Journal: bioRxiv

Article Title: Link between aging and atheroprotection in Mif -deficient atherosclerotic mice

doi: 10.1101/2021.12.14.471281

Figure Lengend Snippet: A-B ) mRNA expression of MIF was assessed by RT-qPCR in spleen ( A ) and liver ( B ) of Apoe −/– mice after 24 and 42 weeks of HFD. Values were normalized to the values of the 30-week-old Apoe −/– controls that received HFD for 24 weeks (n=5-7 mice; results are presented as means ± SD). C ) MIF plasma levels as measured by ELISA in Apoe −/– mice after 24 and 42 weeks of HFD. Values were normalized to the Apoe −/– controls that received HFD for 24 weeks (n=8-9 mice per group; results are presented as means ± SD). Statistics: Mann-Whitney test (no significant differences observed; each data points represents one mouse).

Article Snippet: RT-qPCR was performed using ORA TM SEE qPCR Green ROX H Mix (HighQu, Kraichtal, Germany) and specific mouse primer pairs (Eurofins, Ebersberg, Germany).

Techniques: Expressing, Quantitative RT-PCR, Clinical Proteomics, Enzyme-linked Immunosorbent Assay, MANN-WHITNEY

Journal: bioRxiv

Article Title: Link between aging and atheroprotection in Mif -deficient atherosclerotic mice

doi: 10.1101/2021.12.14.471281

Figure Lengend Snippet: mRNA expression of FoxP3 was assessed by RT-qPCR in spleen of Apoe −/– Mif −/– (blue) after 24 and 42 weeks of HFD and compared to the WT controls (grey). Values were normalized to the values of the 30-week-old Apoe −/– controls that received HFD for 24 weeks (n=6-10 mice per group; results are presented as means ± SD). Statistics: two- way ANOVA (each data point represents one mouse).

Article Snippet: RT-qPCR was performed using ORA TM SEE qPCR Green ROX H Mix (HighQu, Kraichtal, Germany) and specific mouse primer pairs (Eurofins, Ebersberg, Germany).

Techniques: Expressing, Quantitative RT-PCR

Journal: Nucleic Acids Research

Article Title: SETDB1 activity is globally directed by H3K14 acetylation via its Triple Tudor Domain

doi: 10.1093/nar/gkae1053

Figure Lengend Snippet: SETDB1 is recruited to H3K14ac containing target loci. ( A ) Scheme of the cell HCT116 derived lines generated in this study by SETDB1 KO followed by reconstitution with SETDB1 WT or mutants and by HBO1 KO. ( B and C ) H3K9me3 (B) and H3K14ac (C) ChIP-qPCR at known SETDB1 target regions ( , ) showing changes in the histone modification as indicated upon SETDB1 KO and reconstitution with WT SETDB1 of its catalytically inactive mutant H1224K or the 3TD mutant F332A. Moreover, HBO1 KO cells were investigated. ChIP was performed on mononucleosomes isolated from two individual biological replicates from each cell line (represented as dots). Averages of the individual measurements are represented as bars.

Article Snippet: For each region of interest, a master mix was prepared with 7.5 μl of 2X ORATM See qPCR Probe Mix (highQu), 0.4 μl forward primer, 0.4 μl reverse primer and 5.7 μl ddH 2 O.

Techniques: Derivative Assay, Generated, ChIP-qPCR, Modification, Mutagenesis, Isolation

Journal: Scientific Reports

Article Title: NAxtra magnetic nanoparticles for low-cost, efficient isolation of mammalian DNA and RNA

doi: 10.1038/s41598-023-46868-5

Figure Lengend Snippet: Nucleic acid (NA) extraction from 100 to 1,000,000 cells (HAP1), comparing the NAxtra-based method on KingFisher Flex (three independent NA extractions) to the AllPrep DNA/RNA/miRNA Universal Kit (two independent NA extractions). (A) NAs extracted from 1 = 1,000,000 and 2 = 500,000 cells, separated on a 0.4% agarose gel (left, 1% eluate applied for 1,000,000 cells, 2% eluate applied for 500,000 cells) with GeneRuler High Range DNA ladder (Thermo Scientific), or 1.2% agarose gel (right, 4% eluate applied for 1,000,000 cells, 8% eluate applied for 500,000 cells) with GeneRuler 1 kb Plus DNA Ladder (Thermo Scientific). Gel images have been inverted and cropped; original gels are presented in Supplementary Fig. . ( B ) Average NA yields (± 1 SD) from 500,000 and 1,000,000 cells, as measured by Quant-iT RNA/DNA assay (Invitrogen). ( C ) Average cycle threshold (Ct) values (± 1 SD) for DNA target (left; a 305 bp, single-locus genomic DNA amplicon from the KAPA Human Genomic DNA Quantification and QC Kit) and RNA target (right; ACTB) amplified by (RT-)qPCR of NA extracted from 100; 1000; 10,000 and 100,000 cells.

Article Snippet: ACTB mRNA was reverse transcribed and amplified in reactions of 2.5 μl template RNA, 1X ACTB PrimeTime XL PCR Assay Hs.PT.39a.22214747 (Integrated DNA Technologies), and either 1X qScript XLT 1-Step RT-qPCR ToughMix (Quantabio), 1X One-Step Takyon Ultra Probe 4X MasterMix (Eurogentec), or 1X 1Step RT qPCR Probe 4X Kit (highQu) with annealing at 62 °C and remaining reaction conditions according to master mix specifications.

Techniques: Extraction, Agarose Gel Electrophoresis, Amplification, Quantitative RT-PCR

Journal: Scientific Reports

Article Title: NAxtra magnetic nanoparticles for low-cost, efficient isolation of mammalian DNA and RNA

doi: 10.1038/s41598-023-46868-5

Figure Lengend Snippet: Nucleic acids (NA) extracted from adherent cells (HAP1) using the NAxtra-based method on KingFisher Flex (three independent NA extractions) compared to the AllPrep DNA/RNA/miRNA Universal Kit (two independent NA extractions). Average cycle threshold (Ct) values (± 1 SD) for a DNA target (top, MYC) and RNA target (bottom, ACTB) amplified by (RT-)qPCR of NAs extracted from 100 cells and 100,000 cells of HAP1. Two different master mixes were used for each target: RealQ Plus 2 × Master Mix for Probe (Ampliqon) and Luna Universal Probe qPCR Master Mix (NEB), or One-Step Takyon Ultra Probe 4X MasterMix (Eurogentec) and 4X 1Step RT qPCR Probe Kit (highQu).

Article Snippet: ACTB mRNA was reverse transcribed and amplified in reactions of 2.5 μl template RNA, 1X ACTB PrimeTime XL PCR Assay Hs.PT.39a.22214747 (Integrated DNA Technologies), and either 1X qScript XLT 1-Step RT-qPCR ToughMix (Quantabio), 1X One-Step Takyon Ultra Probe 4X MasterMix (Eurogentec), or 1X 1Step RT qPCR Probe 4X Kit (highQu) with annealing at 62 °C and remaining reaction conditions according to master mix specifications.

Techniques: Amplification, Quantitative RT-PCR

Journal: Scientific Reports

Article Title: NAxtra magnetic nanoparticles for low-cost, efficient isolation of mammalian DNA and RNA

doi: 10.1038/s41598-023-46868-5

Figure Lengend Snippet: RNA isolated from triplicates of 1,000,000 cells (HAP1) using the NAxtra-based method compared to the MagMAX mir Vana Total RNA isolation kit (Applied Biosystems) on KingFisher Duo Prime. Statistical analysis was performed by two-sided, unpaired t-tests, in which ns (non-significant) = P > 0.05, * = P ≤ 0.05, ** = P ≤ 0.01, and **** P ≤ 0.0001. ( A ) Total RNA separated on a 1.2% agarose gel (5% eluate applied) with GeneRuler 1 kb Plus DNA Ladder (Thermo Scientific). The gel image has been inverted and cropped; the original gel is presented in Supplementary Fig. . ( B ) Average total RNA yield (± 1 SD), as measured by Quant-iT RNA assay (Invitrogen) ( C ) Average cycle threshold (Ct) values (± 1 SD) for five miRNA targets; hsa-miR-24-3p, hsa-miR-122-5p, hsa-miR-210-5p, hsa-miR-455-5p and hsa-miR-1246, amplified by RT-qPCR. D) Average cycle threshold (Ct) values (± 1 SD) for an mRNA target (ACTB) amplified by RT-qPCR.

Article Snippet: ACTB mRNA was reverse transcribed and amplified in reactions of 2.5 μl template RNA, 1X ACTB PrimeTime XL PCR Assay Hs.PT.39a.22214747 (Integrated DNA Technologies), and either 1X qScript XLT 1-Step RT-qPCR ToughMix (Quantabio), 1X One-Step Takyon Ultra Probe 4X MasterMix (Eurogentec), or 1X 1Step RT qPCR Probe 4X Kit (highQu) with annealing at 62 °C and remaining reaction conditions according to master mix specifications.

Techniques: Isolation, Agarose Gel Electrophoresis, Amplification, Quantitative RT-PCR

Journal: International Journal of Molecular Sciences

Article Title: Prolonged Extracorporeal Circulation Leads to Inflammation and Higher Expression of Mediators of Vascular Permeability Through Activation of STAT3 Signaling Pathway in Macrophages

doi: 10.3390/ijms252212398

Figure Lengend Snippet: List of TaqMan Real-Time PCR Assays for RT-qPCR analysis.

Article Snippet: The expression of target genes and GAPDH as a reference gene control was analyzed by real-time qPCR using TaqMan Gene Expression Assays (summarized in ) and ORA TM SEE qPCR Probe ROX H Mix (highQu, Kraichtal, Germany) according to manufacturers’ recommendations.

Techniques: Real-time Polymerase Chain Reaction

Journal: Microbial Biotechnology

Article Title: Sequential development of several RT‐qPCR tests using LNA nucleotides and dual probe technology to differentiate SARS‐CoV‐2 from influenza A and B

doi: 10.1111/1751-7915.14031

Figure Lengend Snippet: Schematic illustrating SARS‐CoV‐2 genome and regions targeted by RT‐qPCR primers and probes. A. Schematic overview portrays the SARS‐CoV‐2 genome with RdRP and E gene regions magnified to show the locations of primers and probes of the original Charité protocol, vDetect (v1 and v2), and rTEST RT‐qPCR assays. F, forward primer; P, probe; R, reverse primer. The inset boxes (from left to right) illustrate a SARS‐CoV‐2 particle with labelled structural proteins and RNA, legend describing panel A and the primers and probes used in each test to detect RNase P subunit p30 (RPP30). B. Diagram compares the sequences of RdRP and E gene primers and probes for the original Charité protocol, vDetect (v.1) and vDetect v.2 and rTEST RT‐qPCR assays to the Wuhan reference sequence. The numbers written above the Wuhan reference sequence correspond to the start and end base positions of the sequence Reverse primer sequences are written in the reverse complement (rc). Magenta lines and letters represent mixed bases found in the primers and probes in the Charité protocol that were replaced with the correct bases in vDetect v1 (blue lines and letters). Red lines and letters signify LNA‐modified bases.

Article Snippet: RT‐qPCR reactions were optimized on a CFX96 (Bio‐Rad), QuantStudio 5 (Agilent Technologies, CA, USA) and Mx3005P (Agilent Technologies) real time PCR detection systems using the 1Step RT qPCR Probe ROX L Kit (Cat. No. QOP0201, highQu, Germany).

Techniques: Quantitative RT-PCR, Sequencing, Modification

Journal: Microbial Biotechnology

Article Title: Sequential development of several RT‐qPCR tests using LNA nucleotides and dual probe technology to differentiate SARS‐CoV‐2 from influenza A and B

doi: 10.1111/1751-7915.14031

Figure Lengend Snippet: Optimization, analytical sensitivity and clinical performance of a rapid, RNA extraction‐free, multiplexed RT‐qPCR assay. A. Analytical sensitivity of the triplexed E, RdRP and RNase P assay in the rTEST COVID‐19 qPCR Allplex kit. B. Clinical performance of the rTEST COVID‐19 qPCR Allplex kit. C. Optimization of gargle sample input for a rapid, RNA extraction‐free, triplexed rTEST. D. Comparison of four different thermal profiles using 8 μl of gargle input volume in rapid, direct RT‐qPCR. E. Analytical sensitivity of the triplexed E, RdRP and RNase P assay in the RNA extraction‐free rTEST COVID‐19 qPCR Rapid kit. F. Clinical performance of the rTEST COVID‐19 qPCR Rapid kit. The dotted line at C t = 40 (panels A and E) serves as a threshold after which amplification is considered invalid. The dotted lines and shaded areas (panels B and F) indicate samples that were not detected by either the evaluation test, index test or both tests. C t , cycle threshold; E, envelope gene; ND, not detected within 45 cycles; NTC, no template control; RdRP, RNA‐dependent RNA polymerase.

Article Snippet: RT‐qPCR reactions were optimized on a CFX96 (Bio‐Rad), QuantStudio 5 (Agilent Technologies, CA, USA) and Mx3005P (Agilent Technologies) real time PCR detection systems using the 1Step RT qPCR Probe ROX L Kit (Cat. No. QOP0201, highQu, Germany).

Techniques: RNA Extraction, Quantitative RT-PCR, Comparison, Amplification, Control

Journal: Microbial Biotechnology

Article Title: Sequential development of several RT‐qPCR tests using LNA nucleotides and dual probe technology to differentiate SARS‐CoV‐2 from influenza A and B

doi: 10.1111/1751-7915.14031

Figure Lengend Snippet: Schematic illustrating influenza A and B genome and regions targeted by RT‐qPCR primers and probes. (A) Schematic overview portrays the influenza A and B genome with PB1 and PA gene regions magnified to show the locations of primers and probes. Nucleotides labelled in red text indicate mixed bases in the consensus sequences for influenza A and B. BHQ2, black hole quencher 2; F, forward primer; HA, haemagglutinin; M, matrix protein; NA, neuraminidase; NP, nucleoprotein; NS, non‐structural protein; P, probe; PA, polymerase acidic protein; PB1, polymerase basic 1 protein; PB2, polymerase basic 2 protein; R, reverse primer; seg., segment; YY, Yakima Yellow ® .

Article Snippet: RT‐qPCR reactions were optimized on a CFX96 (Bio‐Rad), QuantStudio 5 (Agilent Technologies, CA, USA) and Mx3005P (Agilent Technologies) real time PCR detection systems using the 1Step RT qPCR Probe ROX L Kit (Cat. No. QOP0201, highQu, Germany).

Techniques: Quantitative RT-PCR

Journal: Cancers

Article Title: Tumoricidal, Temozolomide- and Radiation-Sensitizing Effects of K Ca 3.1 K + Channel Targeting In Vitro Are Dependent on Glioma Cell Line and Stem Cell Fraction

doi: 10.3390/cancers14246199

Figure Lengend Snippet: Enrichment of the glioblastoma stem cell fraction. ( A – D ). Culturing murine SMA-560, SMA-540 and GL-261 glioma cells and human U-251MG glioma cells in NSC medium (open circles) increased housekeeper-normalized mRNA abundances of stem cell markers as compared to DMEM medium (closed circles; in addition to the individual values, means ± standard error of three experimental and two observational units each are depicted). The mRNA abundances of four different stem cell markers, ( A ) ALDH1A3 , ( B ) CXCR4 , ( C ) Nestin and ( D ) SOX2 were determined by real-time RT-PCR. Numbers indicate error probability ( p values) as calculated by Welch-corrected two-tailed t -test.

Article Snippet: One step SYBR Green-based reverse transcriptase PCR was accomplished using the 1 Step RT PCR Green ROX L Kit (highQu) following the manufacturer’s instruction.

Techniques: Quantitative RT-PCR, Two Tailed Test