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11 protocols using precellys tube

1

Tear Metabolite Extraction and Analysis

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The Schirmer strip tears collection was performed in fasting patients in the morning using Schirmer-Plus strips (GECIS®, Neung sur Beuvron, France) in sterile conditions, placed at the 2-3/1-3 outer junction of the lower eyelid and left in place for 5 min, without prior local anesthetic. The tear-soaked strips were then placed in Eppendorf® tubes, which were immediately transferred in liquid nitrogen, before being sent to our Biological Resource Center for conservation at −80 °C.
A tear volume of 15 µL was collected as described [11 (link)] by cutting the soaked strips at 21 mm from their edge. The strips were then transferred into precooled 2.0 mL homogenization Precellys tubes (Bertin Technologies, Montigny-le-Bretonneux, France) prefilled with 1.4-mm diameter ceramic beads and 20 μL of cold methanol. The strips were homogenized by two grinding cycles, each at 6500 rpm for 30 s, spaced 20 s apart, using a Precellys® homogenizer kept at +4 °C. The supernatant containing the metabolites was recovered after centrifuging at 20,000× g for 10 min and kept at −80 °C until analysis.
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2

Lung Tissue Sample Preparation and Analysis

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Immediately after exsanguination, the lungs including trachea and larynx were removed en bloc, rinsed in saline, blotted dry, and weighed. The preparation of the lung was performed after placing the lung on weighed cellulose swabs to collect leaking fluid during preparation (Figure 1). The trachea including the larynx was cut just above the first airway bifurcation and transferred to a weighed vial. A small piece (30–60 mg) of parenchyma was cut with a scalpel from the lateral part of the left lung. For preparation of the bronchial sample, the remaining lung was held in place with forceps at the bifurcation while the parenchyma was squished by gently knocking with the back part of curved forceps. Afterwards, the destroyed parenchyma was carefully stripped from the bronchi up to the third airway generation. Finally, the remaining tissue and the cellulose swabs were collected for further analysis. Having finished the preparation, all collected samples were weighed, transferred to 7 mL Precellys® tubes (Bertin Instruments, Montigny-le-Bretonneux, France), and 4 parts of acetonitrile/methanol (1:1) solution were added. Samples were homogenized using a Precellys® homogenizer. After centrifugation, supernatants were stored at −20 °C.
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3

Taenia crassiceps Cyst Extraction

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Taenia crassiceps (Tc) cysts (ORF strain) were extracted from infected mice, washed, and loaded into 2 mL Precellys tubes (Bertin Technologies S.A.S, cat no. SK38). Phosphate-buffered saline (PBS) with a protease inhibitor cocktail was added to bring volumes to the topmost demarcation on the tubes. Using the Precellys 24 (Bertin Instruments, #P000669-PR240-A), tubes were thrice homogenized for 20 seconds at 5000 revolutions per minute (RPM) and then centrifuged for 2 minutes at 2000 RPM. The aqueous phase was then removed and placed into a 50 mL tube (Fisher Scientific, #14-432-22) on ice. Another 1 mL of PBS with protease inhibitor was added to each Precellys tube for a second homogenization. This was repeated twice more for a total of 4 homogenizations. After the final homogenization, all remaining fluid was transferred to a a 50ml conical tube and sonicated on ice at 60 amps for 3 cycles of 60 seconds each with 60 seconds of rest in between. The fluid was transferred into a 125 mL Erlenmeyer flask and a magnetic stir bar was used to stir the solution overnight at 4°C. Finally, the product was centrifuged at 33745 relative centrifugal force (RCF) for 60 minutes at 4°C and the aqueous phase was decanted, filtered through a 45-um filter, aliquoted, and stored overnight at -20°C and then -80°C.
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4

Macaque and Mangabey Fecal Sampling

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Frozen feces and intestinal tissue homogenates were accessed for this study. Approximately 1mL of macaque stool was originally collected fresh from each animal by inserting a sterile swab 2 cm into the rectum and spinning to collect available sample. Approximately 1 gram of mangabey feces was collected opportunistically from all animals within one hour of defecation on grossly uncontaminated surfaces (areas with no other pre-existing urine, water, food, natural substrates, or feces). Collected feces were snap-frozen and stored at −80°C until accession. To obtain intestinal biopsies, animals were sedated with 3-4 mg/kg Telazol administered intramuscular and isoflurane gas by intubation, to effect. Successful anesthetization was monitored by response to stimuli. For rectal biopsies, fecal material was removed from the rectum and biopsies obtained with biopsy forceps. Jejunal biopsies were obtained by video-guided endoscopy. 10 pinch biopsies were obtained per animal. Biopsies were maintained in RPMI-1640 medium for transport, rinsed twice with PBS, and transferred to soil-grinding Precellys tubes (Bertin Technologies, France). Samples were homogenized in 1 mL TRIzol (ThermoFisher Scientific, USA) at room temperature on a Precellys 24 homogenizer at 5000 revolutions per minute (RPM) in 4 successive 20 sec intervals and immediately transferred to −80°C for storage.
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5

Tissue Homogenization and RNA Extraction

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Isolated tissues were removed from RNAlater solution and weighed. Following tissue transfer to Precellys® tubes (Bertin Instruments, one per tissue), 350 µl of RLT buffer with 1% β-mercaptoethanol (QIAGEN) was added for every 10 mg of tissue. Tubes were placed into a Precellys® 24-dual homogenizer and homogenized at 5500 r.p.m. for 20 s. For samples that were insufficiently homogenized, the procedure was repeated. Cell pellets from the MACS purification were resuspended in 300 µl RLT buffer with 1% β-mercaptoethanol for every 1 × 106 cells and incubated for 5 min at room temperature. Lysates were transferred to a QiaShredder tube (QIAGEN) and centrifuged at 13,000 r.c.f. for 2 min.
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6

Recombinant Aspergillus Protein Expression

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The A. fumigatus recombinant (r) proteins were expressed in E. coli Rosetta with IPTG induction as described above and bacterial cell pellets frozen at -80°C, resuspended in PBS or pre-rehydration buffer, and homogenized in precellys tubes (Bertin Technologies, Montigny-le-Bretonneux, France) with quartz sand (0.4 – 0.8 mm, Carl Roth) with a Precellys 24 Homogenzier (6800 rpm 3 x 30 sec twice). After centrifugation, supernatants were stored at -80°C. The acetone precipitation of r proteins was performed as described for A. fumigatus TP, to reduce bacterial product background in one-dimensional (1D) immunoblot analyses.
The acetone precipitated r proteins were used to test their immunoreactivity with the serum samples used before (Table 1). Precipitated bacterial lysates with overexpressed r proteins were separated by (1D) PAGE. As controls, acetone precipitated bacterial lysate before IPTG induction (negative control) and rAsp f 1 pure protein (positive control, kindly provided by Dr. Claudio Rhyner, SIAF, Davos, Switzerland) were included. PAGE, blotting, serum, and detection antibodies (Pan-Ig, IgG4/7, IgG3/5, goat-anti-mouse AlexaFluor® 647) were applied as described above for 2D immunoblots (Table 2).
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7

RT-qPCR Analysis of SARS-CoV-2 in Hamster Lungs

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Hamster lung tissues were collected after sacrifice and were homogenized using bead disruption (Precellys tubes, Bertin Corp., Rockville, MD, USA) in TRK lysis buffer (E.Z.N.A.® Total RNA Kit, Omega Bio-tek, Norcross, GA, USA) and centrifuged (10,000 rpm, 5 min) to pellet the cell debris. RNA was extracted according to the manufacturer’s instructions. Of 50 μL eluate, 4 μL was used as a template in RT-qPCR reactions. RT-qPCR was performed on a LightCycler96 platform (Roche Diagnostics, Diegem, Belgium) using the iTaq Universal Probes One-Step RT-qPCR kit (BioRad, Temse, Belgium) with N2 primers and probes targeting the nucleocapsid [10 (link),11 (link)]. Standards of SARS-CoV-2 cDNA (IDT) were used to express viral genome copies per mg tissue or per mL serum.
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8

Macaque and Mangabey Fecal Sampling

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Frozen feces and intestinal tissue homogenates were accessed for this study. Approximately 1mL of macaque stool was originally collected fresh from each animal by inserting a sterile swab 2 cm into the rectum and spinning to collect available sample. Approximately 1 gram of mangabey feces was collected opportunistically from all animals within one hour of defecation on grossly uncontaminated surfaces (areas with no other pre-existing urine, water, food, natural substrates, or feces). Collected feces were snap-frozen and stored at −80°C until accession. To obtain intestinal biopsies, animals were sedated with 3-4 mg/kg Telazol administered intramuscular and isoflurane gas by intubation, to effect. Successful anesthetization was monitored by response to stimuli. For rectal biopsies, fecal material was removed from the rectum and biopsies obtained with biopsy forceps. Jejunal biopsies were obtained by video-guided endoscopy. 10 pinch biopsies were obtained per animal. Biopsies were maintained in RPMI-1640 medium for transport, rinsed twice with PBS, and transferred to soil-grinding Precellys tubes (Bertin Technologies, France). Samples were homogenized in 1 mL TRIzol (ThermoFisher Scientific, USA) at room temperature on a Precellys 24 homogenizer at 5000 revolutions per minute (RPM) in 4 successive 20 sec intervals and immediately transferred to −80°C for storage.
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9

Tissue Preservation and Protein Extraction

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For protein analysis, dissected tissues were immediately snap frozen, while for RNA analysis, organs were first submerged in RNAlater™ Stabilization Solution (AM7021, ThermoFisher) for 24 h at 4 °C. Tissues were transferred into Precellys® tubes (Bertin Instruments) together with 50 µl/10 mg RLT buffer (79,216, QIAGEN) containing 1% β-mercaptoethanol (M3148, Sigma-Aldrich) for RNAlater stabilized tissues or 100 µl/10 mg RIPA buffer (R0278, Sigma-Aldrich) containing 1X HALT Protease inhibitor Cocktail (1861279, ThermoFisher) for snap frozen tissues. Tissues were homogenized at 5500 rpm for 20 s using a Precellys® 24 homogenizer (Bertin Instruments). After disruption, protein lysates were incubated for 30 min at 4 °C. Lysates were centrifuged for 20 min at 15,294g to pellet cell debris and supernatant was collected. Protein concentration was measured using Pierce™ BCA Protein Assay Kit (23225, ThermoFisher) according to the manufacturer’s instructions.
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10

Total RNA Extraction from Solid Tumor Tissue

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Total RNA from solid tumor tissue of patients with PCa and adjacent normal tissue was extracted using RNeasy kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. Solid tissues were sliced into small pieces and transferred to a Precellys tube pre-filled with 1.4-mm ceramic beads (Bertin Technologies, Saint-Quentin-en-Yvelines Cedex, France) containing lysis buffer. Cells were lysed under rapid agitation at 6,500 rpm for 1 minute in three cycles using a Precellys 24 homogenizer (Bertin Technologies). cDNA was synthesized from 1 μg of total RNA with oligo(dT) primer using an AffinityScript QPCR cDNA synthesis kit (Stratagene, Santa Clara, CA), according to the manufacturer’s instructions. The amount and quality of RNA were analyzed using Nanovue (GE Healthcare, Piscataway, NJ) and bioanalyzer (Agilent Technologies, Palo Alto, CA), respectively.
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