Messageamp 2 bacteria kit

Manufactured by Thermo Fisher Scientific

Sourced in United States

The MessageAmp II-Bacteria kit is a lab equipment product designed for the amplification of bacterial RNA. It provides a streamlined workflow for the extraction and purification of RNA from bacterial samples, enabling researchers to obtain high-quality RNA for downstream applications such as gene expression analysis.

Automatically generated - may contain errors

Lab products found in correlation

Rneasy mini kit, by Qiagen (4 mentions) 2100 bioanalyzer, by Agilent Technologies (3 mentions) Qiaquick pcr purification kit, by Qiagen (3 mentions) Qubit fluorometer, by Thermo Fisher Scientific (2 mentions) Turbo dnase, by Thermo Fisher Scientific (2 mentions) Nanodrop spectrophotometer, by Thermo Fisher Scientific (2 mentions) Universal riboclone cdna synthesis system, by Promega (2 mentions) Model 2100 bioanalyzer, by Agilent Technologies (1 mentions) Biotin 11 ctp, by PerkinElmer (1 mentions) Qubit rna hs assay kit, by Thermo Fisher Scientific (1 mentions) 7gplus genechip scanner, by Thermo Fisher Scientific (1 mentions) Rneasy plus mini kit, by Qiagen (1 mentions) Hiseq 4000 platform, by Illumina (1 mentions) Microbenrich, by Thermo Fisher Scientific (1 mentions) Microbexpress, by Thermo Fisher Scientific (1 mentions) Ribominus plant kit for rna seq, by Thermo Fisher Scientific (1 mentions) Glycoblue coprecipitant, by Thermo Fisher Scientific (1 mentions) Sureprep rna cleanup and concentration kit, by Thermo Fisher Scientific (1 mentions) Dnase 1, by Zymo Research (1 mentions) Clean concentrator kit, by Zymo Research (1 mentions)

12 protocols using messageamp 2 bacteria kit

Transcriptional Analysis of Yersinia Infection

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

Total RNA was isolated using an RNeasy Plus minikit (Qiagen). RNA was isolated from six independent in vitro samples and from four or six independent in vivo samples collected 1 day or 2 weeks after infection, respectively. As a control, RNA was isolated from three independent samples of uninfected flea digestive tracts. The absence of genomic DNA contamination was verified by PCR using primers matching the chromosomal rtn locus sequences that were identical in the two Yersinia species. RNA quality and integrity were verified using a model 2100 Bioanalyzer and the RNA 6000 Nano Kit assay (Agilent) and quantitated using a Qubit fluorometer and a Qubit RNA HS assay kit (Invitrogen). Purified RNA was stored at −80°C until use.
RNA amplification was carried out as previously described (36 (link)). Briefly, 100 ng of total RNA was amplified and labeled with modified biotin-16-UTP (Roche Molecular Biomedicals) and biotin-11-CTP (PerkinElmer) by using a MessageAmp II-Bacteria kit (Thermo Fisher Scientific). Amplified RNA was then fragmented using Ambion fragmentation reagents (Thermo Fisher Scientific) and hybridized to an RML custom Affymetrix GeneChip containing sequences for all Y. pestis CO92, Y. pestis KIM, and Y. pseudotuberculosis IP32953 predicted open reading frames (ORFs) and intergenic regions and scanned using an Affymetrix 7Gplus GeneChip scanner.

Chouikha I., Sturdevant D.E., Jarrett C., Sun Y.C, & Hinnebusch B.J. (2019). Differential Gene Expression Patterns of Yersinia pestis and Yersinia pseudotuberculosis during Infection and Biofilm Formation in the Flea Digestive Tract. mSystems, 4(1), e00217-18.

+ Open protocol

+ Expand

Genome-wide Transcriptome Analysis of Xanthomonas oryzae

Check if the same lab product or an alternative is used in the 5 most similar protocols

DNA microarrays with 50-bp oligo spots representing 3382 ORFs, approximately 3/4 of the Xoo KACC10331 genome, were synthesized and spotted on addressable electrodes of CustomArray™ 12K microarrays. Microarray analysis was performed according to the CustomArray™ 12K microarray protocol provided by CombiMatrix (CombiMatrix Corp.; http://www.combimatrix.com).
RNA was isolated from a stationary phase culture (OD₆₀₀ = 0.8) using an RNeasy mini kit in accordance with the manufacturer’s instructions (Qiagen, Seoul, Korea). Total RNA was eluted with 50 μl of RNase-free water and quantified using an ultraviolet spectrophotometer (ND-1000). Each sample was run on a 1.2% agarose gel to verify the purity and integrity of the RNA. cDNA was synthesized using the MessageAmp™ II-Bacteria Kit (Thermo Scientific). Polyadenylation of the bacterial RNA was performed using Escherichia coli poly(A) polymerase and tailed RNA reverse-transcribed in a reaction mixture primed with an oligo (dT) primer and ArrayScript™ (Thermo Scientific) reverse transcriptase. Second-strand cDNA was synthesized and purified for in vitro transcription in a reaction mixture containing biotinmodified UTP and T7 RNA polymerase.

Kim H.I, & Park Y.J. (2016). DNA Microarray and Gene Ontology Enrichment Analysis Reveals That a Mutation in opsX Affects Virulence and Chemotaxis in Xanthomonas oryzae pv. oryzae. The Plant Pathology Journal, 32(3), 190-200.

+ Open protocol

+ Expand

Bacterial RNA Extraction and Amplification

Check if the same lab product or an alternative is used in the 5 most similar protocols

RNA was extracted following the RNeasy mini kit (Qiagen, Hilden, Germany) procedure and the ethanol precipitation protocol. The remaining DNA was removed with TurboDNase (Invitrogen, Carlsbad, CA, USA) and the efficiency of removal was tested with PCR. Enrichment of RNA was performed with 20 μL of sample RNA following the procedures of the MICROBEnrich (Ambion, Austin, TX, USA) and MICROBExpress (Ambion, Austin, TX, USA) kits. Thereafter, the MessageAmp II-Bacteria kit (Invitrogen) was used to improve the subsequent amplification and purification: enriched RNA was reverse transcribed to cDNA, which was in vitro transcribed back to amplified RNA (aRNA) using the mentioned kit. Quantifications were simultaneously run with a Nanodrop spectrophotometer (Thermo Fisher) and a Qubit fluorometer (Invitrogen, Carlsbad, CA, USA) using the RNA HS Assay kit and an RNA profile generated with a Bioanalyzer 2100 (Agilent Technologies, Böblingen, Germany). aRNA was shotgun sequenced directly in an Illumina HiSeq4000 platform (CNAG, Barcelona, Spain), generating between 28–35 Gb of 2 × 101 bp reads per sample.

Martínez-Pérez C., Greening C., Bay S.K., Lappan R.J., Zhao Z., De Corte D., Hulbe C., Ohneiser C., Stevens C., Thomson B., Stepanauskas R., González J.M., Logares R., Herndl G.J., Morales S.E, & Baltar F. (2022). Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf. Nature Communications, 13, 117.

+ Open protocol

+ Expand

Plant Ribosomal RNA Depletion for RNA-Seq

Check if the same lab product or an alternative is used in the 5 most similar protocols

A RiboMinus™ Plant Kit for RNA-Seq (Invitrogen) was used for the removal of plant ribosomal RNA (rRNA) from total RNA in accordance with the manufacturer's manual. Then, the rRNA-free RNA fraction was concentrated by precipitation with 2 µL of GlycoBlue™ Coprecipitant (15 µg/µL; Invitrogen), 1/10 V of 3 M sodium acetate, pH 5.5 (Invitrogen), and 3 V of 96% ethanol. RNA precipitate was washed with 70% ethanol and resuspended with 40 µL of RNAse free water. Residual oligonucleotides were removed with DNAse I (Zymo Research, Irvine, CA, USA) and RNA was purified using a Clean & Concentrator™ kit (Zymo Research) in accordance with the manufacturer's instructions. The RNA concentration was measured with Qubit 2.0. To obtain a sufficient amount of mRNA for transcriptome analysis and real-time PCR, a single round of RNA amplification was performed with a MessageAmp II Bacteria kit (Invitrogen). Only plant mRNA was amplified because the polyadenylation step was omitted. The cDNA templates were then removed using DNAse I (Zymo Research) and amplified RNA purification was carried out with a SurePrep RNA Cleanup and Concentration Kit (Fisher BioReagents, Pittsburgh, PA, USA) according to the manufacturer's instructions.

Kusakin P.G., Serova T.A., Gogoleva N., Gogolev Y., & Tsyganov V.E. (2021). Laser Microdissection of Pisum sativum L. Nodules Followed by RNA-Seq Analysis Revealed Crucial Transcriptomic Changes during Infected Cell Differentiation. Agronomy, 11(12), 2504-2504.

+ Open protocol

+ Expand

Metatranscriptomic Sequencing of Total RNA

Check if the same lab product or an alternative is used in the 5 most similar protocols

RNA was extracted as previously detailed (Poretsky et al., 2009a (link)). Briefly, filters were shattered with a mallet, vortexed in falcon tubes containing Power Soil beads (Mobio), and the lysate was mixed with 70% ethanol (1:1 volume). RNA extractions were carried out with the RNeasy Mini Kit (Qiagen). RNA was treated with Turbo DNase (Ambion) and the ribosomal RNA was depleted using the mRNA-only isolation kit (Epicenter), the MicrobeExpress, and MicrobeEnrich kits (Ambion). The enriched mRNAs were linearly amplified using the Message Amp II-Bacteria kit (Ambion), reverse transcribed to double-stranded complementary DNA (cDNA) with the Universal Riboclone cDNA synthesis system (Promega) and purified with the QIAQuick PCR purification kit (Qiagen). The eight cDNA samples were subjected to single-end sequencing in an Illumina MiSeq run.

Alonso-Sáez L., Morán X.A, & González J.M. (2020). Transcriptional Patterns of Biogeochemically Relevant Marker Genes by Temperate Marine Bacteria. Frontiers in Microbiology, 11, 465.

+ Open protocol

+ Expand

Isolation and Labeling of Mycobacterial RNA

Check if the same lab product or an alternative is used in the 5 most similar protocols

Mtb RNA from extracellular and intracellular samples was isolated, amplified, and labeled as previously described (Rohde et al., 2007 (link)). In brief, Mtb in guanidine thiocyanate was pelleted, washed once with PBS supplemented with 0.1% Tween 80, and treated with 10 mg/ml lysozyme. Bacilli were then lysed in 65°C TRIzol (Invitrogen) using silicon beads in a BeadBeater. Bacterial lysate was extracted once with chloroform, and total RNA was purified from the aqueous phase using an RNeasy kit (QIAGEN). Eluted RNA samples were treated with DNase I (Ambion) for 45 min at 37°C before storage at −70°C. The MessageAmpII-Bacteria kit (Ambion) was used to generate amplified RNA (aRNA) from 100 ng of total RNA input. Amino-allyl UTP was incorporated into aRNA during in vitro transcription to allow fluorophore labeling. 10 µg of modified aRNA from each sample was then labeled with Alexa Fluors (Invitrogen). After excess dyes were quenched by hydroxylamine, the labeled aRNA was purified using a MegaClear kit (Ambion).

Liu Y., Tan S., Huang L., Abramovitch R.B., Rohde K.H., Zimmerman M.D., Chen C., Dartois V., VanderVen B.C, & Russell D.G. (2016). Immune activation of the host cell induces drug tolerance in Mycobacterium tuberculosis both in vitro and in vivo. The Journal of Experimental Medicine, 213(5), 809-825.

+ Open protocol

+ Expand

Ribosomal RNA Depletion and cDNA Synthesis

Check if the same lab product or an alternative is used in the 5 most similar protocols

Ribosomal RNA (rRNA) was removed from total RNA via a subtractive hybridization process using sample-specific biotinylated rRNA probes [23] (link). rRNA-subtracted RNA was amplified linearly using the MessageAmp II-Bacteria kit (Ambion, Austin, TX, USA). Amplified RNA was converted to double-stranded cDNA using the Universal RiboClone cDNA synthesis system (Promega, Madison, WI, USA) using random hexamer primers [23] (link). The synthesized cDNA was purified with the QIAquick PCR purification kit (Qiagen, Valencia, CA, USA).

Huang Q., Briggs B.R., Dong H., Jiang H., Wu G., Edwardson C., De Vlaminck I, & Quake S. (2014). Taxonomic and Functional Diversity Provides Insight into Microbial Pathways and Stress Responses in the Saline Qinghai Lake, China. PLoS ONE, 9(11), e111681.

+ Open protocol

+ Expand

Peat Soil Nucleic Acid Coextraction

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

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.

+ Open protocol

+ Expand

Sponge mRNA Isolation and Amplification

Check if the same lab product or an alternative is used in the 5 most similar protocols

Total RNA was extracted as described by Moitinho-Silva et al. [33 (link)], and sponge mRNA was isolated from the total RNA (100 μg) using a Poly(A) Purist MAG kit (Ambion, USA) with two rounds of poly(A) purification. The isolated sponge mRNA was linearly amplified using a MessageAmp II-Bacteria kit (Ambion, USA) as described, except that we omitted the polyadenylation of the template RNA (which is required only for prokaryotic RNA). RNA integrity was analysed using an Experion System (Bio-Rad, USA), and the isolated sponge mRNA was stored at − 80 °C until use.

Ryu T., Seridi L., Moitinho-Silva L., Oates M., Liew Y.J., Mavromatis C., Wang X., Haywood A., Lafi F.F., Kupresanin M., Sougrat R., Alzahrani M.A., Giles E., Ghosheh Y., Schunter C., Baumgarten S., Berumen M.L., Gao X., Aranda M., Foret S., Gough J., Voolstra C.R., Hentschel U, & Ravasi T. (2016). Hologenome analysis of two marine sponges with different microbiomes. BMC Genomics, 17, 158.

+ Open protocol

+ Expand

Microbial mRNA Enrichment from Total RNA

Check if the same lab product or an alternative is used in the 5 most similar protocols

Enrichment of microbial messenger RNA (mRNA) from total RNA was performed based on sample-tailored rRNA-subtraction developed by Stewart et al.18 (link), supplemented with an additional step to remove poly(A)-tailed eukaryotic mRNA19 (link) (see Supplementary document for the detailed protocol). In brief, total RNA was hybridized with biotinylated probes targeting small and large subunits of bacterial, archaeal and eukaryotic rRNA (total six probe types). These probes were generated with PCR-amplification of corresponding DNA samples obtained from different disease developmental stages (CP and BBD; i.e. a total of 12 types of rRNA probes were synthesized). Hybridized rRNA was then removed from total RNA with streptavidin-coated magnet beads. To subtract poly(A)-tailed mRNA from the remaining RNA, oligo d(T)-coated magnetic beads were added subsequently and hybridized beads were removed. Enrichment of microbial mRNA was verified on a 2100 Bioanalyzer (Agilent); ensuring a substantial decline of signature peaks for small and large subunit rRNA in RNA size distribution profiles. Microbial mRNA-enriched RNA was linearly amplified using the MessageAmp II Bacteria kit (Ambion), and double-stranded cDNA was synthesized for each CP and BBD sample.

Sato Y., Ling E.Y., Turaev D., Laffy P., Weynberg K.D., Rattei T., Willis B.L, & Bourne D.G. (2017). Unraveling the microbial processes of black band disease in corals through integrated genomics. Scientific Reports, 7, 40455.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!