNA was extracted from mouse ears using the Wizard^® SV Genomic DNA Purification System and used for genotyping transgenic animals.
(3584)

Notes: A panel of 11 Gram-negative and 11 Gram-positive bacterial species was used to develop a real-time PCR detection method. Initially DNA was purified from 1ml of various dilutions of bacteria resuspended in a saline solution using either the QIAamp DNA blood mini kit or the Wizard^® SV Genomic DNA Purification System. The results suggested that the Wizard^® SV Genomic DNA Purification System extraction protocol was superior in disrupting the bacterial cell wall (especially of Gram-positive bacteria), to allow release of bacterial DNA. Using DNA purified with the Wizard^® SV Genomic DNA Purification System, detection of S. aureus and E. coli at concentrations as low as 10¹ CFU per PCR was achieved. The Wizard^® SV Genomic DNA Purification System purification protocol provided in eNotes online (www.promega.com/enotes/applications/ap0051_tabs.htm) was used with the following modifications: The bacterial pellet was resuspended in 400µl of enzymatic lysis solution (47mM EDTA, 25mg/ml lysozyme, 20µg/ml lysostaphin) and incubated for 2 hours at 37°C. Next, 19.2mg/ml proteinase K was added (final concentration 0.4mg/ml), and the mixture was incubated for 1 hour at 55°C. Finally, the Nuclei Lysis Solution and RNase Solution were added, mixed and incubated for 10 minutes at 80°C. For real-time PCR analysis, 2µl of genomic DNA was used. (3676)

Notes: To examine possible Ig gene rearrangement of B-cell neoplasias after Kaposi sarcoma–associated herpesvirus infection, transgenic mice expressing KSHV latency-associated nuclear antigen (LANA) were created. Genomic DNA was isolated from murine spleens using the Wizard^® SV Genomic DNA Purification System, and 1.7ng of the purified genomic DNA was used in PCR analysis. (3414)

Notes: To rapidly characterize somatic mutations in the EGF receptor in lung cancer tissues, genomic DNA was extracted from lung biopsies using the Wizard^® SV Genomic DNA Purification System. The extracted DNA was used in a LightCycler SNP genotyping assay to determine the genotype of common loci associated with improved patient response to the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor. (3588)

Notes: To examine the methylation status of the DPYD promoter, genomic DNA was extracted from an RKO cell line and from peripheral blood mononuclear cells using the Wizard^® SV Genomic DNA Purification System. The isolated DNA was treated by sodium bisulfate modification followed by amplification and sequencing, or by DHPLC to determine CpG island methylation state. (3587)

Notes: Three terminal repeat sequences (TR) from Kaposi's sarcoma-associated herpesvirus (KSHV) were PCR amplified and then purified using the Wizard^® PCR Preps DNA Purification System. The PCR products were 386, 424, and 307 base pairs in size.  These TR products were used in PARP1-DNA ELISA assays.  The authors also used the Wizard^® SV Genomic DNA Purification System to isolate DNA from a BC3 cell line infected with KSHV. The isolated DNA was used in real-time PCR to assess KSHV copy number in cells. (3232)

Notes: The Wizard^® SV Genomic DNA Purification System was used to purify total DNA from plasmid-electroporated EBV-positive D98-HR1 cells. The isolated DNA was digested by two different restriction enzyme combinations and used in Southern blots to identify electroporated plasmid levels. (3231)