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    Structured Review

    Thermo Fisher trizol reagent
    Sample collection, processing and RNA extraction: Whole blood was collected in triplicate followed by peripheral blood mononuclear cells (PBMCs) separation in a subset of samples. The following sample collection tubes were used for the study: RNAgard ® , PAXgene ® RNA, EDTA, ACD-A, and CPT tubes. The <t>PBMC</t> separation was done using standard procedures for CPT tubes, and magnetic bead, LeukoLOCK ™ and LSM methods. The samples were then stored at either 4°C (Cold) or -80°C (Frozen) and shipped overnight (o/n) for follow-up RNA extraction. Next, they were treated with one or more of several different RNA extraction procedures: Biomaxi Precip Buffer/ PAXgene ® Blood miRNA, PAXgene ® Blood miRNA, <t>TRIzol</t> ® LS, ACK Lysing Buffer/ Qiagen miRNeasy, and TRIzol ® Reagent manufacturer’s protocol.
    Trizol Reagent, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 573 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Investigating gene expression profiles of whole blood and peripheral blood mononuclear cells using multiple collection and processing methods"

    Article Title: Investigating gene expression profiles of whole blood and peripheral blood mononuclear cells using multiple collection and processing methods

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0225137

    Sample collection, processing and RNA extraction: Whole blood was collected in triplicate followed by peripheral blood mononuclear cells (PBMCs) separation in a subset of samples. The following sample collection tubes were used for the study: RNAgard ® , PAXgene ® RNA, EDTA, ACD-A, and CPT tubes. The PBMC separation was done using standard procedures for CPT tubes, and magnetic bead, LeukoLOCK ™ and LSM methods. The samples were then stored at either 4°C (Cold) or -80°C (Frozen) and shipped overnight (o/n) for follow-up RNA extraction. Next, they were treated with one or more of several different RNA extraction procedures: Biomaxi Precip Buffer/ PAXgene ® Blood miRNA, PAXgene ® Blood miRNA, TRIzol ® LS, ACK Lysing Buffer/ Qiagen miRNeasy, and TRIzol ® Reagent manufacturer’s protocol.
    Figure Legend Snippet: Sample collection, processing and RNA extraction: Whole blood was collected in triplicate followed by peripheral blood mononuclear cells (PBMCs) separation in a subset of samples. The following sample collection tubes were used for the study: RNAgard ® , PAXgene ® RNA, EDTA, ACD-A, and CPT tubes. The PBMC separation was done using standard procedures for CPT tubes, and magnetic bead, LeukoLOCK ™ and LSM methods. The samples were then stored at either 4°C (Cold) or -80°C (Frozen) and shipped overnight (o/n) for follow-up RNA extraction. Next, they were treated with one or more of several different RNA extraction procedures: Biomaxi Precip Buffer/ PAXgene ® Blood miRNA, PAXgene ® Blood miRNA, TRIzol ® LS, ACK Lysing Buffer/ Qiagen miRNeasy, and TRIzol ® Reagent manufacturer’s protocol.

    Techniques Used: RNA Extraction, Cycling Probe Technology

    Two dimensional Sammon projection using the top 50% of most variable transcripts (25370) for whole blood (red) and PBMC (black). There is a clear distinction in clusters for PBMCs and whole blood sample processing as marked by a black tilted line. All whole blood samples are shown on left side and PBMC samples are on the right side of the plot. The (F) and (C) denotes the frozen and cold conditions for the sample collection and storage. The description of all the legends is given here. PBMCs samples: ACD_Magnetic - blood collected in ACD-A tubes and separated using magnetic method followed by extraction using TRIzol ® method. CPT —blood collected in CPT tubes and PBMCs separation using manufacturer recommendations followed by extraction using TRIzol ® method. EDTA_LSM - blood collected in EDTA tube and PBMC separation using LSM followed by extraction using TRIzol ® method. EDTA_Leukolock - blood collected in EDTA tube, PBMCs separated using LeukoLOCK ™ method followed by extraction using TRIzol ® method. Whole blood samples: ACD - blood collected in ACD-A tube followed by RNA extraction using TRIzol ® LS method. ACD_RBC lysis- blood collected in ACD-A tube followed by RBC lysis using ACK buffer and RNA extraction using miRNAeasy extraction kit. EDTA_RBC lysis -blood collected in EDTA tube followed by RBC lysis using ACK buffer and RNA extraction using miRNAeasy extraction kit. EDTA - blood collected in EDTA tube followed by RNA extraction using TRIzol ® LS method. PAXgene - blood collected in PAXgene ® tube followed by RNA extraction using PAXgene ® blood miRNA kit. RNAgard— blood collected in RNAgard ® tube followed by RNA extraction using Biomaxi ™ Precip Buffer and PAXgene ® Blood miRNA kit.
    Figure Legend Snippet: Two dimensional Sammon projection using the top 50% of most variable transcripts (25370) for whole blood (red) and PBMC (black). There is a clear distinction in clusters for PBMCs and whole blood sample processing as marked by a black tilted line. All whole blood samples are shown on left side and PBMC samples are on the right side of the plot. The (F) and (C) denotes the frozen and cold conditions for the sample collection and storage. The description of all the legends is given here. PBMCs samples: ACD_Magnetic - blood collected in ACD-A tubes and separated using magnetic method followed by extraction using TRIzol ® method. CPT —blood collected in CPT tubes and PBMCs separation using manufacturer recommendations followed by extraction using TRIzol ® method. EDTA_LSM - blood collected in EDTA tube and PBMC separation using LSM followed by extraction using TRIzol ® method. EDTA_Leukolock - blood collected in EDTA tube, PBMCs separated using LeukoLOCK ™ method followed by extraction using TRIzol ® method. Whole blood samples: ACD - blood collected in ACD-A tube followed by RNA extraction using TRIzol ® LS method. ACD_RBC lysis- blood collected in ACD-A tube followed by RBC lysis using ACK buffer and RNA extraction using miRNAeasy extraction kit. EDTA_RBC lysis -blood collected in EDTA tube followed by RBC lysis using ACK buffer and RNA extraction using miRNAeasy extraction kit. EDTA - blood collected in EDTA tube followed by RNA extraction using TRIzol ® LS method. PAXgene - blood collected in PAXgene ® tube followed by RNA extraction using PAXgene ® blood miRNA kit. RNAgard— blood collected in RNAgard ® tube followed by RNA extraction using Biomaxi ™ Precip Buffer and PAXgene ® Blood miRNA kit.

    Techniques Used: Cycling Probe Technology, RNA Extraction, Lysis

    2) Product Images from "Investigating gene expression profiles of whole blood and peripheral blood mononuclear cells using multiple collection and processing methods"

    Article Title: Investigating gene expression profiles of whole blood and peripheral blood mononuclear cells using multiple collection and processing methods

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0225137

    Sample collection, processing and RNA extraction: Whole blood was collected in triplicate followed by peripheral blood mononuclear cells (PBMCs) separation in a subset of samples. The following sample collection tubes were used for the study: RNAgard ® , PAXgene ® RNA, EDTA, ACD-A, and CPT tubes. The PBMC separation was done using standard procedures for CPT tubes, and magnetic bead, LeukoLOCK ™ and LSM methods. The samples were then stored at either 4°C (Cold) or -80°C (Frozen) and shipped overnight (o/n) for follow-up RNA extraction. Next, they were treated with one or more of several different RNA extraction procedures: Biomaxi Precip Buffer/ PAXgene ® Blood miRNA, PAXgene ® Blood miRNA, TRIzol ® LS, ACK Lysing Buffer/ Qiagen miRNeasy, and TRIzol ® Reagent manufacturer’s protocol.
    Figure Legend Snippet: Sample collection, processing and RNA extraction: Whole blood was collected in triplicate followed by peripheral blood mononuclear cells (PBMCs) separation in a subset of samples. The following sample collection tubes were used for the study: RNAgard ® , PAXgene ® RNA, EDTA, ACD-A, and CPT tubes. The PBMC separation was done using standard procedures for CPT tubes, and magnetic bead, LeukoLOCK ™ and LSM methods. The samples were then stored at either 4°C (Cold) or -80°C (Frozen) and shipped overnight (o/n) for follow-up RNA extraction. Next, they were treated with one or more of several different RNA extraction procedures: Biomaxi Precip Buffer/ PAXgene ® Blood miRNA, PAXgene ® Blood miRNA, TRIzol ® LS, ACK Lysing Buffer/ Qiagen miRNeasy, and TRIzol ® Reagent manufacturer’s protocol.

    Techniques Used: RNA Extraction, Cycling Probe Technology

    Two dimensional Sammon projection using the top 50% of most variable transcripts (25370) for whole blood (red) and PBMC (black). There is a clear distinction in clusters for PBMCs and whole blood sample processing as marked by a black tilted line. All whole blood samples are shown on left side and PBMC samples are on the right side of the plot. The (F) and (C) denotes the frozen and cold conditions for the sample collection and storage. The description of all the legends is given here. PBMCs samples: ACD_Magnetic - blood collected in ACD-A tubes and separated using magnetic method followed by extraction using TRIzol ® method. CPT —blood collected in CPT tubes and PBMCs separation using manufacturer recommendations followed by extraction using TRIzol ® method. EDTA_LSM - blood collected in EDTA tube and PBMC separation using LSM followed by extraction using TRIzol ® method. EDTA_Leukolock - blood collected in EDTA tube, PBMCs separated using LeukoLOCK ™ method followed by extraction using TRIzol ® method. Whole blood samples: ACD - blood collected in ACD-A tube followed by RNA extraction using TRIzol ® LS method. ACD_RBC lysis- blood collected in ACD-A tube followed by RBC lysis using ACK buffer and RNA extraction using miRNAeasy extraction kit. EDTA_RBC lysis -blood collected in EDTA tube followed by RBC lysis using ACK buffer and RNA extraction using miRNAeasy extraction kit. EDTA - blood collected in EDTA tube followed by RNA extraction using TRIzol ® LS method. PAXgene - blood collected in PAXgene ® tube followed by RNA extraction using PAXgene ® blood miRNA kit. RNAgard— blood collected in RNAgard ® tube followed by RNA extraction using Biomaxi ™ Precip Buffer and PAXgene ® Blood miRNA kit.
    Figure Legend Snippet: Two dimensional Sammon projection using the top 50% of most variable transcripts (25370) for whole blood (red) and PBMC (black). There is a clear distinction in clusters for PBMCs and whole blood sample processing as marked by a black tilted line. All whole blood samples are shown on left side and PBMC samples are on the right side of the plot. The (F) and (C) denotes the frozen and cold conditions for the sample collection and storage. The description of all the legends is given here. PBMCs samples: ACD_Magnetic - blood collected in ACD-A tubes and separated using magnetic method followed by extraction using TRIzol ® method. CPT —blood collected in CPT tubes and PBMCs separation using manufacturer recommendations followed by extraction using TRIzol ® method. EDTA_LSM - blood collected in EDTA tube and PBMC separation using LSM followed by extraction using TRIzol ® method. EDTA_Leukolock - blood collected in EDTA tube, PBMCs separated using LeukoLOCK ™ method followed by extraction using TRIzol ® method. Whole blood samples: ACD - blood collected in ACD-A tube followed by RNA extraction using TRIzol ® LS method. ACD_RBC lysis- blood collected in ACD-A tube followed by RBC lysis using ACK buffer and RNA extraction using miRNAeasy extraction kit. EDTA_RBC lysis -blood collected in EDTA tube followed by RBC lysis using ACK buffer and RNA extraction using miRNAeasy extraction kit. EDTA - blood collected in EDTA tube followed by RNA extraction using TRIzol ® LS method. PAXgene - blood collected in PAXgene ® tube followed by RNA extraction using PAXgene ® blood miRNA kit. RNAgard— blood collected in RNAgard ® tube followed by RNA extraction using Biomaxi ™ Precip Buffer and PAXgene ® Blood miRNA kit.

    Techniques Used: Cycling Probe Technology, RNA Extraction, Lysis

    3) Product Images from "The herpes simplex virus host shutoff (vhs) RNase limits accumulation of double stranded RNA in infected cells: Evidence for accelerated decay of duplex RNA"

    Article Title: The herpes simplex virus host shutoff (vhs) RNase limits accumulation of double stranded RNA in infected cells: Evidence for accelerated decay of duplex RNA

    Journal: PLoS Pathogens

    doi: 10.1371/journal.ppat.1008111

    Effects of US11 on the stability and immune signaling activity of duplex RNA formed by annealing of partially complementary reporter mRNAs. A ) Schematic of dsRNA generation. MCherry expression plasmids with a fragment of the SRPRα ORF (canine signal recognition particle receptor subunit alpha) inserted in the 3’UTR in the forward (fwd) or reverse (rev) orientation. Co-transfection of both plasmids results in formation of dsRNAs with 5’ and 3’ overhangs. B ) HeLa cells were transfected with fwd and rev together (fwd/rev) along with either pEGFP or pEGFP-US11 for 20 hours. As a control, cells in separate dishes were transfected with either fwd/pEGFP or rev/pEGFP and combined during Trizol lysis (fwd)+(rev). Total RNA was extracted, digested by DNaseI and RNaseA/T1 (high salt conditions) or DNaseI, RNaseIII and RNaseA/T1 and analyzed by Northern blot with a probe specific for the inserted SRPRα fragment. C) Cotransfection of fwd/rev and pEGFP or pEGFP-US11, respectively. Transfected cells were treated with actinomycin D for 0, 2 or 4 hours prior to RNA extraction and processed as in (B). D ) Quantification of the full-length dsRNA SRPRα signal from 3 independent experiments. P-value for pEGFP/4h vs. 0h is 0.010, 4h/pEGFP-US11 is ns/nonsignificant. E) HeLa cells were transfected with fwd or fwd/rev and pcDNA, pEGFP or pEGFP-US11, respectively. After 20 hours cells were treated with actinomycinD for 4 hours. Whole-cell lysates were analyzed by Western blot with the indicated antibodies. Results shown are representative of 3 independent experiments.
    Figure Legend Snippet: Effects of US11 on the stability and immune signaling activity of duplex RNA formed by annealing of partially complementary reporter mRNAs. A ) Schematic of dsRNA generation. MCherry expression plasmids with a fragment of the SRPRα ORF (canine signal recognition particle receptor subunit alpha) inserted in the 3’UTR in the forward (fwd) or reverse (rev) orientation. Co-transfection of both plasmids results in formation of dsRNAs with 5’ and 3’ overhangs. B ) HeLa cells were transfected with fwd and rev together (fwd/rev) along with either pEGFP or pEGFP-US11 for 20 hours. As a control, cells in separate dishes were transfected with either fwd/pEGFP or rev/pEGFP and combined during Trizol lysis (fwd)+(rev). Total RNA was extracted, digested by DNaseI and RNaseA/T1 (high salt conditions) or DNaseI, RNaseIII and RNaseA/T1 and analyzed by Northern blot with a probe specific for the inserted SRPRα fragment. C) Cotransfection of fwd/rev and pEGFP or pEGFP-US11, respectively. Transfected cells were treated with actinomycin D for 0, 2 or 4 hours prior to RNA extraction and processed as in (B). D ) Quantification of the full-length dsRNA SRPRα signal from 3 independent experiments. P-value for pEGFP/4h vs. 0h is 0.010, 4h/pEGFP-US11 is ns/nonsignificant. E) HeLa cells were transfected with fwd or fwd/rev and pcDNA, pEGFP or pEGFP-US11, respectively. After 20 hours cells were treated with actinomycinD for 4 hours. Whole-cell lysates were analyzed by Western blot with the indicated antibodies. Results shown are representative of 3 independent experiments.

    Techniques Used: Activity Assay, Expressing, Cotransfection, Transfection, Lysis, Northern Blot, RNA Extraction, Western Blot

    4) Product Images from "Water Extracts of Hull-less Waxy Barley (Hordeum vulgare L.) Cultivar ‘Boseokchal’ Inhibit RANKL-induced Osteoclastogenesis"

    Article Title: Water Extracts of Hull-less Waxy Barley (Hordeum vulgare L.) Cultivar ‘Boseokchal’ Inhibit RANKL-induced Osteoclastogenesis

    Journal: Molecules

    doi: 10.3390/molecules24203735

    Effects of BSC-W on RANKL-mediated mRNA expression of NFATc1. BMMs were treated with vehicle (0.1% DMSO) or BSC-W (30 μg/mL) and 30 ng/mL M-CSF for 1 h and then 10 ng/mL RANKL at the indicated times. Total RNA was subsequently isolated using TRIzol reagent, after which the mRNA expression levels were evaluated by real-time PCR. ( A ) NFATc1, ( B ) c-Fos, ( C ) TRAP, ( D ) Cathepsin K, and ( E ) DC-STAMP were used. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used as the internal control. *, p
    Figure Legend Snippet: Effects of BSC-W on RANKL-mediated mRNA expression of NFATc1. BMMs were treated with vehicle (0.1% DMSO) or BSC-W (30 μg/mL) and 30 ng/mL M-CSF for 1 h and then 10 ng/mL RANKL at the indicated times. Total RNA was subsequently isolated using TRIzol reagent, after which the mRNA expression levels were evaluated by real-time PCR. ( A ) NFATc1, ( B ) c-Fos, ( C ) TRAP, ( D ) Cathepsin K, and ( E ) DC-STAMP were used. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used as the internal control. *, p

    Techniques Used: Expressing, Isolation, Real-time Polymerase Chain Reaction

    5) Product Images from "The herpes simplex virus host shutoff (vhs) RNase limits accumulation of double stranded RNA in infected cells: Evidence for accelerated decay of duplex RNA"

    Article Title: The herpes simplex virus host shutoff (vhs) RNase limits accumulation of double stranded RNA in infected cells: Evidence for accelerated decay of duplex RNA

    Journal: PLoS Pathogens

    doi: 10.1371/journal.ppat.1008111

    Effects of US11 on the stability and immune signaling activity of duplex RNA formed by annealing of partially complementary reporter mRNAs. A ) Schematic of dsRNA generation. MCherry expression plasmids with a fragment of the SRPRα ORF (canine signal recognition particle receptor subunit alpha) inserted in the 3’UTR in the forward (fwd) or reverse (rev) orientation. Co-transfection of both plasmids results in formation of dsRNAs with 5’ and 3’ overhangs. B ) HeLa cells were transfected with fwd and rev together (fwd/rev) along with either pEGFP or pEGFP-US11 for 20 hours. As a control, cells in separate dishes were transfected with either fwd/pEGFP or rev/pEGFP and combined during Trizol lysis (fwd)+(rev). Total RNA was extracted, digested by DNaseI and RNaseA/T1 (high salt conditions) or DNaseI, RNaseIII and RNaseA/T1 and analyzed by Northern blot with a probe specific for the inserted SRPRα fragment. C) Cotransfection of fwd/rev and pEGFP or pEGFP-US11, respectively. Transfected cells were treated with actinomycin D for 0, 2 or 4 hours prior to RNA extraction and processed as in (B). D ) Quantification of the full-length dsRNA SRPRα signal from 3 independent experiments. P-value for pEGFP/4h vs. 0h is 0.010, 4h/pEGFP-US11 is ns/nonsignificant. E) HeLa cells were transfected with fwd or fwd/rev and pcDNA, pEGFP or pEGFP-US11, respectively. After 20 hours cells were treated with actinomycinD for 4 hours. Whole-cell lysates were analyzed by Western blot with the indicated antibodies. Results shown are representative of 3 independent experiments.
    Figure Legend Snippet: Effects of US11 on the stability and immune signaling activity of duplex RNA formed by annealing of partially complementary reporter mRNAs. A ) Schematic of dsRNA generation. MCherry expression plasmids with a fragment of the SRPRα ORF (canine signal recognition particle receptor subunit alpha) inserted in the 3’UTR in the forward (fwd) or reverse (rev) orientation. Co-transfection of both plasmids results in formation of dsRNAs with 5’ and 3’ overhangs. B ) HeLa cells were transfected with fwd and rev together (fwd/rev) along with either pEGFP or pEGFP-US11 for 20 hours. As a control, cells in separate dishes were transfected with either fwd/pEGFP or rev/pEGFP and combined during Trizol lysis (fwd)+(rev). Total RNA was extracted, digested by DNaseI and RNaseA/T1 (high salt conditions) or DNaseI, RNaseIII and RNaseA/T1 and analyzed by Northern blot with a probe specific for the inserted SRPRα fragment. C) Cotransfection of fwd/rev and pEGFP or pEGFP-US11, respectively. Transfected cells were treated with actinomycin D for 0, 2 or 4 hours prior to RNA extraction and processed as in (B). D ) Quantification of the full-length dsRNA SRPRα signal from 3 independent experiments. P-value for pEGFP/4h vs. 0h is 0.010, 4h/pEGFP-US11 is ns/nonsignificant. E) HeLa cells were transfected with fwd or fwd/rev and pcDNA, pEGFP or pEGFP-US11, respectively. After 20 hours cells were treated with actinomycinD for 4 hours. Whole-cell lysates were analyzed by Western blot with the indicated antibodies. Results shown are representative of 3 independent experiments.

    Techniques Used: Activity Assay, Expressing, Cotransfection, Transfection, Lysis, Northern Blot, RNA Extraction, Western Blot

    6) Product Images from "A Noncanonical Function of Polycomb Repressive Complexes Promotes Human Cytomegalovirus Lytic DNA Replication and Serves as a Novel Cellular Target for Antiviral Intervention"

    Article Title: A Noncanonical Function of Polycomb Repressive Complexes Promotes Human Cytomegalovirus Lytic DNA Replication and Serves as a Novel Cellular Target for Antiviral Intervention

    Journal: Journal of Virology

    doi: 10.1128/JVI.02143-18

    HCMV infection leads to an upregulation of polycomb group proteins. (A and B) HFF cells were infected with the laboratory HCMV strain AD169 (A) and the clinical strain TB40/E (B) at an MOI of 3. Samples were harvested at the indicated time points postinfection, and whole-cell extracts were subjected to subsequent SDS-PAGE and Western blot analysis. Cellular PcG proteins were detected by the indicated antibodies. The detection of viral immediate early (IE1), early (pUL44), and late (pp28, MCP) proteins was used to monitor progression of the replication cycle. β-Actin served as a loading control. (C) HFF cells were infected with AD169 at an MOI of 3 and harvested at the indicated time points postinfection. RNA was isolated using TRIzol and the Direct-zol RNA miniprep kit (Zymo Research) and synthesized into cDNA by RT-PCR. Transcript levels were assessed by SYBR green PCR, and relative mRNA levels were calculated by normalization against the value for the housekeeping gene GAPDH. Values are derived from biological triplicates and represent mean values ± standard deviations (SD). Statistical analysis was performed by ordinary one-way analysis of variance (ANOVA). n.s., not significant; *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001. (D) HFF cells were infected with AD169 at an MOI of 3 and treated with cycloheximide (CHX) (150 μg/ml) in parallel. After the indicated time points postinfection, whole-cell lysates were prepared and subjected to Western blot analysis. Cellular and viral proteins were detected by the indicated antibodies. IE proteins (IE1 or IE2) served as controls for blocked de novo protein synthesis, while pp65 ensured the income of tegument proteins. β-Actin served as a loading control. (E) HFF cells were infected with either AD169 or UV-inactivated AD169 at an MOI of 1. Whole-cell extracts were generated at the indicated time points and subjected to Western blot analysis. Detection of proteins was equivalent to that for panel D.
    Figure Legend Snippet: HCMV infection leads to an upregulation of polycomb group proteins. (A and B) HFF cells were infected with the laboratory HCMV strain AD169 (A) and the clinical strain TB40/E (B) at an MOI of 3. Samples were harvested at the indicated time points postinfection, and whole-cell extracts were subjected to subsequent SDS-PAGE and Western blot analysis. Cellular PcG proteins were detected by the indicated antibodies. The detection of viral immediate early (IE1), early (pUL44), and late (pp28, MCP) proteins was used to monitor progression of the replication cycle. β-Actin served as a loading control. (C) HFF cells were infected with AD169 at an MOI of 3 and harvested at the indicated time points postinfection. RNA was isolated using TRIzol and the Direct-zol RNA miniprep kit (Zymo Research) and synthesized into cDNA by RT-PCR. Transcript levels were assessed by SYBR green PCR, and relative mRNA levels were calculated by normalization against the value for the housekeeping gene GAPDH. Values are derived from biological triplicates and represent mean values ± standard deviations (SD). Statistical analysis was performed by ordinary one-way analysis of variance (ANOVA). n.s., not significant; *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001. (D) HFF cells were infected with AD169 at an MOI of 3 and treated with cycloheximide (CHX) (150 μg/ml) in parallel. After the indicated time points postinfection, whole-cell lysates were prepared and subjected to Western blot analysis. Cellular and viral proteins were detected by the indicated antibodies. IE proteins (IE1 or IE2) served as controls for blocked de novo protein synthesis, while pp65 ensured the income of tegument proteins. β-Actin served as a loading control. (E) HFF cells were infected with either AD169 or UV-inactivated AD169 at an MOI of 1. Whole-cell extracts were generated at the indicated time points and subjected to Western blot analysis. Detection of proteins was equivalent to that for panel D.

    Techniques Used: Infection, SDS Page, Western Blot, Isolation, Synthesized, Reverse Transcription Polymerase Chain Reaction, SYBR Green Assay, Polymerase Chain Reaction, Derivative Assay, Generated

    7) Product Images from "PTBP1-mediated regulation of AXL mRNA stability plays a role in lung tumorigenesis"

    Article Title: PTBP1-mediated regulation of AXL mRNA stability plays a role in lung tumorigenesis

    Journal: Scientific Reports

    doi: 10.1038/s41598-019-53097-2

    Post-transcriptional control of AXL mRNA stability by PTBP1. ( A ) The transcription rate of AXL was similar in different cells. Nuclei from 2 × 10 6 cells were collected and incubated in a reaction buffer containing ATP, GTP, CTP and biotin-16-UTP and subjected to nonradioactive nuclear run-on assay. In some reactions (negative controls), UTP was used in place of biotin-16-UTP. Total RNA was isolated by TRIzol extraction, and biotinylated RNA was purified using agarose-conjugated streptavidin beads. Expression level of AXL mRNA was measured by quantitative real-time RT-PCR. Actin was used as the internal control. The mRNA stability measurement experiments were initiated by adding 10 μg/ml ActD to ( B ) Empty vector-transfected CL1-0 vs. PTBP1-transfected CL1-0 and to ( C ) Empty vector-transfected CL1-5 vs. PTBP1-transfected CL1-5, respectively. Cells were harvested at intervals as indicated and AXL mRNA decay was analyzed by quantitative real-time RT-PCR. The values were derived from three independent experiments. Error bars represent SD. *P
    Figure Legend Snippet: Post-transcriptional control of AXL mRNA stability by PTBP1. ( A ) The transcription rate of AXL was similar in different cells. Nuclei from 2 × 10 6 cells were collected and incubated in a reaction buffer containing ATP, GTP, CTP and biotin-16-UTP and subjected to nonradioactive nuclear run-on assay. In some reactions (negative controls), UTP was used in place of biotin-16-UTP. Total RNA was isolated by TRIzol extraction, and biotinylated RNA was purified using agarose-conjugated streptavidin beads. Expression level of AXL mRNA was measured by quantitative real-time RT-PCR. Actin was used as the internal control. The mRNA stability measurement experiments were initiated by adding 10 μg/ml ActD to ( B ) Empty vector-transfected CL1-0 vs. PTBP1-transfected CL1-0 and to ( C ) Empty vector-transfected CL1-5 vs. PTBP1-transfected CL1-5, respectively. Cells were harvested at intervals as indicated and AXL mRNA decay was analyzed by quantitative real-time RT-PCR. The values were derived from three independent experiments. Error bars represent SD. *P

    Techniques Used: Incubation, Nuclear Run-on Assay, Isolation, Purification, Expressing, Quantitative RT-PCR, Plasmid Preparation, Transfection, Derivative Assay

    8) Product Images from "Anti-PABPC1 Co-Immunoprecipitation for Examining the miRNAs Directly Targeting the 3′-UTR of EED mRNA"

    Article Title: Anti-PABPC1 Co-Immunoprecipitation for Examining the miRNAs Directly Targeting the 3′-UTR of EED mRNA

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0103695

    Time course and efficiency of the anti-Flag PABPC1 RIP. Plasmids containing the 3′-UTR of the wild type or mutant Lin28 (A) or ERBB2 (B) were transfected into the Flag-PABPC1 stable cell line. Anti-Flag PABPC1 RIP was used at four time points (12 h, 18 h, 24 h, and 36 h) after the transfection, and the total RNA in the cell lysate and precipitate was extracted using the TRIzol reagent. The miRNAs were detected by RT-qPCR and the results were analyzed using the Student’s t-test. P
    Figure Legend Snippet: Time course and efficiency of the anti-Flag PABPC1 RIP. Plasmids containing the 3′-UTR of the wild type or mutant Lin28 (A) or ERBB2 (B) were transfected into the Flag-PABPC1 stable cell line. Anti-Flag PABPC1 RIP was used at four time points (12 h, 18 h, 24 h, and 36 h) after the transfection, and the total RNA in the cell lysate and precipitate was extracted using the TRIzol reagent. The miRNAs were detected by RT-qPCR and the results were analyzed using the Student’s t-test. P

    Techniques Used: Mutagenesis, Transfection, Stable Transfection, Quantitative RT-PCR

    9) Product Images from "A role for p53 in the regulation of extracellular matrix metalloproteinase inducer in human cancer cells"

    Article Title: A role for p53 in the regulation of extracellular matrix metalloproteinase inducer in human cancer cells

    Journal:

    doi: 10.4161/cbt.8.18.9207

    Figure 3. EMMPRIN transcription is not affected by p53. (A) LVCaP cells were cultured at 32°C and 39°C for indicated times. Total RNA was extracted by TRIzol ® reagent, and EMMPRIN mRNA was determined by qRT-PCR. The mRNA
    Figure Legend Snippet: Figure 3. EMMPRIN transcription is not affected by p53. (A) LVCaP cells were cultured at 32°C and 39°C for indicated times. Total RNA was extracted by TRIzol ® reagent, and EMMPRIN mRNA was determined by qRT-PCR. The mRNA

    Techniques Used: Cell Culture, Quantitative RT-PCR

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    Article Snippet: .. The PBMC interface was carefully removed by pipetting and was washed twice with 5 mL 1x of DPBS with centrifugation at 250 × g for 10 min. PBMC pellets were resuspended in TRIzol® Reagent (Invitrogen) and immediately frozen. .. EDTA blood tube and LeukoLOCK™ processing One set of the triplicate EDTA blood tubes from each donor was processed through the LeukoLOCK™ Total RNA Isolation System (Life Technologies, Grand Island, NY, USA) according the manufacturer’s procedure.

    Article Title: Comparison of the extraction and determination of serum exosome and miRNA in serum and the detection of miR-27a-3p in serum exosome of ALS patients
    Article Snippet: .. Using the traditional TRIzol reagent method to isolate total RNA from serum exosomes: The extracted exosome was mixed with a proper volume of TRIzol reagent (Invitrogen, Carlsbad, CA, USA), stored at room temperature for 5 min; chloroform was added according to a proportion of 1:5 in order to separated the lysate, transfer the upper aqueous phase to a new collection tube, and add isopropyl alcohol to precipitate the RNA, finally the RNA precipitation was cleaned using 75% ethanol, and then RNA could be precipitated after centrifugation. .. Using Qiagen miRNeasy Mini Kit (Qiagen, Valencia, CA, USA) to isolate total RNA from serum exosomes: the extracted exosomes were washed and centrifuged using Buffer XBP and XWP, and mixed with a proper volume of QIAzol lysate, stored at room temperature for 5 min; and chloroform was added according to the proper proportion to separate the lysate, the upper aqueous phase was transferred to a new collection tube, after addition of 2 volumes of 100% ethanol, the mixture was transferred into an RNeasy MinElute spin column in a 2 ml collection tube, after centrifugation, RNA was combined on the column membrane, and then washed with Buffer RWT and RPE, DNase/RNase-Free water was added and centrifuged 1 min at 12,000 × g, the flow-through collected was the exosome total RNA.

    Amplification:

    Article Title: A Noncanonical Function of Polycomb Repressive Complexes Promotes Human Cytomegalovirus Lytic DNA Replication and Serves as a Novel Cellular Target for Antiviral Intervention
    Article Snippet: RNAs from 6 × 105 mock-infected or infected HFF cells were isolated in triplicate using TRIzol reagent (Invitrogen, Karlsruhe, Germany) and a Direct-zol RNA miniprep kit (Zymo Research, Freiburg, Germany) according to the manufacturers’ instructions. .. For amplification of EED transcripts, the primers EED-fw and EED-rev were used.

    Cycling Probe Technology:

    Article Title: Investigating gene expression profiles of whole blood and peripheral blood mononuclear cells using multiple collection and processing methods
    Article Snippet: Paragraph title: BD vacutainer™ CPT tube procedure ... The PBMC cell pellet was resuspended in 0.5 mL of TRIzol® Reagent (Invitrogen, Life Technologies, Grand Island, NY, USA) and immediately frozen.

    Synthesized:

    Article Title: Group 2 innate lymphoid cells (ILC2) are regulated by stem cell factor during chronic asthmatic disease
    Article Snippet: .. Quantitative RT-PCR Lung tissue was homogenized in TRIzol reagent then RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA). cDNA was synthesized using murine leukemia virus reverse transcriptase (Applied Biosystems, Foster City, CA) and incubated at 37 °C for one hour, followed by incubation at 95 °C for 5 min to stop the reaction. .. Real-time quantitative PCR (qPCR) was multiplexed using Taqman primers, with a FAM-conjugated probe and GAPDH with a VIC-conjugated probe (Applied Biosystems) to measure transcription of GATA3, T-bet, RoRc, TGFb, IL-4, IL-5, IL-9 and IL13 and cytokines receptors.

    Article Title: Water Extracts of Hull-less Waxy Barley (Hordeum vulgare L.) Cultivar ‘Boseokchal’ Inhibit RANKL-induced Osteoclastogenesis
    Article Snippet: .. Total RNA was isolated using TRIzol reagent (Thermo Fisher Scientific Inc., Waltham, MA, USA) according to the manufacturer’s protocols. cDNA was synthesized using a M-MLV cDNA synthesis kit (Enzynomics, Daejeon, Korea) according to the manufacturer’s protocols. .. QPCR was conducted using the TOPreal qPCR 2× PreMIX (BioRad, Hercules, CA, USA) in a Real-Time PCR Detection System (BioRad, Hercules, CA, USA).

    Article Title: Long noncoding RNA DLEU1 aggravates glioma progression via the miR-421/MEF2D axis
    Article Snippet: Quantitative real-time PCR For the detection of DLEU1 and myocyte enhancer factor 2D (MEF2D) expression, total RNA from tissues and cultured glioma cells was extracted using TRIzol reagent (Invitrogen). .. Single-stranded cDNA was synthesized using a Reverse Transcription Kit (Takara, Dalian, China), then was quantified using SYBR Select Master Mix (Thermo Fisher Scientific, Waltham, MA, USA) under a model 7900 Fast Real-Time PCR System following the manufacturer’s instructions.

    Article Title: The Transcription Factor CREB Enhances Interleukin-17A Production and Inflammation in a Mouse Model of Atherosclerosis
    Article Snippet: The Lipofectin transfection reagent (15596018), CM-H2DCFDA (C6827), DHE , BCECF-AM (B1170), and TRIzol reagent were obtained from Invitrogen. .. The following phosphorothiolate-modified antisense oligonucleotides were synthesized by IDT: hControl ASO: 5′-GGGGGUTCTCTGCGTACGGTGCUAGU-3’; hp47Phox ( ) ASO1: 5′-GGGCUCAGGGTCTTCCGTCUCGUC-3’; hp47Phox ASO2: 5′-GUUGGGCTCAGGGTCTTCCGUCUC-3’; hXO ( ) ASO1: 5′-CCCAUCTCCTCCACAGCAUCCACC-3’; hXO ASO2: 5′-GCCUCCTCCCATTCTCTTCACUCG-3’; hSyk ( ) ASO1: 5′-CCCAUCCGCTCTCCTUUCUC-3’; hSyk ASO2: 5′-CUUCCCTGTCTTGTCUUUGU-3’; hSyk ASO3: 5′-UUCCCTGTCTTGTCTUUGUC-3’; hPyk2 ( ) ASO1: 5′-GGCGGUTCTGCGTACGGTGCUAGU-3’; hPyk2 ASO2: 5′-GGUCUGTACTTAGGTCGGCUGGGC-3’; hPyk2 ASO3: 5′-CCUGUGTCCATAGCCCAGAGUACC-3’; hCREB ( ) ASO1: 5′-CUCUGCTGGTTCTCGGCUCC-3’; hCREB ASO2: 5′-GUGGCAATCTGTGGCUGGGC-3’; and hCREB ASO3: ‘5-GCUGCTTCCCTGTTCUUCAU-3’. h, human.

    Quantitative RT-PCR:

    Article Title: Group 2 innate lymphoid cells (ILC2) are regulated by stem cell factor during chronic asthmatic disease
    Article Snippet: .. Quantitative RT-PCR Lung tissue was homogenized in TRIzol reagent then RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA). cDNA was synthesized using murine leukemia virus reverse transcriptase (Applied Biosystems, Foster City, CA) and incubated at 37 °C for one hour, followed by incubation at 95 °C for 5 min to stop the reaction. .. Real-time quantitative PCR (qPCR) was multiplexed using Taqman primers, with a FAM-conjugated probe and GAPDH with a VIC-conjugated probe (Applied Biosystems) to measure transcription of GATA3, T-bet, RoRc, TGFb, IL-4, IL-5, IL-9 and IL13 and cytokines receptors.

    Article Title: Silencing MR-1 attenuates atherosclerosis in ApoE−/− mice induced by angiotensin II through FAK-Akt–mTOR-NF-kappaB signaling pathway
    Article Snippet: .. Quantitative RT-PCR Homogenized aortic samples (50~100 mg) or confluent cells in a 100 mm dish were lysed in 1 ml TRIzol Reagent (Invitrogen). ..

    Real-time Polymerase Chain Reaction:

    Article Title: Group 2 innate lymphoid cells (ILC2) are regulated by stem cell factor during chronic asthmatic disease
    Article Snippet: Quantitative RT-PCR Lung tissue was homogenized in TRIzol reagent then RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA). cDNA was synthesized using murine leukemia virus reverse transcriptase (Applied Biosystems, Foster City, CA) and incubated at 37 °C for one hour, followed by incubation at 95 °C for 5 min to stop the reaction. .. Real-time quantitative PCR (qPCR) was multiplexed using Taqman primers, with a FAM-conjugated probe and GAPDH with a VIC-conjugated probe (Applied Biosystems) to measure transcription of GATA3, T-bet, RoRc, TGFb, IL-4, IL-5, IL-9 and IL13 and cytokines receptors.

    Article Title: Water Extracts of Hull-less Waxy Barley (Hordeum vulgare L.) Cultivar ‘Boseokchal’ Inhibit RANKL-induced Osteoclastogenesis
    Article Snippet: Paragraph title: 4.5. Real-Time PCR ... Total RNA was isolated using TRIzol reagent (Thermo Fisher Scientific Inc., Waltham, MA, USA) according to the manufacturer’s protocols. cDNA was synthesized using a M-MLV cDNA synthesis kit (Enzynomics, Daejeon, Korea) according to the manufacturer’s protocols.

    Article Title: Long noncoding RNA DLEU1 aggravates glioma progression via the miR-421/MEF2D axis
    Article Snippet: .. Quantitative real-time PCR For the detection of DLEU1 and myocyte enhancer factor 2D (MEF2D) expression, total RNA from tissues and cultured glioma cells was extracted using TRIzol reagent (Invitrogen). .. Single-stranded cDNA was synthesized using a Reverse Transcription Kit (Takara, Dalian, China), then was quantified using SYBR Select Master Mix (Thermo Fisher Scientific, Waltham, MA, USA) under a model 7900 Fast Real-Time PCR System following the manufacturer’s instructions.

    Incubation:

    Article Title: Oxidative stress and apoptosis in a pig model of brain death (BD) and living donation (LD)
    Article Snippet: Between 50 mg to 100 mg tissue (liver, heart, and kidney) were homogenized by either cutting the tissue into sections with a cryomicrotome and disrupting it in 1 ml TRIzol reagent (Invitrogen, Carlsbad, CA, US) by passing the suspension through a 23 gauge needle or by homogenizing the tissue in 1 ml TRIzol reagent using a MagNA Lyser (Roche Diagnostics GmbH, Mannheim, Germany). .. In brief, disrupted tissue was incubated for 15 minutes at room temperature and treated with 100 μl 1-Bromo-3-chloropropane (Sigma, St. Louis, MO, US) per ml TRIzol reagent.

    Article Title: The herpes simplex virus host shutoff (vhs) RNase limits accumulation of double stranded RNA in infected cells: Evidence for accelerated decay of duplex RNA
    Article Snippet: Digestion of RNA with single or double strand- specific RNases RNA was extracted using 1ml TRIzol reagent (Life Technologies) according to the manufacturer’s instructions, then treated with DNaseI (Invitrogen/Ambion) for 15 minutes at 37°C. .. Samples were then incubated with a mix of RNase A/T1 (Invitrogen/Ambion) under high salt conditions (350nM NaCl2 , 10mM TrisHCl pH7.5, 5mM EDTA) for 15 minutes at 37°C or RNase III (Invitrogen/Ambion) followed by RNase A/T1 (high salt) for 15min each at 37°C.

    Article Title: Group 2 innate lymphoid cells (ILC2) are regulated by stem cell factor during chronic asthmatic disease
    Article Snippet: .. Quantitative RT-PCR Lung tissue was homogenized in TRIzol reagent then RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA). cDNA was synthesized using murine leukemia virus reverse transcriptase (Applied Biosystems, Foster City, CA) and incubated at 37 °C for one hour, followed by incubation at 95 °C for 5 min to stop the reaction. .. Real-time quantitative PCR (qPCR) was multiplexed using Taqman primers, with a FAM-conjugated probe and GAPDH with a VIC-conjugated probe (Applied Biosystems) to measure transcription of GATA3, T-bet, RoRc, TGFb, IL-4, IL-5, IL-9 and IL13 and cytokines receptors.

    Article Title: Unveiling MYCN regulatory networks in neuroblastoma via integrative analysis of heterogeneous genomics data
    Article Snippet: Double-stranded oligonucleotide was diluted into 250 μl of serum-free DMEM, mixed with 250 μl serum-free DMEM containing 7.5 μl of Lipofectamine 2000 reagent (Invitrogen, Carlsbad, CA, USA), and incubated for 20 min at room temperature, before being added to the cells growing in 1.5 ml of complete medium. .. After 48 h of transfection, cells were harvested using 1 ml TRIzol reagent, and RNA was extracted using TRIzol reagent (Invitrogen) as indicated in the manufacturer's protocol.

    Article Title: The herpes simplex virus host shutoff (vhs) RNase limits accumulation of double stranded RNA in infected cells: Evidence for accelerated decay of duplex RNA
    Article Snippet: Total RNA was extracted using TRIzol reagent (Life Technologies) according to the manufacturer’s instructions. .. After blocking in 5% skim milk in TBS for 1 hour the membrane was incubated with the dsRNA-specific antibody (mouse, J2, Scions) in Odyssey blocking buffer (LICOR) at 4°C overnight.

    Luciferase:

    Article Title: ROS-dependent Syk and Pyk2-mediated STAT1 activation is required for 15(S)-Hydroxyeicosatetraenoic acid-induced CD36 expression and foam cell formation
    Article Snippet: .. Alexa Fluor 488-conjugated goat anti-rabbit secondary antibodies , CM-H2DCFDA [5-(6)-chloromethyl-2',7'-dichlorodihydrofluorescein diacetate] (C6827), Lipofectin transfection reagent (15596018) and TRIzol reagent were obtained from Invitrogen (Grand Island, NY). pGL3 basic vector and Luciferase assay system (E4530) were purchased from Promega (Madison, WI). .. Apolipoproteins (BT927), Dil-OxLDL (BT-920), and OxLDL (BT-910) were obtained from Biomedical Technologies (Stoughton, MA).

    Cell Culture:

    Article Title: Water Extracts of Hull-less Waxy Barley (Hordeum vulgare L.) Cultivar ‘Boseokchal’ Inhibit RANKL-induced Osteoclastogenesis
    Article Snippet: BMMs were cultured with RANKL (10 ng/mL) and M-CSF (30 ng/mL) in 10% FBS α-MEM for 0, 1, 2, or 3 days in the presence of 0.1% DMSO or BSC-W. For real-time PCR, primer sets were designed ( ) using the online primer3 program [ ]. .. Total RNA was isolated using TRIzol reagent (Thermo Fisher Scientific Inc., Waltham, MA, USA) according to the manufacturer’s protocols. cDNA was synthesized using a M-MLV cDNA synthesis kit (Enzynomics, Daejeon, Korea) according to the manufacturer’s protocols.

    Article Title: Long noncoding RNA DLEU1 aggravates glioma progression via the miR-421/MEF2D axis
    Article Snippet: .. Quantitative real-time PCR For the detection of DLEU1 and myocyte enhancer factor 2D (MEF2D) expression, total RNA from tissues and cultured glioma cells was extracted using TRIzol reagent (Invitrogen). .. Single-stranded cDNA was synthesized using a Reverse Transcription Kit (Takara, Dalian, China), then was quantified using SYBR Select Master Mix (Thermo Fisher Scientific, Waltham, MA, USA) under a model 7900 Fast Real-Time PCR System following the manufacturer’s instructions.

    Expressing:

    Article Title: Long noncoding RNA DLEU1 aggravates glioma progression via the miR-421/MEF2D axis
    Article Snippet: .. Quantitative real-time PCR For the detection of DLEU1 and myocyte enhancer factor 2D (MEF2D) expression, total RNA from tissues and cultured glioma cells was extracted using TRIzol reagent (Invitrogen). .. Single-stranded cDNA was synthesized using a Reverse Transcription Kit (Takara, Dalian, China), then was quantified using SYBR Select Master Mix (Thermo Fisher Scientific, Waltham, MA, USA) under a model 7900 Fast Real-Time PCR System following the manufacturer’s instructions.

    Western Blot:

    Article Title: The Transcription Factor CREB Enhances Interleukin-17A Production and Inflammation in a Mouse Model of Atherosclerosis
    Article Snippet: The Lipofectin transfection reagent (15596018), CM-H2DCFDA (C6827), DHE , BCECF-AM (B1170), and TRIzol reagent were obtained from Invitrogen. .. The ECL Western blotting detection reagents (RPN2106) were obtained from GE Health Care.

    Allele-specific Oligonucleotide:

    Article Title: The Transcription Factor CREB Enhances Interleukin-17A Production and Inflammation in a Mouse Model of Atherosclerosis
    Article Snippet: The Lipofectin transfection reagent (15596018), CM-H2DCFDA (C6827), DHE , BCECF-AM (B1170), and TRIzol reagent were obtained from Invitrogen. .. The following phosphorothiolate-modified antisense oligonucleotides were synthesized by IDT: hControl ASO: 5′-GGGGGUTCTCTGCGTACGGTGCUAGU-3’; hp47Phox ( ) ASO1: 5′-GGGCUCAGGGTCTTCCGTCUCGUC-3’; hp47Phox ASO2: 5′-GUUGGGCTCAGGGTCTTCCGUCUC-3’; hXO ( ) ASO1: 5′-CCCAUCTCCTCCACAGCAUCCACC-3’; hXO ASO2: 5′-GCCUCCTCCCATTCTCTTCACUCG-3’; hSyk ( ) ASO1: 5′-CCCAUCCGCTCTCCTUUCUC-3’; hSyk ASO2: 5′-CUUCCCTGTCTTGTCUUUGU-3’; hSyk ASO3: 5′-UUCCCTGTCTTGTCTUUGUC-3’; hPyk2 ( ) ASO1: 5′-GGCGGUTCTGCGTACGGTGCUAGU-3’; hPyk2 ASO2: 5′-GGUCUGTACTTAGGTCGGCUGGGC-3’; hPyk2 ASO3: 5′-CCUGUGTCCATAGCCCAGAGUACC-3’; hCREB ( ) ASO1: 5′-CUCUGCTGGTTCTCGGCUCC-3’; hCREB ASO2: 5′-GUGGCAATCTGTGGCUGGGC-3’; and hCREB ASO3: ‘5-GCUGCTTCCCTGTTCUUCAU-3’. h, human.

    Transfection:

    Article Title: Unveiling MYCN regulatory networks in neuroblastoma via integrative analysis of heterogeneous genomics data
    Article Snippet: .. After 48 h of transfection, cells were harvested using 1 ml TRIzol reagent, and RNA was extracted using TRIzol reagent (Invitrogen) as indicated in the manufacturer's protocol. .. Small RNA sequencing and analysis RNA concentration and purity were determined photometrically using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc, Rockland, DE); absorbance was measured at 260 nm and the A260/A280 ratio was calculated.

    Article Title: ROS-dependent Syk and Pyk2-mediated STAT1 activation is required for 15(S)-Hydroxyeicosatetraenoic acid-induced CD36 expression and foam cell formation
    Article Snippet: .. Alexa Fluor 488-conjugated goat anti-rabbit secondary antibodies , CM-H2DCFDA [5-(6)-chloromethyl-2',7'-dichlorodihydrofluorescein diacetate] (C6827), Lipofectin transfection reagent (15596018) and TRIzol reagent were obtained from Invitrogen (Grand Island, NY). pGL3 basic vector and Luciferase assay system (E4530) were purchased from Promega (Madison, WI). .. Apolipoproteins (BT927), Dil-OxLDL (BT-920), and OxLDL (BT-910) were obtained from Biomedical Technologies (Stoughton, MA).

    Article Title: The Transcription Factor CREB Enhances Interleukin-17A Production and Inflammation in a Mouse Model of Atherosclerosis
    Article Snippet: .. The Lipofectin transfection reagent (15596018), CM-H2DCFDA (C6827), DHE , BCECF-AM (B1170), and TRIzol reagent were obtained from Invitrogen. .. Human recombinant IL-17 (317-ILB-050), IL-17–specific neutralizing antibody (AF-317-NA), and the IL-10 ELISA kit (M10000B) were obtained from R & D Systems.

    SYBR Green Assay:

    Article Title: A Noncanonical Function of Polycomb Repressive Complexes Promotes Human Cytomegalovirus Lytic DNA Replication and Serves as a Novel Cellular Target for Antiviral Intervention
    Article Snippet: Paragraph title: RNA isolation and SYBR green reverse transcription-quantitative PCR. ... RNAs from 6 × 105 mock-infected or infected HFF cells were isolated in triplicate using TRIzol reagent (Invitrogen, Karlsruhe, Germany) and a Direct-zol RNA miniprep kit (Zymo Research, Freiburg, Germany) according to the manufacturers’ instructions.

    Infection:

    Article Title: A Noncanonical Function of Polycomb Repressive Complexes Promotes Human Cytomegalovirus Lytic DNA Replication and Serves as a Novel Cellular Target for Antiviral Intervention
    Article Snippet: .. RNAs from 6 × 105 mock-infected or infected HFF cells were isolated in triplicate using TRIzol reagent (Invitrogen, Karlsruhe, Germany) and a Direct-zol RNA miniprep kit (Zymo Research, Freiburg, Germany) according to the manufacturers’ instructions. .. First-strand cDNA synthesis was performed with 1 μg of total RNA using a Maxima first-strand cDNA synthesis kit (Thermo Fisher Scientific, Waltham, MA, USA).

    Article Title: The herpes simplex virus host shutoff (vhs) RNase limits accumulation of double stranded RNA in infected cells: Evidence for accelerated decay of duplex RNA
    Article Snippet: HFF and HeLa cells were mock infected or infected with the indicated viruses at MOI 10 for 12 hours. .. Total RNA was extracted using TRIzol reagent (Life Technologies) according to the manufacturer’s instructions.

    TaqMan microRNA Assay:

    Article Title: Long noncoding RNA DLEU1 aggravates glioma progression via the miR-421/MEF2D axis
    Article Snippet: Quantitative real-time PCR For the detection of DLEU1 and myocyte enhancer factor 2D (MEF2D) expression, total RNA from tissues and cultured glioma cells was extracted using TRIzol reagent (Invitrogen). .. The TaqMan MicroRNA assay Kit (Thermo Fisher Scientific, Inc.) was used to examine miR-421 under a model 7900 Fast Real-Time PCR System according to the manufacturer’s instructions.

    Polymerase Chain Reaction:

    Article Title: Silencing MR-1 attenuates atherosclerosis in ApoE−/− mice induced by angiotensin II through FAK-Akt–mTOR-NF-kappaB signaling pathway
    Article Snippet: Quantitative RT-PCR Homogenized aortic samples (50~100 mg) or confluent cells in a 100 mm dish were lysed in 1 ml TRIzol Reagent (Invitrogen). .. RNA samples then reverse-transcribed into cDNA by using a TaqMan Reverse Transcription Reagent kit (Applied Bio systems) and a TaqMan PCR Core Reagent Kit (Applied Bio systems) with gene-specific sense and antisense primers ( ).

    Article Title: A Noncanonical Function of Polycomb Repressive Complexes Promotes Human Cytomegalovirus Lytic DNA Replication and Serves as a Novel Cellular Target for Antiviral Intervention
    Article Snippet: Paragraph title: RNA isolation and SYBR green reverse transcription-quantitative PCR. ... RNAs from 6 × 105 mock-infected or infected HFF cells were isolated in triplicate using TRIzol reagent (Invitrogen, Karlsruhe, Germany) and a Direct-zol RNA miniprep kit (Zymo Research, Freiburg, Germany) according to the manufacturers’ instructions.

    Recombinant:

    Article Title: The Transcription Factor CREB Enhances Interleukin-17A Production and Inflammation in a Mouse Model of Atherosclerosis
    Article Snippet: The Lipofectin transfection reagent (15596018), CM-H2DCFDA (C6827), DHE , BCECF-AM (B1170), and TRIzol reagent were obtained from Invitrogen. .. Human recombinant IL-17 (317-ILB-050), IL-17–specific neutralizing antibody (AF-317-NA), and the IL-10 ELISA kit (M10000B) were obtained from R & D Systems.

    Immunofluorescence:

    Article Title: The herpes simplex virus host shutoff (vhs) RNase limits accumulation of double stranded RNA in infected cells: Evidence for accelerated decay of duplex RNA
    Article Snippet: Digestion of RNA with single or double strand- specific RNases RNA was extracted using 1ml TRIzol reagent (Life Technologies) according to the manufacturer’s instructions, then treated with DNaseI (Invitrogen/Ambion) for 15 minutes at 37°C. .. RNA digests on immunofluorescence samples were performed after the fixation and permeabilization step with RNase III/RNase III buffer or RNase A/T1 and high salt buffer for 15 min in the 37°C incubator.

    Mutagenesis:

    Article Title: ROS-dependent Syk and Pyk2-mediated STAT1 activation is required for 15(S)-Hydroxyeicosatetraenoic acid-induced CD36 expression and foam cell formation
    Article Snippet: Alexa Fluor 488-conjugated goat anti-rabbit secondary antibodies , CM-H2DCFDA [5-(6)-chloromethyl-2',7'-dichlorodihydrofluorescein diacetate] (C6827), Lipofectin transfection reagent (15596018) and TRIzol reagent were obtained from Invitrogen (Grand Island, NY). pGL3 basic vector and Luciferase assay system (E4530) were purchased from Promega (Madison, WI). .. Quick-change site-directed mutagenesis kit was purchased from Stratagene (La Jolla, CA).

    Isolation:

    Article Title: Oxidative stress and apoptosis in a pig model of brain death (BD) and living donation (LD)
    Article Snippet: Paragraph title: RNA Isolation and reverse transcription ... Between 50 mg to 100 mg tissue (liver, heart, and kidney) were homogenized by either cutting the tissue into sections with a cryomicrotome and disrupting it in 1 ml TRIzol reagent (Invitrogen, Carlsbad, CA, US) by passing the suspension through a 23 gauge needle or by homogenizing the tissue in 1 ml TRIzol reagent using a MagNA Lyser (Roche Diagnostics GmbH, Mannheim, Germany).

    Article Title: Water Extracts of Hull-less Waxy Barley (Hordeum vulgare L.) Cultivar ‘Boseokchal’ Inhibit RANKL-induced Osteoclastogenesis
    Article Snippet: .. Total RNA was isolated using TRIzol reagent (Thermo Fisher Scientific Inc., Waltham, MA, USA) according to the manufacturer’s protocols. cDNA was synthesized using a M-MLV cDNA synthesis kit (Enzynomics, Daejeon, Korea) according to the manufacturer’s protocols. .. QPCR was conducted using the TOPreal qPCR 2× PreMIX (BioRad, Hercules, CA, USA) in a Real-Time PCR Detection System (BioRad, Hercules, CA, USA).

    Article Title: Molecular Characterization and Differential Expression of Olfactory Genes in the Antennae of the Black Cutworm Moth Agrotis ipsilon
    Article Snippet: RNA extraction and cDNA library construction 400 antennae from each sex were polled for total RNA extraction using TRIzol reagent using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. .. Approximately 500 ng messenger RNA was further purified from 50 µg total RNA using a PolyATtract mRNA Isolation System III (Promega, Madison, WI, USA).

    Article Title: A Noncanonical Function of Polycomb Repressive Complexes Promotes Human Cytomegalovirus Lytic DNA Replication and Serves as a Novel Cellular Target for Antiviral Intervention
    Article Snippet: .. RNAs from 6 × 105 mock-infected or infected HFF cells were isolated in triplicate using TRIzol reagent (Invitrogen, Karlsruhe, Germany) and a Direct-zol RNA miniprep kit (Zymo Research, Freiburg, Germany) according to the manufacturers’ instructions. .. First-strand cDNA synthesis was performed with 1 μg of total RNA using a Maxima first-strand cDNA synthesis kit (Thermo Fisher Scientific, Waltham, MA, USA).

    Article Title: Comparison of the extraction and determination of serum exosome and miRNA in serum and the detection of miR-27a-3p in serum exosome of ALS patients
    Article Snippet: Paragraph title: 2.3. Isolation of total RNA from serum exosomes ... Using the traditional TRIzol reagent method to isolate total RNA from serum exosomes: The extracted exosome was mixed with a proper volume of TRIzol reagent (Invitrogen, Carlsbad, CA, USA), stored at room temperature for 5 min; chloroform was added according to a proportion of 1:5 in order to separated the lysate, transfer the upper aqueous phase to a new collection tube, and add isopropyl alcohol to precipitate the RNA, finally the RNA precipitation was cleaned using 75% ethanol, and then RNA could be precipitated after centrifugation.

    Flow Cytometry:

    Article Title: Comparison of the extraction and determination of serum exosome and miRNA in serum and the detection of miR-27a-3p in serum exosome of ALS patients
    Article Snippet: Using the traditional TRIzol reagent method to isolate total RNA from serum exosomes: The extracted exosome was mixed with a proper volume of TRIzol reagent (Invitrogen, Carlsbad, CA, USA), stored at room temperature for 5 min; chloroform was added according to a proportion of 1:5 in order to separated the lysate, transfer the upper aqueous phase to a new collection tube, and add isopropyl alcohol to precipitate the RNA, finally the RNA precipitation was cleaned using 75% ethanol, and then RNA could be precipitated after centrifugation. .. Using Qiagen miRNeasy Mini Kit (Qiagen, Valencia, CA, USA) to isolate total RNA from serum exosomes: the extracted exosomes were washed and centrifuged using Buffer XBP and XWP, and mixed with a proper volume of QIAzol lysate, stored at room temperature for 5 min; and chloroform was added according to the proper proportion to separate the lysate, the upper aqueous phase was transferred to a new collection tube, after addition of 2 volumes of 100% ethanol, the mixture was transferred into an RNeasy MinElute spin column in a 2 ml collection tube, after centrifugation, RNA was combined on the column membrane, and then washed with Buffer RWT and RPE, DNase/RNase-Free water was added and centrifuged 1 min at 12,000 × g, the flow-through collected was the exosome total RNA.

    Size-exclusion Chromatography:

    Article Title: Molecular Characterization and Differential Expression of Olfactory Genes in the Antennae of the Black Cutworm Moth Agrotis ipsilon
    Article Snippet: RNA extraction and cDNA library construction 400 antennae from each sex were polled for total RNA extraction using TRIzol reagent using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. .. The mRNAs were then sheared into approximately 800 nucleotides via RNA Fragmentation Solution (Autolab, Beijing, China) at 70°C for 30 sec, then cleaned and condensed using an RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA, USA).

    Dot Blot:

    Article Title: The herpes simplex virus host shutoff (vhs) RNase limits accumulation of double stranded RNA in infected cells: Evidence for accelerated decay of duplex RNA
    Article Snippet: Paragraph title: DsRNA dot blot ... Total RNA was extracted using TRIzol reagent (Life Technologies) according to the manufacturer’s instructions.

    Blocking Assay:

    Article Title: The herpes simplex virus host shutoff (vhs) RNase limits accumulation of double stranded RNA in infected cells: Evidence for accelerated decay of duplex RNA
    Article Snippet: Total RNA was extracted using TRIzol reagent (Life Technologies) according to the manufacturer’s instructions. .. After blocking in 5% skim milk in TBS for 1 hour the membrane was incubated with the dsRNA-specific antibody (mouse, J2, Scions) in Odyssey blocking buffer (LICOR) at 4°C overnight.

    cDNA Library Assay:

    Article Title: Molecular Characterization and Differential Expression of Olfactory Genes in the Antennae of the Black Cutworm Moth Agrotis ipsilon
    Article Snippet: .. RNA extraction and cDNA library construction 400 antennae from each sex were polled for total RNA extraction using TRIzol reagent using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. .. The quantity of RNA samples was determined using a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and 1.1% agarose electrophoresis.

    Purification:

    Article Title: Molecular Characterization and Differential Expression of Olfactory Genes in the Antennae of the Black Cutworm Moth Agrotis ipsilon
    Article Snippet: RNA extraction and cDNA library construction 400 antennae from each sex were polled for total RNA extraction using TRIzol reagent using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. .. Approximately 500 ng messenger RNA was further purified from 50 µg total RNA using a PolyATtract mRNA Isolation System III (Promega, Madison, WI, USA).

    Plasmid Preparation:

    Article Title: ROS-dependent Syk and Pyk2-mediated STAT1 activation is required for 15(S)-Hydroxyeicosatetraenoic acid-induced CD36 expression and foam cell formation
    Article Snippet: .. Alexa Fluor 488-conjugated goat anti-rabbit secondary antibodies , CM-H2DCFDA [5-(6)-chloromethyl-2',7'-dichlorodihydrofluorescein diacetate] (C6827), Lipofectin transfection reagent (15596018) and TRIzol reagent were obtained from Invitrogen (Grand Island, NY). pGL3 basic vector and Luciferase assay system (E4530) were purchased from Promega (Madison, WI). .. Apolipoproteins (BT927), Dil-OxLDL (BT-920), and OxLDL (BT-910) were obtained from Biomedical Technologies (Stoughton, MA).

    Electrophoresis:

    Article Title: Molecular Characterization and Differential Expression of Olfactory Genes in the Antennae of the Black Cutworm Moth Agrotis ipsilon
    Article Snippet: RNA extraction and cDNA library construction 400 antennae from each sex were polled for total RNA extraction using TRIzol reagent using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. .. The quantity of RNA samples was determined using a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and 1.1% agarose electrophoresis.

    RNA Extraction:

    Article Title: Molecular Characterization and Differential Expression of Olfactory Genes in the Antennae of the Black Cutworm Moth Agrotis ipsilon
    Article Snippet: .. RNA extraction and cDNA library construction 400 antennae from each sex were polled for total RNA extraction using TRIzol reagent using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. .. The quantity of RNA samples was determined using a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and 1.1% agarose electrophoresis.

    Enzyme-linked Immunosorbent Assay:

    Article Title: The Transcription Factor CREB Enhances Interleukin-17A Production and Inflammation in a Mouse Model of Atherosclerosis
    Article Snippet: The Lipofectin transfection reagent (15596018), CM-H2DCFDA (C6827), DHE , BCECF-AM (B1170), and TRIzol reagent were obtained from Invitrogen. .. Human recombinant IL-17 (317-ILB-050), IL-17–specific neutralizing antibody (AF-317-NA), and the IL-10 ELISA kit (M10000B) were obtained from R & D Systems.

    Spectrophotometry:

    Article Title: Molecular Characterization and Differential Expression of Olfactory Genes in the Antennae of the Black Cutworm Moth Agrotis ipsilon
    Article Snippet: RNA extraction and cDNA library construction 400 antennae from each sex were polled for total RNA extraction using TRIzol reagent using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. .. The quantity of RNA samples was determined using a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and 1.1% agarose electrophoresis.

    Article Title: Comparison of the extraction and determination of serum exosome and miRNA in serum and the detection of miR-27a-3p in serum exosome of ALS patients
    Article Snippet: Using the traditional TRIzol reagent method to isolate total RNA from serum exosomes: The extracted exosome was mixed with a proper volume of TRIzol reagent (Invitrogen, Carlsbad, CA, USA), stored at room temperature for 5 min; chloroform was added according to a proportion of 1:5 in order to separated the lysate, transfer the upper aqueous phase to a new collection tube, and add isopropyl alcohol to precipitate the RNA, finally the RNA precipitation was cleaned using 75% ethanol, and then RNA could be precipitated after centrifugation. .. The concentration and purity of RNA samples were detected by Thermo micro spectrophotometer NanoDrop2000, and values were recorded.

    Concentration Assay:

    Article Title: Comparison of the extraction and determination of serum exosome and miRNA in serum and the detection of miR-27a-3p in serum exosome of ALS patients
    Article Snippet: Using the traditional TRIzol reagent method to isolate total RNA from serum exosomes: The extracted exosome was mixed with a proper volume of TRIzol reagent (Invitrogen, Carlsbad, CA, USA), stored at room temperature for 5 min; chloroform was added according to a proportion of 1:5 in order to separated the lysate, transfer the upper aqueous phase to a new collection tube, and add isopropyl alcohol to precipitate the RNA, finally the RNA precipitation was cleaned using 75% ethanol, and then RNA could be precipitated after centrifugation. .. The concentration and purity of RNA samples were detected by Thermo micro spectrophotometer NanoDrop2000, and values were recorded.

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  • 90
    Thermo Fisher trizol reagent
    Trizol Reagent, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 722 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/trizol reagent/product/Thermo Fisher
    Average 90 stars, based on 722 article reviews
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    trizol reagent - by Bioz Stars, 2020-01
    90/100 stars
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    This system includes both TRIzol LS Reagent and Invitrogen Phasemaker Tubes TRIzol LS Reagent is a complete ready to use reagent for the isolation of high quality total RNA from
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