Lysis matrix e tubes

Manufactured by MP Biomedicals

Sourced in United States, United Kingdom

Lysis Matrix E tubes are laboratory equipment designed for efficient cell lysis. The tubes contain a matrix that facilitates the disruption of cell membranes, allowing for the release of cellular contents. This core function makes the Lysis Matrix E tubes suitable for various applications that require the extraction of biomolecules, such as DNA, RNA, or proteins, from a wide range of sample types.

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Lab products found in correlation

Nanodrop 2000, by Thermo Fisher Scientific (2 mentions) Agilent high sensitivity d5000 screentape, by Agilent Technologies (1 mentions) Qubit dsdna hs assay, by Thermo Fisher Scientific (1 mentions) Nextera dna flex library prep kit, by Illumina (1 mentions) Nextseq 500 sequencer, by Illumina (1 mentions) Synergy htx plate reader, by Agilent Technologies (1 mentions) Magattract powermicrobiome dna rna ep kit, by Qiagen (1 mentions) Agilent 4200 tapestation, by Agilent Technologies (1 mentions) Qubit 2.0 fluorometer, by Thermo Fisher Scientific (1 mentions) Precellys 24 tissue homogenizer, by Bertin Technologies (1 mentions) Vortex mixer, by Thermo Fisher Scientific (1 mentions) Rnaprotect bacteria reagent handbook, by Qiagen (1 mentions) Rneasy mini kit, by Qiagen (1 mentions) Fastprep machine, by MP Biomedicals (1 mentions) Messageamp 2 bacteria kit, by Thermo Fisher Scientific (1 mentions) Tapestation 4200, by Agilent Technologies (1 mentions) Qiaamp fast dna stool mini kit, by Qiagen (1 mentions) Flow cell adapters and indexing barcodes, by Illumina (1 mentions) Agencourt ampure beads, by Beckman Coulter (1 mentions) Miseq system, by Illumina (1 mentions)

6 protocols using lysis matrix e tubes

Metagenomic Analysis of Stool Samples

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Stool samples were collected at different time points per individual (Supplementary Table 3). DNA was extracted from ~50 mg of stool samples in two stages: an initial homogenization in Lysis Matrix E tubes (MP Biomedicals) with a Precellys 24 Tissue Homogenizer (Bertin Instruments) and processing of the resultant supernatant using the MagAttract PowerMicrobiome DNA/RNA EP kit (Qiagen) on an Eppendorf automated liquid handling system as per the manufacturer’s instructions.
Isolated DNA was checked for concentration and quality on a BioTek Synergy HTX plate reader.
Metagenomic libraries were prepared using the Nextera DNA Flex Library Prep Kit (Illumina) per the manufacturer’s instructions with 100 ng of DNA as sample input. The concentration of the libraries was quantified using the Qubit dsDNA HS assay on a Qubit 2.0 fluorometer (Life Technologies). Library size and quality were assessed via the Agilent High Sensitivity D5000 ScreenTape on an Agilent 4200 Tapestation.
Metagenomic libraries were normalized to an equimolar concentration and pooled. The pool was diluted to 1.8 pM, mixed with a 1% PhiX control library and paired-end sequenced (2 × 75 bp) using a NextSeq 500/550 High Output v2 150-cycle Reagent Cartridge on a NextSeq 500 sequencer (Illumina).

Link V.M., Subramanian P., Cheung F., Han K.L., Stacy A., Chi L., Sellers B.A., Koroleva G., Courville A.B., Mistry S., Burns A., Apps R., Hall K.D, & Belkaid Y. (2024). Differential peripheral immune signatures elicited by vegan versus ketogenic diets in humans. Nature Medicine, 30(2), 560-572.

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Soil and root microbiome fractionation

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A. thaliana plants were harvested from three natural populations: two in Germany (Geyen, Pulheim) and one in France (Saint-Dié). For each population, 16 plant individuals were dug out with their surrounding soil, transferred into sterile falcons and transported on ice to the laboratory. Sample fractionation into soil, root episphere and root endosphere compartments was performed within 12 hours after harvesting (Figure S1B). Soil particles not in contact with roots were transferred to 2 mL Lysis Matrix E tubes (MP Biomedicals, Solon, USA) and are defined as the soil fraction. Plant roots were cut and thoroughly washed with sterile water to remove visible soil particles. Epiphytic microbes were washed away from root systems using extensive shaking in TE buffer supplemented with 0.1% Triton X-100. These washes were filtered through 0.22-μM pore size membranes and considered as the epiphytic fraction. Root systems were then washed successively in 80% EtOH and 0.25% NaOCl to further clean the root surfaces from living microorganisms and subsequently washed three times (1 min each) in sterile water. These microbially-enriched endosphere fractions were transferred to 2 mL tubes. Each of the four biological replicates consists of a pool of four plant individuals.

Durán P., Thiergart T., Garrido-Oter R., Agler M., Kemen E., Schulze-Lefert P, & Hacquard S. (2018). Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival. Cell, 175(4), 973-983.e14.

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RNA Isolation from Bacterial Cells

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RNA isolation was performed in an RNAse-free environment at room temperature using the RNeasy Mini Kit (Qiagen) per the manufacturer's instructions. For B. cereus ATCC 14579 and S. lividans TK24, cells were initially disrupted using a modified bead-beating procedure: cells were resuspended in 400 µl Soil Pro Lysis Buffer (MP Bio), transferred to Lysis Matrix E tubes (MP Bio), and agitated horizontally on a Vortex Mixer (Fisher) with Vortex Adapter (Ambion) for 10 min at speed 10. Beads and cellular debris were pelleted by centrifugation at 16,000 × g for 5 min. 200 µl of the supernatant was used for subsequent RNA isolation. Cell pellets for all other organisms were disrupted according to the ‘Enzymatic Lysis Protocol’ in the RNAprotect Bacteria Reagent Handbook (Qiagen); lysozyme (Thermo-Pierce) was used at 15 mg ml⁻¹. RNA concentrations were determined by absorption at 260 nm using the Nanodrop 2000 (Thermo) and absorption ratios A₂₆₀/A₂₈₀ and A₂₆₀/A₂₃₀ were used to assess sample integrity and purity. Isolated RNA was stored at −80°C until further use.

Zhao S., Sakai A., Zhang X., Vetting M.W., Kumar R., Hillerich B., San Francisco B., Solbiati J., Steves A., Brown S., Akiva E., Barber A., Seidel R.D., Babbitt P.C., Almo S.C., Gerlt J.A, & Jacobson M.P. (2014). Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. eLife, 3, e03275.

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Peat Soil Nucleic Acid Coextraction

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The frozen samples from series D of batch e previously incubated at 3, 4, 5, 14, 15, 16, 24, 25, and 26 °C were homogenized separately with mortar and pestle in liquid nitrogen. Coextraction of RNA and DNA from peat soil was performed as previously described (20 (link)). Briefly, a cetrimonium bromide-containing lysis buffer and phenol:chloroform:isoamylalcohol (25:24:1) were added to all peat samples in lysis matrix E tubes (MP Biomedicals) containing silica beads and exposed to 30 s of vigorous shaking in a FastPrep machine (MP Biomedicals) for the extraction of nucleic acids. After PEG precipitation, ethanol washing and dissolution of pellets in nuclease-free water, nucleic acids were treated with DNase or RNase before metatranscriptome and metagenome generation, respectively. Total RNA was amplified using the MessageAmp II-Bacteria Kit (Ambion Life Technologies) following the kit protocol, except that the linear amplification step was carried out for 14 h. Paired-end 101-bp reads were sequenced using the Illumina HighSeq2000 sequencer (Illumina) at the Norwegian Sequencing Centre (University of Oslo, Oslo, Norway).

Tveit A.T., Urich T., Frenzel P, & Svenning M.M. (2015). Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming. Proceedings of the National Academy of Sciences of the United States of America, 112(19), E2507-E2516.

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Comprehensive Fecal Sample Processing

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Immediately upon receipt, the fecal samples were homogenized, aliquoted, and stored at −80°C until the day of analysis. Total DNA was extracted from fecal samples using the Qiagen Fast QiaAmp DNA Stool Mini Kit (QIAGEN, Valencia, CA, USA) according to the manufacturer’s protocol with the inclusion of a physical lysis step. The sample was lysed in FastPrep-24 (MPBio, Derby, UK) with lysis matrix E tubes (MPBio, Derby, UK) twice at 6.5 m/s for 45 seconds. The hypervariable V4 region of the 16s rRNA gene was amplified by polymerase chain reaction with 515-806 primers tailed with sequences to incorporate Illumina flow cell adapters and indexing barcodes (Illumina, San Diego, USA).
Primer dimers and low-molecular-weight products were removed using Agencourt Ampure Beads (Beckman Coulter, Spain) and samples were quantified and quality checked for amplicon size using the 4200 TapeStation (Agilent Technologies, Santa Clara, CA, USA). Amplicons were pooled in equimolar amounts and sequenced (2 × 250) on an Illumina Miseq system (Illumina, San Diego, USA) according to standard protocols.

Vázquez-Cuesta S., Villar L., García N.L., Fernández A.I., Olmedo M., Alcalá L., Marín M., Muñoz P., Bouza E, & Reigadas E. (2023). Characterization of the gut microbiome of patients with Clostridioides difficile infection, patients with non–C. difficile diarrhea, and C. difficile–colonized patients. Frontiers in Cellular and Infection Microbiology, 13, 1130701.

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Propleural Plate Dissection for RNA Extraction

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At the end of the 10-day feeding experiment, the propleural plates of the propleura were removed from the ventral exoskeleton using a dissection microscope and fine sterile tweezers. Propleural plates from each of the 22 ants in each group were placed together in lysis matrix E tubes (MP Biomedicals) on dry ice, before being snap frozen in liquid nitrogen. A modified version of the Qiagen RNeasy Micro Kit protocol was used for all RNA extractions (Supplementary Note 1). The quantity and purity of all RNA samples was checked using a nanodrop spectrophotometer and a Qubit™ RNA HS assay kit (Invitrogen™).

Worsley S.F., Innocent T.M., Holmes N.A., Al‐Bassam M.M., Wilkinson B., Murrell J.C., Boomsma J.J., Yu D.W., & Hutchings M.I. (2020). Competition-based screening secures the evolutionary stability of a defensive microbiome.

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