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11 protocols using precellys system

1

Quantitative RT-PCR for RRV Detection

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20 µL of blood were used for RNA extraction using the Nucleospin 96 RNA kit (Macherey Nagel) according to the manufacturer’s instructions.
Tissues samples collected and frozen at −80 °C, were weighed and grinded in Macherey Nagel RA1 Lysis buffer with a Precellys system® and ceramic beads tubes, Bertin technologies (Montigny Le Bretonneux, France). Total RNA was extracted using Nucleospin RNA II kit (Macherey Nagel) according to manufacturer’s instructions.
Quantitative reverse transcriptase polymerase chain reactions (qRT-PCR) were performed in an Applied Biosystems 7500 fast thermocycler (ThermoFisher Scientific). The sequences of the primers (400 nM) and probe (200 nM) are the following:
RRV-F (position 10407): AGCAACAATCAGGATCAGTTAT;
RRV-R (position 10616): AATCTACCCGGCTGGCCTG;
RRV-Probe (position 10511): [FAM]TCTCAACAGCTTGGTCACCGTT [TAM].
qRT-PCR was performed on 5 µL of the extracted RNA with the following cycling conditions: 30 min at 56 °C, 5 min at 95 °C and 40 cycles at 95 °C for 15 s, 60 °C for 1 min.
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2

Lipid Extraction from Spinal Cord and Muscle

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Tissue samples (25 mg for lumbar spinal cord, and 25–50 mg for soleus muscle) were gently thawed on crushed ice and homogenized with 335 µl precooled methanol. Lipids were extracted by orbital agitation using a Precellys system (Bertin Technologies, Saint-Quentin-en-Yvelines, France) in a propylene tube containing ceramic beads. Two homogenization steps at 5000 rpm for 30 s each were performed at room temperature. Homogenates were transferred into glass conic tubes. To recover the maximum volume of homogenate, Precellys tubes, beads and tips were washed with additional 335 µl precooled methanol. Then, homogenates were mixed with 1340 µl chloroform and centrifuged at 2000 rpm for 5 min at 4°C. The organic phase was transferred into a conical glass tube and washed with 400 µl precooled 0.9% NaCl. After centrifugation at 2000 rpm for 5 min at 4°C, the organic phase was evaporated to dryness at 30°C under nitrogen. Residues were reconstituted with acetonitrile/isopropanol (1:1) (100 µl for lumbar spinal cord, and 60 µl for soleus muscle) and further diluted with solvent mixture before injection (1/40 for lumbar spinal cord, and 1/10 for soleus muscle).
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3

RNA Extraction and RT-qPCR Analysis

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Small intestine (duodenum to ileum) was homogenized in 7 mL tubes containing a mix of 1.4 and 2.8 mm glass beads and 2 mL Trizol (ThermoFisher), respectively using the Precellys system (Bertin Technologies). RNA extraction from organs and cultured cells, RNA clean-up and DNase treatment were performed using the Nucleospin RNA kit (Macherey-Nagel) according to the manufacturer’s instructions.
RNA was quantified using the NanoDrop ND-100 (ThermoFisher) and cDNA synthesis was performed from 1 μg of RNA using oligo-dT (ThermoFisher) and SuperScript IV RT (ThermoFisher). RT-qPCR was performed using Power SYBR Green PCR system (ThermoFisher) and specific primers listed in Supplementary file 1 on the LightCycler 480 Real-Time PCR System (Roche). Relative quantification of gene expression was performed using the comparative 2-ΔΔCt method. Results were normalized using Actin as the housekeeping gene.
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4

Bacterial Identification from Stool and Ileum

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Stool samples and ileum were homogenized in 2-ml tubes containing a mixture of 1.4-mm-diameter and 2.8-mm-diameter glass beads and 1 ml sterile water using a Precellys system (Bertin Technologies). Serial dilutions were plated on selective media (see the supplemental material) for bacterial identification by matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (Bruker) and CFU counts.
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5

Efficient Viral and Bacterial Nucleic Acid Extraction

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Viral RNA and bacterial DNA were extracted from 170-μl amounts of nasal swab, raw BAL fluid, and fecal swab samples using the NucleoMag pathogen kit (Macherey-Nagel, Germany) on the KingFisher Flex purification system (Thermo Fisher Scientific, MA, USA) according to the manufacturer’s instructions. Total RNA was extracted from pelleted cells of BAL fluid samples with the NucleoMag RNA kit (Macherey-Nagel, Germany) on the KingFisher Flex purification system (Thermo Fisher Scientific, MA, USA). Extraction of viral RNA and bacterial DNA from tissues (30-mg amounts of nasal turbinate, trachea, and lung lobe samples) were obtained by lysis in Precellys lysing kit tubes (catalog number P000912-LYSKO-A; Bertin Technologies, France) with 500 μl of Opti-MEM on a Precellys system (Bertin Technologies, France). Nucleic acids were then extracted using the NucleoSpin RNA virus kit (Macherey-Nagel, Germany).
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6

Synaptophysin expression in rat atrium

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The right atria were homogenized in ice-cold RIPA buffer supplemented with protease inhibitors (AEBSF, 2 mM; aprotinin, 0.3 μM; bestatin, 130 μM; E-64, 14 μM; leupeptin, 1 μM) using the Precellys system (Bertin Technologies, France). Proteins (10 μg) were separated on a 4-15% SDS-PAGE (Biorad, Denmark) and blotted onto hybond-P polyvinylidene fluoride transfer membranes (Amersham Biosciences, Denmark). Membranes were incubated with anti-synaptophysin antibody (0.2 μg/ml, Santa Cruz Biotechnology, USA). Synaptophysin is essential for synaptic vesicle regulation neurons and is a marker of nerve synapses. Immunoreactive proteins were detected by HRP-linked donkey anti-rabbit antibody (8 ng/ml, Jackson Immunosearch Laboratories, UK). Membranes were stripped and re-probed with anti-actin antibody (MAB1501, Millipore, Denmark). Protein band density was quantified as a Gaussian densiometric trace on the exposed films and processed equally. Immunoblotting was repeated three times and the average ratio of Synaptophysin/Actin bands density was calculated for each sample and used for the comparison between groups.
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7

Pneumonia Induction Protocol in Mice

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For induction of pneumonia (Inoshima et al., 2011 (link); Popov et al., 2015 (link)), centrifuged bacteria (see above) were resuspended in endotoxin-free PBS at a density of approximately 1010 CFUs/ml (for experiments performed at Stanford University) or approximately 2x 109 CFUs/ml (for experiments performed at the Medical University of Vienna) – the different inoculates of bacteria used were applied due to differing susceptibilities of wildtype mice in pilot experiments (data not shown), which might be explained by differences in housing conditions or microbiome composition. Anesthetized mice were intranasally inoculated with 30 μl in the left nostril (to achieve inoculates of approximately 3x 108 or 6x 107 CFUs/mouse, respectively). Body temperature was measured using a rectal thermometer.
Tissues for bacterial quantification, RNA and protein analysis were homogenized using the Precellys system (Bertin Instruments).
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8

Quantifying Intratissular Bacteria

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Organs were homogenized in 2 mL (brain, spleen, intestine, Peyer’s patches, MLN) or 7 mL tubes (liver) containing a mix of 1.4 and 2.8 mm glass beads and sterile water using the Precellys system (Bertin Technologies). For quantification of intratissular bacteria, small intestine and Peyer’s patches were treated with 200 mg/L gentamicin for 2 hr at room temperature to kill extratissular bacteria before being washed three times in PBS and homogenized. Cultured cells were lysed with ice-cold water.
Serial dilutions were plated on Todd Hewitt medium (Becton Dickinson), and on Granada medium (bioMérieux) for intestine, Peyer’s patches, and MLN. Plates were incubated 24 hr at 37°C in aerobic (Todd Hewitt medium) or anaerobic (Granada medium) atmosphere.
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9

Efficient RNA Extraction from Tissues

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Distal jejunum and liver left lobe were homogenized in 2-ml and 7-ml tubes containing a mix of 1.4-diameter and 2.8-mm-diameter glass beads and 1 ml and 2 ml Trizol, respectively, using a Precellys system (Bertin Technologies). RNA extractions from organs and cultured cells were performed using a NucleoSpin RNA II kit (Macherey-Nagel) before cDNA synthesis and RT-qPCR were performed with the primers listed in Table S6 in the supplemental material.
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10

Efficient Viral and Bacterial Nucleic Acid Extraction

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Viral RNA and bacterial DNA were extracted from 170-μl amounts of nasal swab, raw BAL fluid, and fecal swab samples using the NucleoMag pathogen kit (Macherey-Nagel, Germany) on the KingFisher Flex purification system (Thermo Fisher Scientific, MA, USA) according to the manufacturer’s instructions. Total RNA was extracted from pelleted cells of BAL fluid samples with the NucleoMag RNA kit (Macherey-Nagel, Germany) on the KingFisher Flex purification system (Thermo Fisher Scientific, MA, USA). Extraction of viral RNA and bacterial DNA from tissues (30-mg amounts of nasal turbinate, trachea, and lung lobe samples) were obtained by lysis in Precellys lysing kit tubes (catalog number P000912-LYSKO-A; Bertin Technologies, France) with 500 μl of Opti-MEM on a Precellys system (Bertin Technologies, France). Nucleic acids were then extracted using the NucleoSpin RNA virus kit (Macherey-Nagel, Germany).
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