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High pure isolation kit

Manufactured by Roche
Sourced in Germany, United States

The High Pure Isolation Kit is a laboratory equipment designed for the rapid and efficient isolation of nucleic acids, including DNA and RNA, from various biological samples. The kit utilizes a silica-based membrane technology to capture and purify the target nucleic acids, allowing for easy separation and downstream processing.

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30 protocols using high pure isolation kit

1

RNA Extraction from N. tardaugens

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Total RNA of N. tardaugens cells was extracted from cultures grown in minimal medium with 20 mM CDX and TES or pyruvate as carbon sources. Cells where harvested in mid exponential phase (OD600 0.6) and stored at −80 °C. Pellets where thawed and cells were lysed in 400 µL TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 7.5) containing lysozyme (50 mg/mL) following three freezing–thawing cycles. High Pure Isolation Kit (Roche), followed by DNA-free DNA Removal Kit (Invitrogen) treatment, was used to obtained pure RNA. Purity and concentration were measured in a ND1000 spectrophotometer (Nanodrop Technologies).
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2

Detecting Shigella Virulence Genes

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Total genomic DNA was extracted using High Pure Isolation Kit (Roche, Mannheim, Germany) according to the manufacturer’s instruction. The quality and quantity of extracted DNA was assessed via NanoDrup (Denovix, Wilmington, USA)
The presence of the virulence genes encoding T3SS effector proteins, including ipaH, ipaB, ipaC, ipaD, ipgD, sen, and virA, was investigated using polymerase chain reaction (PCR) using specific primers (Table S1 and Figures S1–S7). Each PCR reaction was performed in a total volume of 25 μL containing 12.5 μL of 2X master mix (Genet bio, Korea), 1μL (10 pM/µL) of each primer, 8.5 μL of distilled water, and 2 μL of DNA (10 ng) template. The cycling programs were preceded by 5 min at 95° C and consisted of 35 cycles of 94° C for 1 min, 1 min annealing at specific temperature for each primer set (Table S1), and 72° C for 1 min, followed by a final extension step at 72° C for 5 min. PCR amplicons were separated using 1.2% agarose gel and visualized by staining with safe stain (CinnaGen, Iran). S. flexneri ATCC 12022 was used as positive control.
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3

RNA Isolation, cDNA Synthesis, and qPCR Quantification

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RNA was isolated and converted to cDNA using the High Pure Isolation Kit (Roche) and the Transcriptor First Strand cDNA Synthesis Kit (Roche), respectively. For cDNA synthesis, a 1:1 mixture of random hexamer and oligodT was used. PCR amplification and quantification was performed using the SYBR Green I Master reaction mix (Roche) on a Roche LightCycler 480. Relative amounts of target cDNAs were normalized to peptidylprolyl isomerase A (PPIA). Oligonucleotides used are described in S1 Supplementary Materials.
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4

Quantitative Real-Time PCR Gene Expression

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Total RNA was isolated with High Pure Isolation Kit (11828665001, Roche). For cDNA synthesis M-MLV reverse transcriptase, random nonamers and oligo (dT)23 (Sigma-Aldrich) were used according to manufacturer’s instructions.
To estimate the expression of genes of interest we performed the qRT-PCR reaction with primers designed with NCBI tool (and custom-synthesized by Sigma-Aldrich) (listed in Additional file 2: Table S4) or TaqMan® Gene Expression Assays (Thermo Fisher Scientific) (listed in Additional file 2: Table S5).
For the qRT-PCR reaction we used the KAPA SYBR FAST qPCR Master Mix (2X) Universal Kit (KK4618, KapaBiosystems) or TaqMan® Gene Expression Master Mix (4369016, ThermoFisher Scientific) and a 7900HT Fast Real-Time PCR thermocycler (Applied Biosystems). At least two technical repeats per experimental condition were done. The expression of targets were normalized to the level of housekeeping genes ACTB, B2M, and GAPDH and presented as fold changes.
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5

Extracting Total RNA from N. tardaugens

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Total RNA of N. tardaugens cells was extracted from cultures grown on minimal medium with 20 mM CDX and E2 or PYR as carbon sources as described previously (Ibero et al., 2019a (link)). Briefly, cells where harvested in mid exponential phase (OD600 0.6) and stored at −80°C. Pellets where thawed and cells were lysed in 400 μl TE buffer (10 mM Tris–HCl, 1 mM EDTA, pH 7.5) containing lysozyme (50 mg/ml) following three freezing–thawing cycles. High Pure Isolation Kit (Roche), followed by DNA-free DNA Removal Kit (Invitrogen) treatment, was used to obtained pure RNA. Purity and concentration were measured in a ND1000 spectrophotometer (Nanodrop Technologies).
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6

Transcriptomic Analysis of Labrenzia sp. PHM005 Pederin Cluster

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Mutant strain PHM005ΔPKS4 was cultured in MBM + vit medium and the total RNA was extracted by High-pure Isolation Kit (Roche) after 24 h. Extracted RNA was additionally treated by DNA-free DNaseTreatment and Removal Reagents (Ambion). The RNA concentration was measured by using a NanoPhotometer (Implen). Reverse transcription of 1 μg of DNA-free RNA per sample was done using the Transcriptor First Strand cDNA Synthesis Kit (Roche) to generate cDNA and RT-PCR semi-quantitative analyses were carried out to check the mRNA levels. The rpoD gene was used as the housekeeping gene. Primers for RT–PCR for Labrenzia sp. PHM005 pederin cluster genes, as well as the housekeeping rpoD gene, were designed using Primer3 implemented by Geneious v.10.0.2 (Supplementary Table S2). Relative mRNA expression was visualized in 1.5% agarose gel. Negative controls contained RNA samples without the reverse transcriptase. The RNA extraction from the strain PHM005 for the transcriptomics analysis was performed in the early exponential phase (12 h) as described previously. Transcriptomics and bioinformatics analyses were carried out by Vertis Biotechnologie AG. The percentage of the mapped reads to annotated genes is 78.4, 80.8, and 77.0% for each replicate sample. The results represent a mean of three replicates.
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7

Quantitative Gene Expression Analysis

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Total RNA was isolated from cells with High Pure Isolation Kit (Roche). For cDNA synthesis random nonamers, oligo(dT)23 and M-MLV reverse transcriptase (Sigma-Aldrich) were used according to the manufacturer’s instructions. To estimate the expression of genes of interest we used primers designed with NCBI tool (and custom-synthesized by Sigma-Aldrich) listed in Supplementary file 1-Table 5. The qRT-PCR reaction was performed with the Kapa Sybr Fast ABI Prism qPCR Kit (KapaBiosystems) using a 7900HT Fast Real-Time PCR thermocycler (Applied Biosystems) with at least three technical repeats per experimental condition. The data were normalized according to the expression level of housekeeping gene, GAPDH (in K562 cells) or RPL19 (in mouse fetal liver erythroblasts) and presented as fold changes.
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8

Quantitative Gene Expression Analysis

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Total RNA was isolated with High Pure Isolation Kit (Roche, 11828665001). For cDNA synthesis random nonamers, oligo(dT)23 and M‐MLV reverse transcriptase (Sigma‐Aldrich, R7647, O4387, and M1302, respectively) were used according to manufacturer's instructions. Expression of genes of interest was measured using primers designed with the NCBI tool (and custom‐synthesized by Sigma‐Aldrich) listed in Appendix Table S2 or the following TaqMan® Gene Expression Assays: Hs99999903_m1 for ACTB, Hs00203085_m1 for VPS4A and Hs00191617_m1 for VPS4B (Thermo Fisher Scientific). The qRT–PCR mixture was performed with the Kapa Sybr Fast qPCR Kit (KapaBiosystems, KK4618) or TaqMan® Gene Expression Master Mix (Thermo Fisher Scientific, 4369016) using a 7900HT Fast Real‐Time PCR thermocycler (Applied Biosystems) with two technical repeats per experimental condition. The data were normalized according to the level of housekeeping genes ACTB or Rpl19 and presented as fold changes.
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9

Evaluating Bax and Bcl2 Gene Expression in U87MG Cells

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In order to evaluate the expressions of Bax and Bcl2 genes, U87MG cells (104 cells) were treated with CA (8 μg/mL) individually or in combination with DOX (5 μg/mL). After 24 h treatment, total RNA of cells (7 × 105 cells) was extracted using high pure isolation kit (Roche, Mannheim, Germany) according to the manufacturer’s instructions. Total RNA was assessed qualitatively and quantitatively using a spectrophotometer (NanoDrop™ 2000, USA) and samples stored at -80 °C for further investigations. A one-step quantitative test was performed on RNA expression using CYBR Green kit. The primer sequences were completely similar to those performed in our previous study (20 ). The cDNA synthesis was carried out at thermal cycler conditions corresponding to 15 min at 50 °C, 10 min at 95 °C followed by 40 cycles of 15 s at 95 °C to denature DNA and 45 s at 60 °C to anneal and extend the template (20 ). The melting curve was analyzed at temperatures in range of 65-95 °C with a temperature transient rate of 0.1 °C/s. All reactions were performed in triplicate in a Stratagene MX 3000P system (USA). The values obtained for the target gene expression were normalized to β-actin and analyzed by the relative gene expression 2-ΔΔCT method (20 ) using the following equation:
-ΔΔCT = (CT target - CT β-actin) Unknown - (CT target - CT β-actin) calibrator
where, CT is threshold cycle.
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10

Evaluating β-TC3 Cell DNA Damage

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β-TC3 cells (2 × 106 cells/well) were seeded in 6 well plates and allowed to adhere for 24 h and then treated with 200 μL of STZ alone or with INF (0.5 mg/ml). Plates were then incubated for 24 h at 37°C in humidified atmosphere of 95% air and 5% CO2. Total DNA from β-TC3 cells was extracted using high pure isolation kit (Roche, Mannheim, Germany) according to the manufacturer instruction. 20 μl of DNA eluted sample was mixed with 4 μl of novel juice dye and run on 1.2% agarose gel at 75 V for 1 h and visualized using an ultraviolet transilluminator and then photographed.[26 (link)]
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