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Spin column

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Spin columns are a type of laboratory equipment used for the purification and separation of various biological molecules, such as DNA, RNA, and proteins. The core function of spin columns is to facilitate the efficient extraction and concentration of the desired target molecules from complex mixtures through a centrifugation process.

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95 protocols using spin column

1

Fetal DNA Isolation and Y-Chromosome Detection

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Blood samples from the peripheral blood of pregnant women were collected in 2–3 ml EDTA-K2 anticoagulative tubes. Plasma separation from these blood samples was performed using a two-step centrifugation method, as previously described (22 (link)). Then, 20 µl Protease K (20 mg/ml) and 200 µl plasma were mixed, and centrifuged briefly after adding 200 µl Buffer AL (Qiagen, Dusseldorf, Germany). The solution was incubated at 56°C for 10 min, centrifuged briefly, 200 µl absolute ethyl alcohol was added, mixed, and subsequently transferred to the spin columns (Qiagen). The spin columns were centrifuged for 1 min at 6,000 × g, 500 µl Buffer AW2 (Qiagen) was added prior to centrifugation for 3 min at 20,000 × g, and then the filtrate was discarded. Next, the spin columns were centrifuged for 1 min at 20,000 × g, and the DNA was eluted with 60 µl Buffer AE (Qiagen), separated into aliquots and stored at −80°C prior to use.
The amplification of the SRY gene (Y chromosomal material) using nested PCR was performed as previously described (22 (link)). The primers used for this nested PCR were as follows: SRY-138 forward (F) (5′-TACAGGCCATGCACAGAGAG-3′) and SRY-138 reverse (R) (5′-TGTTGTCCAGTTGCACTTCG-3′) (first round); and SRY-116F (5′-GCACAGAGAGAAATACCCGAAT-3′) and SRY-116R (5′-GCACTTCGCTGCAGAGTACC-3′) (second round).
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2

R. typhi Isolation and DNA Extraction

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The R. typhi isolates (Table 1) were obtained as yolk sac seeds and passaged one to six times in confluent Vero cells (strain C1008, green monkey kidney cells, obtained originally from the American Type Culture Collection, Manassas, VA) in RPMI 1640 supplemented with 2% fetal bovine serum, 2 mM L-glutamine and 5% tryptose phosphate broth. DNA was isolated from infected cell cultures and supernatants which had been harvested with 5 mm glass beads, pelleted at 12,000 rpm for 20 minutes in a Sorvall GSA rotor, and the pellet washed in PBS (1.0 ml per T150 flask). 0.25 ml of suspension was then lysed and extracted using QIAamp DNA Mini kit reagents (AL buffer plus proteinase K at 50°C overnight) and spin columns from Qiagen (Valencia, CA). DNA was eluted with 0.2 ml of AE buffer, diluted to 1.0 ml and stored at 4°C prior to analysis. Working DNA stocks (diluted 1:10 in water) were generally used for all analyses.
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3

Generating Mutant CDH1 Protein Libraries

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DNA libraries encoding the open reading frame containing the CDH1 stalling sequence in Fig. 1b, with stretches of 4 random codons encoded by NNK sequences (N=any nucleotide, K=G or T) to introduce random mutations in different sites of the CDH1 nascent chain within the ribosome exit tunnel, were generated by PCR amplification. PCR products were purified using spin columns (Qiagen, catalog number: 28506), then treated with Dpn1 nuclease at 37 °C for 1 hour to remove template DNA. A double-stranded DNA fragment encoding a T7 RNA polymerase promoter was then ligated to the 5’ end of the treated DNA, along with a double-stranded DNA encoding a poly-A tail to the 3’ end, using T4 DNA ligase and T4 Polynucleotide Kinase at 16 °C overnight. The ligation reaction was followed by PCR amplification using primers flanking the T7 promoter and poly-A tail to generate the final DNA library. The oligonucleotides used to prepare the DNA libraries are presented in Supplementary Table 3.
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4

Nucleic Acid Extraction from Frozen Tumor Tissue

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All samples were processed following one standard operating protocol to isolate high quality nucleic acids. Each frozen tumor was serially sectioned for DNA and RNA isolation (30 × 30 μm serial sections for both). DNA was isolated using the DNeasy kit for purification of total DNA for animal tissues using two spin columns (Qiagen). On each column samples were eluted twice with 100 μl volumes of buffer AE for a final volume of 400 μl. For RNA extraction, depending on the size of the tumor sample, 20–30 sections of 30 μm were used for RNA extraction. Sections were homogenized in Qiazol (Qiagen) using a tissue lyser (Qiagen) and total RNA was isolated with Qiazol according the manufacturer's instructions. The RNA was further purified using the RNeasy Mini Kit (Qiagen).
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5

RNA Extraction and Quality Control for Microarray Analysis

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RNA from approximately 25 mg tissue (mid-level hippocampus containing all
hippocampal subregions) was extracted using Trizol, treated with DNAse, and
purified using Qiagen spin columns as described previously (Berchtold et al., 2008 (link)). RNA quality was assessed
using the Agilent Bioanalyzer and RNA integrity number (RIN), and samples with
RIN ≥ 6.5 were further processed on microarrays. CEL file quality control
was assessed using the affyQC automated R workflow available through
ArrayAnalysis (http://www.arrayanalysis.org). Quality control parameters were:
beta-actin 3’/5’ ratio < 3, GAPDH 3’/5’ ratio
< 1.25, internal hybridization control signal (BioB=Present), Percent
Present ≥ 49%, Percent Present spread ≤ 10%, Background spread
≤ 20%) and log scale factor spread ≤ 3.
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6

RNA Extraction from Corneal Endothelium

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An RNA extraction kit (RNeasy Mini Kit; Qiagen) was used to extract total RNA from the corneal endothelium obtained from the 203 FECD patients during DMEK. Briefly, Descemet membranes with corneal endothelium were lysed, and the lysate was applied to spin columns (Qiagen) with ethanol. The total RNA was eluted from columns, and cDNA was synthesized using a master mix (SuperScript VILO Master Mix; Thermo Fisher Scientific Inc., Waltham, MA, USA). As a control, Descemet membranes with corneal endothelium were peeled from the 35 non-FECD donor corneas, and cDNA was synthesized from the extracted total RNA.
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7

Bacterial RNA Extraction Protocol

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After harvesting the bacteria by centrifuging the cultures at 4800× g for 10 min, the bacterial pellet was suspended in 500 µL of ice-cold phosphate buffer solution (PBS). The suspension was then centrifuged at 500× g for 10 min at 4 °C. This washing step was repeated twice. The RNA was extracted by a combination of the CTAB and QIAGEN RNeasy Mini Kit methods. In short, CTAB/PVP/BME solution was added to the bacteria pellet and, after resuspension, subjected to three cycles of deep freezing at −80 °C, followed by thawing at room temperature to allow the lysing of the cells, and was subsequently processed as described by Jordon-Thaden et al. [27 (link)], albeit after DNAse treatment with a TURBO DNA-free kit, a phenol/chloroform/IAA step was included, followed by two cycles of chloroform/IAA extractions. For precipitation, a 1/20th volume of 5 M NaCl and two volumes of ethanol were added, and then the solution was incubated for 20 min at −20 °C. RNA purification was carried out with Qiagen spin columns, washing with Qiagen washing solutions, and finally elution with 50 microliters of RNase-free water. The quantity and purity of the total RNA samples were assessed by ultraviolet spectroscopy using a DS-11 spectrophotometer (DeNovix, Inc., Wilmington, North Carolina, USA).
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8

Molecular Typing of MRSA Isolates

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Molecular characterization was carried out using the StaphyType DNA microarray (Alere Technologies, Jena, Germany). The included target genes, primer and probe sequences and procedures have been published previously [10] (link). Briefly, MRSA isolates were collected from Columbia blood agar, and DNA extraction was carried out by enzymatic lysis [10] (link) followed by purification using a commercially available kit utilizing spin columns (Qiagen, Hilden, Germany). The purified DNA was used as template in a linear primer elongation reaction, during which biotin-16-dUTP was incorporated into the resulting amplicons and the single-stranded DNA products were hybridized stringently to the microarray. Incubation with horseradish peroxidase–streptavidin conjugate, which binds to biotin labels, was carried out, and a dye was added which precipitated in the presence of the peroxidase, resulting in the formation of visible spots where hybridization had occurred. Microarray images were taken and analysed with a dedicated reader and software (Alere Technologies). Assignment to clonal complexes and sequence types, as well as identification of epidemic strains was carried out fully automatically with the same software module [8] (link), [10] (link).
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9

ChIP Analysis of c-Jun Binding

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ChIP analysis was performed as previously described 11 (link). Chromatin solutions were precipitated overnight at 4 °C using c-Jun antibody or rabbit Ig control (Abcam, Cambridge, MA). The input DNA and the immunoprecipitated DNA were extracted using Qiagen spin columns and were analyzed by PCR or real-time PCR assays using Ei and E3′ specific primers (Table S1).
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10

DNA Extraction from Single Specimens

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Individual ethanol-preserved specimens were lysed in ATL lysis buffer (cat. no. 19076, Qiagen, Hilden, Germany), with Proteinase K (cat. no. 19133, Qiagen, Hilden, Germany), followed by DNA purification with the DNAeasy Blood and Tissue Kit (Qiagen, Hilden, Germany) and Qiagen Spin Columns according to standard protocols (https://www.qiagen.com/us/resources/resourcedetail?id=6b09dfb8-6319-464d-996c-79e8c7045a50&lang=en). Elution with Low TE (Invitrogen, Carlsbad, CA) used a small volume (28 μl) since the resultant purified DNA is from a single microscopic organism.
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