Trizol

Manufactured by Next Advance

Sourced in United States

TRIZOL is a reagent used for the isolation and purification of total RNA from a variety of biological samples, including cells, tissues, and organs. It is a mono-phasic solution containing phenol and guanidine isothiocyanate, which facilitates the effective lysis of cells and the subsequent separation of RNA from DNA and proteins.

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Lab products found in correlation

Bullet blender, by Next Advance (3 mentions) Trizol, by Thermo Fisher Scientific (2 mentions) Ion torrent personal genome machine, by Thermo Fisher Scientific (2 mentions) Miniprep kit, by Zymo Research (1 mentions) Superscript first strand synthesis system, by Thermo Fisher Scientific (1 mentions) Rneasy, by Qiagen (1 mentions) Rnase free dnase, by Qiagen (1 mentions) Primescript rt reagent kit with gdna eraser, by Takara Bio (1 mentions) Nebnext ultra directional rna library prep kit, by New England Biolabs (1 mentions) Miracloth, by Merck Group (1 mentions) Trizol, by Takara Bio (1 mentions) 2100 bioanalyzer, by Agilent Technologies (1 mentions) Hiseq 2500 platform, by Illumina (1 mentions) Agilent rna 6000 nano kit, by Agilent Technologies (1 mentions)

6 protocols using trizol

RNA Extraction and Sequencing Protocol

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RNA was collected as three independent biological replicates from mixed sex groups of each life stage (10 adults, approximately 500 eggs, 10 larvae, and 10 pupae per replicate). Tissue was pulverized in TRIZOL (BulletBlender, Next Advance Inc., Averill Park, NY, USA) at speed 8 for 2 min with RNAse-free ziroconium oxide beads. RNA extraction and purification were with a Zymo mini prep kit (Irvine, CA, USA). From the total RNA, DIRECTbeads (Agilient, Santa Clara, CA, USA) were used to isolate polyA mRNA, and libraries were made with a 200 bp RNA-Seq v2 kit (Life Technologies, Grand Island, NY, USA). Samples were sequenced on 318v2 chips on the Ion Torrent Personal Genome Machine (PGM, Life Technologies). Each run provided approximately 1–5 million reads, with a total of 5–12 million reads per life stage (Perkin, Elpidina & Oppert, 2016 (link)). Life stage sequences were deposited at NCBI SRA as part of BioProject PRJNA299695.

Perkin L.C, & Oppert B. (2019). Gene expression in Tribolium castaneum life stages: Identifying a species-specific target for pest control applications. PeerJ, 7, e6946.

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BoNT-A Induced Muscle Tissue RNA Extraction

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Samples were prepared for 5 groups (n =4/group)
that included tissue from TAs of BoNT-A–injected rats at 1, 4, 12, and
52 weeks after injection. Control tissue was obtained from the contralateral TA
of saline-injected rats euthanized at 12 weeks. RNA was extracted with Trizol
(Invitrogen, Carlsbad, California) and RNeasy (Qiagen, Valencia, California).
Briefly, 30 mg of frozen tissue was mixed with 0.5 ml of Trizol and homogenized
at 4°C in a bullet blender (Next Advance, Inc., Averill Park, New York).
The homogenate was mixed with 100 μl of chloroform, and
samples were incubated for 2 minutes at room temperature and spun at 4°C
for 15 minutes. The aqueous portion was removed and mixed with equal amounts of
70% ethyl alcohol. The solution was then washed through an RNeasy spin
column, incubated for 15 minutes with RNAse-free DNAse (Qiagen), washed 3 times,
and eluted according to the manufacturer’s instructions. Absorbance was
measured at 260 nm to determine RNA concentration, and the 260/280-nm absorbance
ratio was calculated to determine RNA purity. RNA was reverse-transcribed into
cDNA using a synthesis system (SuperScript First-Strand Synthesis System; Life
Technologies, Grand Island, New York).

MUKUND K., MATHEWSON M., MINAMOTO V., WARD S.R., SUBRAMANIAM S, & LIEBER R.L. (2014). SYSTEMS ANALYSIS OF TRANSCRIPTIONAL DATA PROVIDES INSIGHTS INTO MUSCLE’S BIOLOGICAL RESPONSE TO BOTULINUM TOXIN. Muscle & nerve, 50(5), 744-758.

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Transcriptome Analysis of Lesser Grain Borer Larvae

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To obtain larvae for dissection, infested wheat kernels with 3–4-week-old R. dominica larvae (30 °C, 65% R.H.; tempered wheat; 100+ adults/jar/week) were X-rayed as in [51 (link)]. A detailed description of the dissection procedure with diagrams is found in File S1.
RNA was extracted and sequenced as in [52 (link)]. Briefly, RNA was collected as three independent biological replicates from each larval tissue (head, gut, carcass). The tissue was pulverized in TRIZOL (BulletBlender, Next Advance Inc., Averill Park, NY, USA) at speed 8 for 2 min with RNAse-free ziroconium oxide beads. RNA extraction and purification were with a Zymo mini prep kit (Irvine, CA, USA). DIRECTbeads (Agilient, Santa Clara, CA, USA) were used to isolate polyA mRNA from total RNA, and libraries were made with a 200 bp RNA-Seq v2 kit (Life Technologies, Grand Island, NY, USA). Samples were sequenced on 318v2 chips on the Ion Torrent Personal Genome Machine (PGM, Life Technologies). Total reads per sample were: head—216,180; gut—263,938; carcass—268,508. Reads for the R. dominica head, gut, carcass data were submitted to SRA SUB6755681.
Differential expression of transcriptome data was determined using ArrayStar (DNAStar Lasergene). Reads were mapped to the R. dominica genome assembly. Read counts were normalized by Reads Per Kilobase of template per Million mapped reads (RPKM, [53 (link)]).

Oppert B., Muszewska A., Steczkiewicz K., Šatović-Vukšić E., Plohl M., Fabrick J.A., Vinokurov K.S., Koloniuk I., Johnston J.S., Smith T.P., Guedes R.N., Terra W.R., Ferreira C., Dias R.O., Chaply K.A., Elpidina E.N., Tereshchenkova V.F., Mitchell R.F., Jenson A.J., McKay R., Shan T., Cao X., Miao Z., Xiong C., Jiang H., Morrison WR I.I.I., Koren S., Schlipalius D., Lorenzen M.D., Bansal R., Wang Y.H., Perkin L., Poelchau M., Friesen K., Olmstead M.L., Scully E, & Campbell J.F. (2022). The Genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success. Genes, 13(3), 446.

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RNA Extraction and RT-qPCR Analysis

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Mycelia were harvested and washed with cold water followed by freezing in liquid nitrogen in the presence of 1ml TRIzol (Ambion, cat. no. 135405) before storing at -80°C until use. Cell lysis was carried out through six cycles of 3 minutes beating in 1 ml ice-cold TRIzol with ~100 μl volume of silica beads using Bullet Blender (Next Advance). Total RNA was extracted as previously described [115 (link)] and the quality was checked on 2% agarose gel. One μg of total RNAs was subjected to reverse transcription into cDNAs using PrimeScript RT reagent Kit with gDNA Eraser (Takara, cat. no. RR047A) according to manufacturer’s protocol. The resultant cDNA samples were diluted twenty folds and 2 μl of diluted samples were subjected to real-time qPCR analysis as described above.

Colabardini A.C., Wang F., Miao Z., Pardeshi L., Valero C., de Castro P.A., Akiyama D.Y., Tan K., Nora L.C., Silva-Rocha R., Marcet-Houben M., Gabaldón T., Fill T., Wong K.H, & Goldman G.H. (2022). Chromatin profiling reveals heterogeneity in clinical isolates of the human pathogen Aspergillus fumigatus. PLoS Genetics, 18(1), e1010001.

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RNA Extraction and Sequencing of Life Stages

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RNA was collected from each of the three biological replicates of each life stage (10 adults, approximately 500 eggs, 10 larvae, and 10 pupae per replicate). All samples were pulverized in TRIZOL (BulletBlender, Next Advance Inc., Averill Park, NY, USA) at speed 8 for 2 min with RNAse-free ziroconium oxide beads. RNA extraction and purification was with a Zymo mini prep kit (Irvine, CA, USA). To obtain mRNA, DIRECTbeads (Agilient, Santa Clara, CA, USA) were used to select polyA RNA, and libraries were made with the 200 base pair RNA-seq v2 kit (Life Technologies, Grand Island, NY, USA). Samples were sequenced on 318v2 chips on the Ion Torrent Personal Genome Machine (PGM) (Life Technologies). Each run provided approximately 1–5 million reads, with a total of 5–12 million reads per life stage (Table S1).

Perkin L., Elpidina E.N, & Oppert B. (2016). Expression patterns of cysteine peptidase genes across the Tribolium castaneum life cycle provide clues to biological function. PeerJ, 4, e1581.

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Fungal Transcriptome Analysis via RNA-seq

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Strains were grown as described above with 1% glucose as the sole carbon source, and mycelia were harvested through filtering using Miracloth (Millipore, Billerica MA, USA), rinsed with cold double-distilled water (ddH₂O), and pressed-dried on paper towel. The dried mycelium pad was immediately frozen in liquid N₂ and kept at –80°C until use. RNA was extracted with TRIzol (9109; TaKaRa) according to the manufacturer's protocol with a modification in the mycelium lysis step, in which mycelia were lysed in TRIzol with five rounds of 3 min beating using a Bullet Blender (Next Advance) with at least 3 min of cooling between cycles. Homogenized samples were incubated at 56°C for 10 min to dissociate the nucleoprotein complex completely before adding chloroform. RNA integrity was analyzed on an Agilent Bioanalyzer 2100 (Stockport, UK) using an Agilent RNA 6000 Nano kit (no. 9780). RNA libraries were prepared using a NEBNext Ultra directional RNA library prep kit (7760; NEB) as per the manufacturer’s instructions and sequenced on the Illumina HiSeq2500 platform at the Genomics and Single-Cell Analysis Core facility at the University of Macau.

Chen Y., Dong L., Alam M.A., Pardeshi L., Miao Z., Wang F., Tan K., Hynes M.J., Kelly J.M, & Wong K.H. (2022). Carbon Catabolite Repression Governs Diverse Physiological Processes and Development in Aspergillus nidulans. mBio, 13(1), e03734-21.

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