Log In Sign up
The largest database of trusted experimental protocols

Diethylpyrocarbonate treated water

Manufactured by Merck Group
Visit Supplier
Sourced in China

Diethylpyrocarbonate-treated water is a laboratory reagent used to inactivate ribonucleases (RNases) in aqueous solutions. It is commonly employed in RNA-based experiments to prevent degradation of RNA samples.

Automatically generated - may contain errors

Lab products found in correlation

Rnase r, by Geneseed (3 mentions) Neutral buffered formalin, by Merck Group (2 mentions) Microtome, by Leica (2 mentions) Dimethyl sulfoxide (dmso), by Merck Group (2 mentions) Actinomycin d, by Merck Group (2 mentions) Nanodrop 2000 spectrophotometer, by Thermo Fisher Scientific (2 mentions) Trizol reagent, by Merck Group (1 mentions) Rnase r, by Merck Group (1 mentions) Sybr premix ex taq reagent, by Takara Bio (1 mentions) Cfx96 real time system, by Bio-Rad (1 mentions) Microm hm 355s microtome, by Thermo Fisher Scientific (1 mentions) Histoclear, by National Diagnostics (1 mentions) Nanodropr nd 1000 spectrophotometer, by Thermo Fisher Scientific (1 mentions) Trizol reagent, by Takara Bio (1 mentions) Primescript rt reagent kit with gdna eraser, by Takara Bio (1 mentions) 15 mer poly dt oligonucleotide, by Thermo Fisher Scientific (1 mentions) Superscript reverse transcriptase, by Thermo Fisher Scientific (1 mentions) Trizol reagent, by Molecular Research Center (1 mentions)

Close spelling variants of this product

Diethylpyrocarbonate water (3 citations)

10 protocols using diethylpyrocarbonate treated water

1

Intestinal Tissue Harvesting and Histological Processing

Check if the same lab product or an alternative is used in the 5 most similar protocols
Either the entire intestinal tract was removed and divided into small
intestine (proximal, middle, and distal) and colon, or in case of
wounding/colitis experiments, only the colon was removed. The intestines were
flushed with phosphate-buffered saline, opened longitudinally using a gut
preparation apparatus, and fixed overnight in 10% neutral buffered formalin
(Merck, Readington, NJ). The tissues were then embedded in paraffin and
sectioned at 4 μm using a microtome (Leica, Buffalo
Grove, IL) with diethylpyrocarbonate-treated water (Merck) in the water
bath.
To find the ulcers generated by biopsy wounding, the entire tissue block
was sectioned, and 4 serial sections collected, followed by a
50-μm trim (discarded), throughout the block.
H&E staining was performed on 1 of 4 sections of each series following
standard procedures, leaving 3 blank slides per series for other stains. The
mid-ulcer series of sections was determined for all ulcers by identifying their
range within the entire set of H&E slides per block. For whole-mount
scanning, colons were washed with cold phosphate-buffered saline, whole-mounted,
and fixed in 4% paraformaldehyde for 3 hours at room temperature. In situ
hybridization, immunohistochemistry, multiplex, and whole-mount staining were
completed using standard techniques described in detail in the Supplementary
Methods.
Koppens M.A., Davis H., Valbuena G.N., Mulholland E.J., Nasreddin N., Colombe M., Antanaviciute A., Biswas S., Friedrich M., Lee L., Wang L.M., Koelzer V.H., East J.E., Simmons A., Winton D.J, & Leedham S.J. (2021). Bone Morphogenetic Protein Pathway Antagonism by Grem1 Regulates Epithelial Cell Fate in Intestinal Regeneration. Gastroenterology, 161(1), 239-254.e9.
+ Open protocol
+ Expand
2

Intestinal Tissue Harvesting and Histological Processing

Check if the same lab product or an alternative is used in the 5 most similar protocols
Either the entire intestinal tract was removed and divided into small
intestine (proximal, middle, and distal) and colon, or in case of
wounding/colitis experiments, only the colon was removed. The intestines were
flushed with phosphate-buffered saline, opened longitudinally using a gut
preparation apparatus, and fixed overnight in 10% neutral buffered formalin
(Merck, Readington, NJ). The tissues were then embedded in paraffin and
sectioned at 4 μm using a microtome (Leica, Buffalo
Grove, IL) with diethylpyrocarbonate-treated water (Merck) in the water
bath.
To find the ulcers generated by biopsy wounding, the entire tissue block
was sectioned, and 4 serial sections collected, followed by a
50-μm trim (discarded), throughout the block.
H&E staining was performed on 1 of 4 sections of each series following
standard procedures, leaving 3 blank slides per series for other stains. The
mid-ulcer series of sections was determined for all ulcers by identifying their
range within the entire set of H&E slides per block. For whole-mount
scanning, colons were washed with cold phosphate-buffered saline, whole-mounted,
and fixed in 4% paraformaldehyde for 3 hours at room temperature. In situ
hybridization, immunohistochemistry, multiplex, and whole-mount staining were
completed using standard techniques described in detail in the Supplementary
Methods.
Koppens M.A., Davis H., Valbuena G.N., Mulholland E.J., Nasreddin N., Colombe M., Antanaviciute A., Biswas S., Friedrich M., Lee L., Wang L.M., Koelzer V.H., East J.E., Simmons A., Winton D.J, & Leedham S.J. (2021). Bone Morphogenetic Protein Pathway Antagonism by Grem1 Regulates Epithelial Cell Fate in Intestinal Regeneration. Gastroenterology, 161(1), 239-254.e9.
+ Open protocol
+ Expand
3

Validating circVPS33B Stability in XGC-1 Cells

Check if the same lab product or an alternative is used in the 5 most similar protocols
To verify the stability of circVPS33B in XGC-1 cells, we performed actinomycin D treatment and RNase R digestion. For actinomycin D treatment, XGC-1 cells were cultured in a complete medium supplemented with 2 μg/mL actinomycin D (Sigma, St Louis, MO, USA) or dimethyl sulfoxide (Sigma). For RNA digestion, total RNA from XGC-1 cells was incubated with 3 U/μg RNase R (Geneseed, Guangzhou, China) or diethylpyrocarbonate-treated water (Sigma).
Lu Y., Cheng J., Cai W., Zhuo H., Wu G, & Cai J. (2021). Inhibition of circRNA circVPS33B Reduces Warburg Effect and Tumor Growth Through Regulating the miR-873-5p/HNRNPK Axis in Infiltrative Gastric Cancer. OncoTargets and therapy, 14, 3095-3108.
+ Open protocol
+ Expand
4

Transcriptome analysis of Antarctic alga

Check if the same lab product or an alternative is used in the 5 most similar protocols
Cell cultures of E. focardii constantly grown at 4 °C were incubated at 0 °C, 4 °C and 12 °C, for 1 and 2 hours. Total RNA was extracted from ~20000 cells (representing a mix of both TN1 and TN15 strains) using TRIzol reagent (Sigma, Milan, Italy) according to manufacturer’s instructions. Isolated RNA was resuspended in diethylpyrocarbonate treated water (Sigma) and subjected to DNase I (from Carlo Erba, Milan Italy) treatment to remove genomic DNA. Total RNA concentration was measured at 260 nm with UV spectrophotometer (UV 1600PC). RNA integrity was verified by denaturing electrophoresis of a 2 µg sample on 1% agarose gel. DNase I-treated RNA samples were used as the template to amplify the E. focardii SSUrRNA gene to verify the absence of genomic DNA contamination. First strand cDNA was synthesized at 42 °C for 1 h from 2 µg of total RNA using random hexamer primers (5 ng/µl final concentration) and Moloney murine leukemia virus reverse transcriptase (Lucigen, Middleton, WI, USA).
Pischedda A., Ramasamy K.P., Mangiagalli M., Chiappori F., Milanesi L., Miceli C., Pucciarelli S, & Lotti M. (2018). Antarctic marine ciliates under stress: superoxide dismutases from the psychrophilic Euplotes focardii are cold-active yet heat tolerant enzymes. Scientific Reports, 8, 14721.
+ Open protocol
+ Expand
5

Determining CircABCA1 Structural Stability

Check if the same lab product or an alternative is used in the 5 most similar protocols
The ring structure of circABCA1 was determined by actinomycin D and RNaseR treatment. Total RNA from VSMCs was incubated with 3 U/μg RNase R (Geneseed, China) or diethylpyrocarbonate-treated water (Sigma) at 37 °C.
To test for genetic stability, transfected VSMCs were treated with 4 μM actinomycin D for 0 h, 2 h, 4 h and 6 h, and analyzed by quantitative PCR to determine circABCA1 or GAPDH levels.
Yu F., Liu J, & Wei X. (2024). Circ-ABCA1 promotes oxidized low-density lipoprotein-induced inflammation and phenotypic switch in vascular smooth muscle cells. Clinics, 79, 100343.
+ Open protocol
+ Expand
6

Stability of circSOD2 in AML12 Cells

Check if the same lab product or an alternative is used in the 5 most similar protocols
To ascertain the stability of circSOD2 within AML12 cells, we employed treatments with Actinomycin D and RNase R. AML12 cells (1 × 106) were incubated in complete medium supplemented with 2 μg/mL Actinomycin D (Sigma) or Dimethyl Sulfoxide (Sigma) as a control. For RNA digestion, total RNA from AML12 cells (1 × 105) was incubated with 3 Units/μg RNase R (Geneseed, Guangzhou, China) or Diethyl Pyrocarbonate-treated water (Sigma) as a control. circSOD2 and linear Glyceraldehyde 3-Phosphate Dehydrogenase (GAPDH) mRNA were quantified via quantitative Reverse Transcription Polymerase Chain Reaction (RT-qPCR).
Chen F., Xing Y., Chen Z., Chen X., Li J., Gong S., Luo F, & Cai Q. (2024). Competitive adsorption of microRNA-532-3p by circular RNA SOD2 activates Thioredoxin Interacting Protein/NLR family pyrin domain containing 3 pathway and promotes pyroptosis of non-alcoholic fatty hepatocytes. European Journal of Medical Research, 29, 250.
+ Open protocol
+ Expand
7

Tissue-Specific RNA Extraction and Expression Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
Total RNA was extracted from longissimus dorsi muscle, adipose, liver, and proximal colon tissues using TRIzol reagent (Waltham, MA, USA). The final RNA was eluted in an appropriate amount of 0.1% diethylpyrocarbonate-treated water (Sigma-Aldrich, Inc., St. Louis, MO, USA), and the total RNA concentration was determined using a NanoDrop™ 2000 spectrophotometer (Thermo Scientific, Waltham, MA, USA). For cDNA preparation, total RNA was reverse-transcribed using ImProm-II™ Reverse Transcriptase reagent (Promega, Madison, WI, USA). The expression levels of the target mRNAs were amplified by PCR using SYBR premix ExTaq reagents (TaKaRa Bio, Mountain View, CA, USA) and CFX96™ Real-Time System (BIO-RAD, Hercules, CA, USA) in the Bio-Health Materials Core-Facility, Jeju National University. The specific primers used for amplifying the representative genes are listed in Supplementary Table S2. Gene expression levels were calculated using the 2−ΔΔCT method. The mRNA levels of the tested genes were normalized to that of glyceraldehyde-3-phosphate dehydrogenase (GAPDH).
Kim D., Min Y., Yang J., Heo Y., Kim M., Hur C.G., Lee S.C., Lee H.K., Song K.D., Heo J., Son Y.O, & Lee D.S. (2021). Multi-Probiotic Lactobacillus Supplementation Improves Liver Function and Reduces Cholesterol Levels in Jeju Native Pigs. Animals : an Open Access Journal from MDPI, 11(8), 2309.
+ Open protocol
+ Expand
8

Tissue Harvesting and Histological Processing

Check if the same lab product or an alternative is used in the 5 most similar protocols
Animals were killed by an overdose of isoflurane (Piramal Critical Care, West Drayton, UK) and exsanguination from the inferior vena cava. Blood was collected using heparinised needles. AGs for RT-qPCR were dissected into ice-cold phosphate buffered saline (PBS, in mM: 137 NaCl, 2.7 KCl, 4 Na2H2PO4.7H2O, 1.5 KH2PO4) in diethyl pyrocarbonate-treated water (0.1%, v/v, Sigma). For histology, mice were perfused-fixed with 5 mL PBS followed by 5 mL 4% paraformaldehyde (PFA)/PBS (w/v) (Sigma). Dissected AGs were fixed in 4% PFA/PBS overnight, transferred into 70% (v/v) ethanol then dehydrated in an ascending ethanol series ending in histoclear (National Diagnostics, Atlanta, US), embedded in 60°C paraffin and sectioned to 4 μm thickness with a Microm HM 355S microtome (Thermo Fisher Scientific).
Eckardt L., Prange-Barczynska M., Hodson E.J., Fielding J.W., Cheng X., Lima J.D., Kurlekar S., Douglas G., Ratcliffe P.J, & Bishop T. (2021). Developmental role of PHD2 in the pathogenesis of pseudohypoxic pheochromocytoma. Endocrine-Related Cancer, 28(12), 757-772.
+ Open protocol
+ Expand
9

Quantitative RNA Expression Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
Total RNA was extracted from DI using Trizol reagent (Takara, Beijing) and electrophoresed on a 1.2% agarose gel to evaluate the integrity, with RNA concentration assessed using NanoDrop R ND-1000 spectrophotometer (Thermo Scientific, Waltham, MA, United States). The first cDNA strand was synthesized by reversely transcribing purified 1 µg total RNA using PrimeScript RT reagent Kit with gDNA Eraser (RR047A; Takara Biotech) according to the manufacturer's indication. The real-time qPCR (rt-qPCR) assays were performed in a total volume of 25 µL consisted of 1 µL of 200 ng/µL complementary cDNA product, 1 µL of each specific primer (10 µM), 12.5 µL of TYBR Green PCR Master Mix [c R Premix Ex Taq TM (Tli RNase H Plus)] (Takara, Japan), 9.5 µL of diethylpyrocarbonate-treated water (Sigma-Aldrich). The reaction conditions of qPCR amplification were employed as following conditions: 95 • C for 2 min and then 40 cycles of 95 • C for 10 s, 60 • C for 20 s, and 72 • C for 20 s. A melting curve analysis was performed after each amplification phase to confirm that any product detected was specific to the desired amplicon. Fold changes were calculated after normalization to reference gene β-actin using relative quantitative method (2 -CT ). Primer sequences are listed in Table 2.
Dai J., Ou W., Yu G., Ai Q., Zhang W., Mai K., & Zhang Y. (2020). The Antimicrobial Peptide Cecropin AD Supplement Alleviated Soybean Meal-Induced Intestinal Inflammation, Barrier Damage, and Microbial Dysbiosis in Juvenile Turbot, Scophthalmus maximus. Frontiers in Marine Science, 7.
+ Open protocol
+ Expand
10

Quantifying hNIS Expression in Lymphoid Tissues

Check if the same lab product or an alternative is used in the 5 most similar protocols
Organs were removed from immunized mice and lysed using a homogenizer. Total RNA was extracted from lysates in the presence of RNase inhibitors using TRIzol reagent (Molecular Research Center, Cincinnati, OH, USA). Isolated RNA was dissolved in diethyl pyrocarbonatetreated water (Sigma-Aldrich, St. Louis, MO, USA) and used to generate cDNA using a 15mer poly dT oligonucleotide (Invitrogen, Carlsbad, CA, USA) and Superscript reverse transcriptase (Gibco) with incubation at 37°C for 1 h according to the manufacturer's protocol.
Expression of the hNIS gene was detected in dLNs, non-dLNs, and spleen by RT-PCR using the primers: 5'-GGCTCCTCGGTGACTCTAGGATGC-3' (forward) and 5'-CATGAATTCTGGGCTCAATTTTCTTGTCC-3' (reverse). To confirm DNA integrity, the mouse β-actin gene (codons 135-223) was amplified with the primers 5'-GGCTCCTCGGTGACTCTAGGATGC-3' (forward) and 5'-CATGAATTCTGGGCTCAATTTTCTTGTCC-3' (reverse) under the following conditions: 34 cycles of 94°C at 60 s, 55°C at 60 s, and 72°C at 60 s.
Son H.Y., Apostolopoulos V., Chung J.K., Kim C.W, & Park J.U. (2018). Protective efficacy of a plasmid DNA vaccine against transgene-specific tumors by Th1 cellular immune responses after intradermal injection. Cellular immunology, 329.
+ 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?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!