microrna marker  (New England Biolabs)


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    Name:
    microRNA Marker
    Description:
    microRNA Marker 100 gel lanes
    Catalog Number:
    n2102s
    Price:
    70
    Size:
    100 gel lanes
    Category:
    RNA Molecular Weight Markers
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    New England Biolabs microrna marker
    microRNA Marker
    microRNA Marker 100 gel lanes
    https://www.bioz.com/result/microrna marker/product/New England Biolabs
    Average 93 stars, based on 111 article reviews
    Price from $9.99 to $1999.99
    microrna marker - by Bioz Stars, 2020-05
    93/100 stars

    Images

    1) Product Images from "Down‐regulation of genes coding for core RNAi components and disease resistance proteins via corresponding microRNAs might be correlated with successful Soybean mosaic virus infection in soybean"

    Article Title: Down‐regulation of genes coding for core RNAi components and disease resistance proteins via corresponding microRNAs might be correlated with successful Soybean mosaic virus infection in soybean

    Journal: Molecular Plant Pathology

    doi: 10.1111/mpp.12581

    Transient expression assay for the verification of microRNA (miRNA)–target relationships. The target gene name is shown at the top. Target oligonucleotides from each target gene were cloned under the firefly luciferase (F‐Luc) reporter gene driven by the constitutive p35S promoter in the 3′‐untranslated region (3′‐UTR) sensor. A renilla luciferase (R‐Luc) coding gene on the same vector was used for normalization. A control β‐glucuronidase (GUS)‐based competitor vector, miRNA overexpression vector and short tandem target mimic (STTM)‐based miRNA inhibitory vector were transformed into Agrobacterium tumefaciens strain GV3101 (pMP90 pSoup) separately, and transiently overexpressed, together with the corresponding recombinant 3′‐UTR sensor with an F‐Luc‐target cassette, in the same leaves of N. benthamiana . Leaf discs were collected 48 h after infiltration. Dual‐luciferase assays were performed for the detection of the F‐Luc/R‐Luc protein ratio (open bars), and quantitative real‐time polymerase chain reaction (qRT‐PCR) experiments were performed for the detection of the F‐Luc / R‐Luc mRNA ratio (filled bars). Three biological replications, each with two technical replicates, were carried out for each treatment. t ‐test was performed to evaluate protein ratio differences between miRNA overexpression and STTM groups with the control GUS‐based competitor group. REST 2009 software was used to analyse significant differences for qPCR data. A single asterisk indicates a significant difference at P
    Figure Legend Snippet: Transient expression assay for the verification of microRNA (miRNA)–target relationships. The target gene name is shown at the top. Target oligonucleotides from each target gene were cloned under the firefly luciferase (F‐Luc) reporter gene driven by the constitutive p35S promoter in the 3′‐untranslated region (3′‐UTR) sensor. A renilla luciferase (R‐Luc) coding gene on the same vector was used for normalization. A control β‐glucuronidase (GUS)‐based competitor vector, miRNA overexpression vector and short tandem target mimic (STTM)‐based miRNA inhibitory vector were transformed into Agrobacterium tumefaciens strain GV3101 (pMP90 pSoup) separately, and transiently overexpressed, together with the corresponding recombinant 3′‐UTR sensor with an F‐Luc‐target cassette, in the same leaves of N. benthamiana . Leaf discs were collected 48 h after infiltration. Dual‐luciferase assays were performed for the detection of the F‐Luc/R‐Luc protein ratio (open bars), and quantitative real‐time polymerase chain reaction (qRT‐PCR) experiments were performed for the detection of the F‐Luc / R‐Luc mRNA ratio (filled bars). Three biological replications, each with two technical replicates, were carried out for each treatment. t ‐test was performed to evaluate protein ratio differences between miRNA overexpression and STTM groups with the control GUS‐based competitor group. REST 2009 software was used to analyse significant differences for qPCR data. A single asterisk indicates a significant difference at P

    Techniques Used: Expressing, Clone Assay, Luciferase, Plasmid Preparation, Over Expression, Transformation Assay, Recombinant, Real-time Polymerase Chain Reaction, Quantitative RT-PCR, Software

    Validation of microRNA (miRNA) target cleavage sites by RNA ligase‐mediated rapid amplification of cDNA ends (RLM‐RACE) assay. Adaptor‐ligated RNA was reverse transcribed and amplified sequentially by two rounds of real‐time polymerase chain reaction (RT‐PCR) using gene‐specific outer and inner primers together with adaptor primer. The amplicons were gel purified, ligated into pGEM‐T vector and sequenced. The sequences were aligned with adaptor sequences and the cleavage sites on target genes were identified. The cleavage sites are indicated by triangles above the target mRNA with the frequency of cleavage events obtained from the sequencing of independent clones. Watson–Crick pairing (A:U, G:C) is indicated by vertical dashes, and G:U wobble pairing is indicated by open circles.
    Figure Legend Snippet: Validation of microRNA (miRNA) target cleavage sites by RNA ligase‐mediated rapid amplification of cDNA ends (RLM‐RACE) assay. Adaptor‐ligated RNA was reverse transcribed and amplified sequentially by two rounds of real‐time polymerase chain reaction (RT‐PCR) using gene‐specific outer and inner primers together with adaptor primer. The amplicons were gel purified, ligated into pGEM‐T vector and sequenced. The sequences were aligned with adaptor sequences and the cleavage sites on target genes were identified. The cleavage sites are indicated by triangles above the target mRNA with the frequency of cleavage events obtained from the sequencing of independent clones. Watson–Crick pairing (A:U, G:C) is indicated by vertical dashes, and G:U wobble pairing is indicated by open circles.

    Techniques Used: Rapid Amplification of cDNA Ends, Amplification, Real-time Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, Purification, Plasmid Preparation, Sequencing, Clone Assay

    2) Product Images from "Mature and functional viral miRNAs transcribed from novel RNA polymerase III promoters"

    Article Title: Mature and functional viral miRNAs transcribed from novel RNA polymerase III promoters

    Journal: RNA

    doi: 10.1261/rna.1873910

    Northern blot analysis of γHV68 pol III-1 during lytic infection. ( A ) Schematic of the predicted γHV68 pol III-1 transcript. RNA pol III type 2 internal promoter elements are shown as solid gray boxes. γHV68 miRNA miR-M1-1 is represented
    Figure Legend Snippet: Northern blot analysis of γHV68 pol III-1 during lytic infection. ( A ) Schematic of the predicted γHV68 pol III-1 transcript. RNA pol III type 2 internal promoter elements are shown as solid gray boxes. γHV68 miRNA miR-M1-1 is represented

    Techniques Used: Northern Blot, Infection

    Demonstration of RNA pol III transcription of γHV68 miRNAs. 293 cells were infected with γHV68 and treated with α-amanitin at the indicated concentration. ( A ) RT-PCR analysis, with relative abundance of each RT-PCR product determined
    Figure Legend Snippet: Demonstration of RNA pol III transcription of γHV68 miRNAs. 293 cells were infected with γHV68 and treated with α-amanitin at the indicated concentration. ( A ) RT-PCR analysis, with relative abundance of each RT-PCR product determined

    Techniques Used: Infection, Concentration Assay, Reverse Transcription Polymerase Chain Reaction

    Confirmation of the production of the γHV68 miRNAs by RNA pol III using the Left End plasmids. ( A ) Schematic of the γHV68 RNA pol III promoter deletion strategy. ( B ) RLM-RT-PCR for miRNAs in 293 cells transfected with either pLE-WT or
    Figure Legend Snippet: Confirmation of the production of the γHV68 miRNAs by RNA pol III using the Left End plasmids. ( A ) Schematic of the γHV68 RNA pol III promoter deletion strategy. ( B ) RLM-RT-PCR for miRNAs in 293 cells transfected with either pLE-WT or

    Techniques Used: Reverse Transcription Polymerase Chain Reaction, Transfection

    Detection of mature miRNAs using RLM-RT-PCR. ( A ) Schematic of the RLM-RT-PCR process for the detection of mature miRNAs. ( B ) RLM-RT-PCR of miRNAs miR-M1-1 and miR-M1-5 produced from the dicer substrates in transfected cells. Total RNA from the indicated
    Figure Legend Snippet: Detection of mature miRNAs using RLM-RT-PCR. ( A ) Schematic of the RLM-RT-PCR process for the detection of mature miRNAs. ( B ) RLM-RT-PCR of miRNAs miR-M1-1 and miR-M1-5 produced from the dicer substrates in transfected cells. Total RNA from the indicated

    Techniques Used: Reverse Transcription Polymerase Chain Reaction, Produced, Transfection

    3) Product Images from "Biochemical analysis of the Cas6-1 RNA endonuclease associated with the subtype I-D CRISPR-Cas system in Synechocystis sp. PCC 6803"

    Article Title: Biochemical analysis of the Cas6-1 RNA endonuclease associated with the subtype I-D CRISPR-Cas system in Synechocystis sp. PCC 6803

    Journal: RNA Biology

    doi: 10.1080/15476286.2018.1447742

    Purification and in vitro cleavage assay of Synechocystis WT Cas6-1 and mutated Cas6-1 proteins. (A) Coomassie-stained 15% SDS-PAGE of heterologously overexpressed and purified Cas6-1 protein variants. The expected molecular weight of Cas6-1_6xHis is ∼ 30 kDa. 66.67 pmol recombinant enzyme was loaded on each lane and PageRuler™ Prestained Protein Ladder (Thermo Fisher Scientific) served for protein size estimation. (B, C) In in vitro cleavage assays both the (B) CRISPR1 RNA oligo repeat sequence and the (C) pre-acrRNA cassette is processed with variable efficiency by the purified Cas6-1 protein variants shown in (A). After incubation at 30°C the RNA fragments were electrophoretically size separated on a 15% PAA sequencing gel and visualized with SYBR® Gold Nucleic Acid Gel Stain. The processing results in a pattern of RNA fragments of distinct lengths. Cleavage assays were conducted with a three-fold excess (B) or a 1:1 ratio (C) of protein to RNA-substrate in cleavage buffer and incubated at 30°C for the indicated time. Expected RNA fragments and their corresponding sizes are illustrated by cartoons. Another Cas6-1 WT protein sample, which was overexpressed and purified independently, is indicated by an asterisk. Negative controls were complemented with 1 μL of H 2 O or 1 μL eluate of a mock control. Two additional nucleotides resulting from in vitro transcription were added to the 215 nt long acrRNA yielding a 217 nt long pre-acrRNA. For RNA size estimation a CRISPR1 repeat oligo ladder (C1L), RiboRuler low range RNA ladder (Thermo Fisher Scientific), low range ssRNA ladder or microRNA marker (both from New England Biolabs) were used.
    Figure Legend Snippet: Purification and in vitro cleavage assay of Synechocystis WT Cas6-1 and mutated Cas6-1 proteins. (A) Coomassie-stained 15% SDS-PAGE of heterologously overexpressed and purified Cas6-1 protein variants. The expected molecular weight of Cas6-1_6xHis is ∼ 30 kDa. 66.67 pmol recombinant enzyme was loaded on each lane and PageRuler™ Prestained Protein Ladder (Thermo Fisher Scientific) served for protein size estimation. (B, C) In in vitro cleavage assays both the (B) CRISPR1 RNA oligo repeat sequence and the (C) pre-acrRNA cassette is processed with variable efficiency by the purified Cas6-1 protein variants shown in (A). After incubation at 30°C the RNA fragments were electrophoretically size separated on a 15% PAA sequencing gel and visualized with SYBR® Gold Nucleic Acid Gel Stain. The processing results in a pattern of RNA fragments of distinct lengths. Cleavage assays were conducted with a three-fold excess (B) or a 1:1 ratio (C) of protein to RNA-substrate in cleavage buffer and incubated at 30°C for the indicated time. Expected RNA fragments and their corresponding sizes are illustrated by cartoons. Another Cas6-1 WT protein sample, which was overexpressed and purified independently, is indicated by an asterisk. Negative controls were complemented with 1 μL of H 2 O or 1 μL eluate of a mock control. Two additional nucleotides resulting from in vitro transcription were added to the 215 nt long acrRNA yielding a 217 nt long pre-acrRNA. For RNA size estimation a CRISPR1 repeat oligo ladder (C1L), RiboRuler low range RNA ladder (Thermo Fisher Scientific), low range ssRNA ladder or microRNA marker (both from New England Biolabs) were used.

    Techniques Used: Purification, In Vitro, Cleavage Assay, Staining, SDS Page, Molecular Weight, Recombinant, Sequencing, Incubation, Marker

    In vitro cleavage assays of Cas6-1 WT reveals a single turnover mechanism. In vitro cleavage assays with varying enzyme to substrate (CRISPR1 repeat RNA oligo) ratios revealed a single turnover mechanism for the WT Cas6-1. Protein to RNA ratios were applied as indicated above the respective image. RNA cleavage was visualized on a SYBR® Gold stained 15% PAA gel and analyzed with Quantity One software (BIO-RAD). Negative controls were complemented with 1 μL of H 2 O or 1 μL eluate of a mock control. The low molecular weight band of ∼20 nt visible in all lanes is a synthesis by-product. The microRNA marker (New England Biolabs) served for RNA size estimation. (B) ImageJ was used to calculate the percentage of cleaved RNA from the gel images by the amount of product divided by the sum of the amount of product and substrate multiplied by 100 and plotted against time. Standard errors of the mean (SEM) are indicated by vertical bars. A representative of three independent replicates is shown.
    Figure Legend Snippet: In vitro cleavage assays of Cas6-1 WT reveals a single turnover mechanism. In vitro cleavage assays with varying enzyme to substrate (CRISPR1 repeat RNA oligo) ratios revealed a single turnover mechanism for the WT Cas6-1. Protein to RNA ratios were applied as indicated above the respective image. RNA cleavage was visualized on a SYBR® Gold stained 15% PAA gel and analyzed with Quantity One software (BIO-RAD). Negative controls were complemented with 1 μL of H 2 O or 1 μL eluate of a mock control. The low molecular weight band of ∼20 nt visible in all lanes is a synthesis by-product. The microRNA marker (New England Biolabs) served for RNA size estimation. (B) ImageJ was used to calculate the percentage of cleaved RNA from the gel images by the amount of product divided by the sum of the amount of product and substrate multiplied by 100 and plotted against time. Standard errors of the mean (SEM) are indicated by vertical bars. A representative of three independent replicates is shown.

    Techniques Used: In Vitro, Staining, Software, Molecular Weight, Marker

    4) Product Images from "Oral Delivery of Double-Stranded RNAs and siRNAs Induces RNAi Effects in the Potato/Tomato Psyllid, Bactericerca cockerelli"

    Article Title: Oral Delivery of Double-Stranded RNAs and siRNAs Induces RNAi Effects in the Potato/Tomato Psyllid, Bactericerca cockerelli

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0027736

    Northern blot detection of small RNA in BC-Actin dsRNA-fed psyllids. Teneral adult psyllids were allowed to feed for 72h on artificial diet containing 700 ng/µL of BC-Actin , BC-ATPase or GFP dsRNAs. Subsequently, small RNAs were isolated from group of ∼80 individuals, and 1 µg small RNA was separated on a 15% PAGE gel containing 8M Urea and transferred to a nylon membrane. 32 P-UTP-l abeled negative strand BC-Actin (A), BC-ATPase (B) or GFP (C) RNA transcripts were used as a probe for the corresponding blot. MicroRNA markers were analyzed on the same gel and sizes are indicated to the right of each blot. As a positive control, a TMV vector pJL36 containing BC-Actin, BC-ATPase or GFP fragment was agro-infiltrated into N. benthamiana and siRNAs were isolated after 2 weeks. (A) Lane 1, pJL36- BC-Actin -infected N. benthamiana ; Lane 2, BC-Actin dsRNA-fed psyllids; Lane 3, GFP dsRNA-fed psyllids; Lane 4, sucrose-fed psyllids. The arrow on the left indicates the position of the siRNAs. (B) Lane 1, pJL36- BC-ATPase -infected N. benthamiana ; Lane 2, BC-ATPase dsRNA-fed psyllids; Lane 3, GFP dsRNA-fed psyllids; Lane 4, sucrose-fed psyllids. (C) Lane 1, pJL36-GFP-infected N. benthamiana ; Lane 2, GFP dsRNA-fed psyllids; Lane 3, GFP dsRNA-fed psyllids were transferred to and fed on tomato seedling for 48h; Lane 4, GFP dsRNA-fed psyllids were transferred to and fed on tomato seedling for 96h; Lane 5, sucrose-fed psyllids. The panels at the bottom show ethidium bromide stained rRNA as a loading control. The exposure times for BC-Actin , BC-ATPase and GFP were 15 h, 19 h and 8 h, respectively.
    Figure Legend Snippet: Northern blot detection of small RNA in BC-Actin dsRNA-fed psyllids. Teneral adult psyllids were allowed to feed for 72h on artificial diet containing 700 ng/µL of BC-Actin , BC-ATPase or GFP dsRNAs. Subsequently, small RNAs were isolated from group of ∼80 individuals, and 1 µg small RNA was separated on a 15% PAGE gel containing 8M Urea and transferred to a nylon membrane. 32 P-UTP-l abeled negative strand BC-Actin (A), BC-ATPase (B) or GFP (C) RNA transcripts were used as a probe for the corresponding blot. MicroRNA markers were analyzed on the same gel and sizes are indicated to the right of each blot. As a positive control, a TMV vector pJL36 containing BC-Actin, BC-ATPase or GFP fragment was agro-infiltrated into N. benthamiana and siRNAs were isolated after 2 weeks. (A) Lane 1, pJL36- BC-Actin -infected N. benthamiana ; Lane 2, BC-Actin dsRNA-fed psyllids; Lane 3, GFP dsRNA-fed psyllids; Lane 4, sucrose-fed psyllids. The arrow on the left indicates the position of the siRNAs. (B) Lane 1, pJL36- BC-ATPase -infected N. benthamiana ; Lane 2, BC-ATPase dsRNA-fed psyllids; Lane 3, GFP dsRNA-fed psyllids; Lane 4, sucrose-fed psyllids. (C) Lane 1, pJL36-GFP-infected N. benthamiana ; Lane 2, GFP dsRNA-fed psyllids; Lane 3, GFP dsRNA-fed psyllids were transferred to and fed on tomato seedling for 48h; Lane 4, GFP dsRNA-fed psyllids were transferred to and fed on tomato seedling for 96h; Lane 5, sucrose-fed psyllids. The panels at the bottom show ethidium bromide stained rRNA as a loading control. The exposure times for BC-Actin , BC-ATPase and GFP were 15 h, 19 h and 8 h, respectively.

    Techniques Used: Northern Blot, Isolation, Polyacrylamide Gel Electrophoresis, Positive Control, Plasmid Preparation, Infection, Staining

    Related Articles

    Marker:

    Article Title: Silencing of Aphid Genes by dsRNA Feeding from Plants
    Article Snippet: .. MicroRNA marker (NEB, Hitchin, UK) consisting of three synthetic single-stranded RNA oligonucleotides of 17, 21 and 25 residues was loaded in gels and hybridized on blots with corresponding microRNA probe to determine size of siRNA between 21–23 nucleotides. .. The signals were detected after 3-day exposure to phosphor storage plates (GE Healthcare, Little Chalfont, UK) scanned with a Typhoon™ 9200 scanner (GE Healthcare) and analyzed using ImageQuant™ (GE Healthcare).

    Article Title: Oral Delivery of Double-Stranded RNAs and siRNAs Induces RNAi Effects in the Potato/Tomato Psyllid, Bactericerca cockerelli
    Article Snippet: .. MicroRNA Marker (New England Biolabs; catalog NO. N2102S) was used on the same gel to estimate RNA sizes. ..

    Article Title: Transcriptome-wide measurement of translation by ribosome profiling
    Article Snippet: .. Additionally, in order to facilitate the isolation of the small footprints described by Lareau et al. [ ], load 12 µl of NEB miRNA marker in similar positions. .. Separate by electrophoresis for 65 minutes at 200 V. Stain the gel for 3 minutes with 1X SYBR Gold in 1X TBE running buffer on a gentle shaker.

    Article Title: Mature and functional viral miRNAs transcribed from novel RNA polymerase III promoters
    Article Snippet: .. While prerunning the gel, samples consisting of 20 μg of total cellular RNA, the miRNA Marker ladder (New England BioLabs), and the BrightStar Biotinylated RNA Century Plus Markers ladder (Ambion) were each brought to a final total volume of 40 μL using gel loading buffer II (Ambion) and boiled for 5 min at 95°C. .. The gel was stained with 1 μg/mL of ethidium bromide in 1× TBE for 5 min, and destained in 1× TBE for 2 min.

    Article Title: Biochemical analysis of the Cas6-1 RNA endonuclease associated with the subtype I-D CRISPR-Cas system in Synechocystis sp. PCC 6803
    Article Snippet: .. The low range ssRNA ladder (ssRNA marker) (New England Biolabs), the RiboRuler low range RNA ladder (Thermo Fisher Scientific) and the microRNA marker (New England Biolabs) served as RNA ladders for size estimation. .. The CRISPR1 repeat oligo ladder (C1L) was generated by alkaline hydrolysis (50 mM Tris-HCl pH 8.5, 20 mM MgCl2 ) with 25 pmol substrate and was incubated for 72 h to 96 h at 30°C.

    Article Title: Enhanced Whitefly Resistance in Transgenic Tobacco Plants Expressing Double Stranded RNA of v-ATPase A Gene
    Article Snippet: .. MicroRNA marker (NEB, UK) having 17, 21 and 25 residues of single-stranded RNA oligonucleotides was used as size standards to determine size of siRNA between 21–23 nucleotides. .. Loading of comparable amounts of RNA was assessed by ethidium bromide staining.

    Article Title: Down‐regulation of genes coding for core RNAi components and disease resistance proteins via corresponding microRNAs might be correlated with successful Soybean mosaic virus infection in soybean
    Article Snippet: .. RNAs were fixed with 1‐ethyl‐3‐(3‐dimethylaminopropyl) carbodiimide following the protocol described previously (Kim et al ., ). miRNA Marker (New England Biolabs, N2102S, Ipswich, MA, USA) was analysed on the same gel to estimate small RNA sizes. .. Oligonucleotides for complementary sequences of mature miRNAs were synthesized and digoxigenin (DIG) labelled by digoxigenin‐11‐dUTP (Roche, 11558706910, Basel, Switzerland) following the supplier's instructions (Table S8).

    Isolation:

    Article Title: Transcriptome-wide measurement of translation by ribosome profiling
    Article Snippet: .. Additionally, in order to facilitate the isolation of the small footprints described by Lareau et al. [ ], load 12 µl of NEB miRNA marker in similar positions. .. Separate by electrophoresis for 65 minutes at 200 V. Stain the gel for 3 minutes with 1X SYBR Gold in 1X TBE running buffer on a gentle shaker.

    Staining:

    Article Title: Characterization of microRNA Expression Profiles in Leishmania Infected Human Phagocytes
    Article Snippet: .. Total RNA was electrophoresed on a 15% TBE urea pre-cast gel (Novex), following manufacturer instructions, alongside flanking microRNA markers (New England Biolabs), and stained with SYBR Gold Nucleic Acid Gel Stain (Life Technologies). .. Gel sections of RNA samples in the range of 17 to 25nt were cut using clean instruments and small RNA was extracted from the sections by diffusion as previously described ( ).

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    New England Biolabs microrna marker
    Transient expression assay for the verification of <t>microRNA</t> (miRNA)–target relationships. The target gene name is shown at the top. Target oligonucleotides from each target gene were cloned under the firefly luciferase (F‐Luc) reporter gene driven by the constitutive p35S promoter in the 3′‐untranslated region (3′‐UTR) sensor. A renilla luciferase (R‐Luc) coding gene on the same vector was used for normalization. A control β‐glucuronidase (GUS)‐based competitor vector, miRNA overexpression vector and short tandem target mimic (STTM)‐based miRNA inhibitory vector were transformed into Agrobacterium tumefaciens strain GV3101 (pMP90 pSoup) separately, and transiently overexpressed, together with the corresponding recombinant 3′‐UTR sensor with an F‐Luc‐target cassette, in the same leaves of N. benthamiana . Leaf discs were collected 48 h after infiltration. Dual‐luciferase assays were performed for the detection of the F‐Luc/R‐Luc protein ratio (open bars), and quantitative real‐time polymerase chain reaction (qRT‐PCR) experiments were performed for the detection of the F‐Luc / R‐Luc mRNA ratio (filled bars). Three biological replications, each with two technical replicates, were carried out for each treatment. t ‐test was performed to evaluate protein ratio differences between miRNA overexpression and STTM groups with the control GUS‐based competitor group. REST 2009 software was used to analyse significant differences for qPCR data. A single asterisk indicates a significant difference at P
    Microrna Marker, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/microrna marker/product/New England Biolabs
    Average 93 stars, based on 24 article reviews
    Price from $9.99 to $1999.99
    microrna marker - by Bioz Stars, 2020-05
    93/100 stars
      Buy from Supplier

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    Transient expression assay for the verification of microRNA (miRNA)–target relationships. The target gene name is shown at the top. Target oligonucleotides from each target gene were cloned under the firefly luciferase (F‐Luc) reporter gene driven by the constitutive p35S promoter in the 3′‐untranslated region (3′‐UTR) sensor. A renilla luciferase (R‐Luc) coding gene on the same vector was used for normalization. A control β‐glucuronidase (GUS)‐based competitor vector, miRNA overexpression vector and short tandem target mimic (STTM)‐based miRNA inhibitory vector were transformed into Agrobacterium tumefaciens strain GV3101 (pMP90 pSoup) separately, and transiently overexpressed, together with the corresponding recombinant 3′‐UTR sensor with an F‐Luc‐target cassette, in the same leaves of N. benthamiana . Leaf discs were collected 48 h after infiltration. Dual‐luciferase assays were performed for the detection of the F‐Luc/R‐Luc protein ratio (open bars), and quantitative real‐time polymerase chain reaction (qRT‐PCR) experiments were performed for the detection of the F‐Luc / R‐Luc mRNA ratio (filled bars). Three biological replications, each with two technical replicates, were carried out for each treatment. t ‐test was performed to evaluate protein ratio differences between miRNA overexpression and STTM groups with the control GUS‐based competitor group. REST 2009 software was used to analyse significant differences for qPCR data. A single asterisk indicates a significant difference at P

    Journal: Molecular Plant Pathology

    Article Title: Down‐regulation of genes coding for core RNAi components and disease resistance proteins via corresponding microRNAs might be correlated with successful Soybean mosaic virus infection in soybean

    doi: 10.1111/mpp.12581

    Figure Lengend Snippet: Transient expression assay for the verification of microRNA (miRNA)–target relationships. The target gene name is shown at the top. Target oligonucleotides from each target gene were cloned under the firefly luciferase (F‐Luc) reporter gene driven by the constitutive p35S promoter in the 3′‐untranslated region (3′‐UTR) sensor. A renilla luciferase (R‐Luc) coding gene on the same vector was used for normalization. A control β‐glucuronidase (GUS)‐based competitor vector, miRNA overexpression vector and short tandem target mimic (STTM)‐based miRNA inhibitory vector were transformed into Agrobacterium tumefaciens strain GV3101 (pMP90 pSoup) separately, and transiently overexpressed, together with the corresponding recombinant 3′‐UTR sensor with an F‐Luc‐target cassette, in the same leaves of N. benthamiana . Leaf discs were collected 48 h after infiltration. Dual‐luciferase assays were performed for the detection of the F‐Luc/R‐Luc protein ratio (open bars), and quantitative real‐time polymerase chain reaction (qRT‐PCR) experiments were performed for the detection of the F‐Luc / R‐Luc mRNA ratio (filled bars). Three biological replications, each with two technical replicates, were carried out for each treatment. t ‐test was performed to evaluate protein ratio differences between miRNA overexpression and STTM groups with the control GUS‐based competitor group. REST 2009 software was used to analyse significant differences for qPCR data. A single asterisk indicates a significant difference at P

    Article Snippet: RNAs were fixed with 1‐ethyl‐3‐(3‐dimethylaminopropyl) carbodiimide following the protocol described previously (Kim et al ., ). miRNA Marker (New England Biolabs, N2102S, Ipswich, MA, USA) was analysed on the same gel to estimate small RNA sizes.

    Techniques: Expressing, Clone Assay, Luciferase, Plasmid Preparation, Over Expression, Transformation Assay, Recombinant, Real-time Polymerase Chain Reaction, Quantitative RT-PCR, Software

    Validation of microRNA (miRNA) target cleavage sites by RNA ligase‐mediated rapid amplification of cDNA ends (RLM‐RACE) assay. Adaptor‐ligated RNA was reverse transcribed and amplified sequentially by two rounds of real‐time polymerase chain reaction (RT‐PCR) using gene‐specific outer and inner primers together with adaptor primer. The amplicons were gel purified, ligated into pGEM‐T vector and sequenced. The sequences were aligned with adaptor sequences and the cleavage sites on target genes were identified. The cleavage sites are indicated by triangles above the target mRNA with the frequency of cleavage events obtained from the sequencing of independent clones. Watson–Crick pairing (A:U, G:C) is indicated by vertical dashes, and G:U wobble pairing is indicated by open circles.

    Journal: Molecular Plant Pathology

    Article Title: Down‐regulation of genes coding for core RNAi components and disease resistance proteins via corresponding microRNAs might be correlated with successful Soybean mosaic virus infection in soybean

    doi: 10.1111/mpp.12581

    Figure Lengend Snippet: Validation of microRNA (miRNA) target cleavage sites by RNA ligase‐mediated rapid amplification of cDNA ends (RLM‐RACE) assay. Adaptor‐ligated RNA was reverse transcribed and amplified sequentially by two rounds of real‐time polymerase chain reaction (RT‐PCR) using gene‐specific outer and inner primers together with adaptor primer. The amplicons were gel purified, ligated into pGEM‐T vector and sequenced. The sequences were aligned with adaptor sequences and the cleavage sites on target genes were identified. The cleavage sites are indicated by triangles above the target mRNA with the frequency of cleavage events obtained from the sequencing of independent clones. Watson–Crick pairing (A:U, G:C) is indicated by vertical dashes, and G:U wobble pairing is indicated by open circles.

    Article Snippet: RNAs were fixed with 1‐ethyl‐3‐(3‐dimethylaminopropyl) carbodiimide following the protocol described previously (Kim et al ., ). miRNA Marker (New England Biolabs, N2102S, Ipswich, MA, USA) was analysed on the same gel to estimate small RNA sizes.

    Techniques: Rapid Amplification of cDNA Ends, Amplification, Real-time Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, Purification, Plasmid Preparation, Sequencing, Clone Assay

    Northern blot analysis of γHV68 pol III-1 during lytic infection. ( A ) Schematic of the predicted γHV68 pol III-1 transcript. RNA pol III type 2 internal promoter elements are shown as solid gray boxes. γHV68 miRNA miR-M1-1 is represented

    Journal: RNA

    Article Title: Mature and functional viral miRNAs transcribed from novel RNA polymerase III promoters

    doi: 10.1261/rna.1873910

    Figure Lengend Snippet: Northern blot analysis of γHV68 pol III-1 during lytic infection. ( A ) Schematic of the predicted γHV68 pol III-1 transcript. RNA pol III type 2 internal promoter elements are shown as solid gray boxes. γHV68 miRNA miR-M1-1 is represented

    Article Snippet: While prerunning the gel, samples consisting of 20 μg of total cellular RNA, the miRNA Marker ladder (New England BioLabs), and the BrightStar Biotinylated RNA Century Plus Markers ladder (Ambion) were each brought to a final total volume of 40 μL using gel loading buffer II (Ambion) and boiled for 5 min at 95°C.

    Techniques: Northern Blot, Infection

    Demonstration of RNA pol III transcription of γHV68 miRNAs. 293 cells were infected with γHV68 and treated with α-amanitin at the indicated concentration. ( A ) RT-PCR analysis, with relative abundance of each RT-PCR product determined

    Journal: RNA

    Article Title: Mature and functional viral miRNAs transcribed from novel RNA polymerase III promoters

    doi: 10.1261/rna.1873910

    Figure Lengend Snippet: Demonstration of RNA pol III transcription of γHV68 miRNAs. 293 cells were infected with γHV68 and treated with α-amanitin at the indicated concentration. ( A ) RT-PCR analysis, with relative abundance of each RT-PCR product determined

    Article Snippet: While prerunning the gel, samples consisting of 20 μg of total cellular RNA, the miRNA Marker ladder (New England BioLabs), and the BrightStar Biotinylated RNA Century Plus Markers ladder (Ambion) were each brought to a final total volume of 40 μL using gel loading buffer II (Ambion) and boiled for 5 min at 95°C.

    Techniques: Infection, Concentration Assay, Reverse Transcription Polymerase Chain Reaction

    Confirmation of the production of the γHV68 miRNAs by RNA pol III using the Left End plasmids. ( A ) Schematic of the γHV68 RNA pol III promoter deletion strategy. ( B ) RLM-RT-PCR for miRNAs in 293 cells transfected with either pLE-WT or

    Journal: RNA

    Article Title: Mature and functional viral miRNAs transcribed from novel RNA polymerase III promoters

    doi: 10.1261/rna.1873910

    Figure Lengend Snippet: Confirmation of the production of the γHV68 miRNAs by RNA pol III using the Left End plasmids. ( A ) Schematic of the γHV68 RNA pol III promoter deletion strategy. ( B ) RLM-RT-PCR for miRNAs in 293 cells transfected with either pLE-WT or

    Article Snippet: While prerunning the gel, samples consisting of 20 μg of total cellular RNA, the miRNA Marker ladder (New England BioLabs), and the BrightStar Biotinylated RNA Century Plus Markers ladder (Ambion) were each brought to a final total volume of 40 μL using gel loading buffer II (Ambion) and boiled for 5 min at 95°C.

    Techniques: Reverse Transcription Polymerase Chain Reaction, Transfection

    Detection of mature miRNAs using RLM-RT-PCR. ( A ) Schematic of the RLM-RT-PCR process for the detection of mature miRNAs. ( B ) RLM-RT-PCR of miRNAs miR-M1-1 and miR-M1-5 produced from the dicer substrates in transfected cells. Total RNA from the indicated

    Journal: RNA

    Article Title: Mature and functional viral miRNAs transcribed from novel RNA polymerase III promoters

    doi: 10.1261/rna.1873910

    Figure Lengend Snippet: Detection of mature miRNAs using RLM-RT-PCR. ( A ) Schematic of the RLM-RT-PCR process for the detection of mature miRNAs. ( B ) RLM-RT-PCR of miRNAs miR-M1-1 and miR-M1-5 produced from the dicer substrates in transfected cells. Total RNA from the indicated

    Article Snippet: While prerunning the gel, samples consisting of 20 μg of total cellular RNA, the miRNA Marker ladder (New England BioLabs), and the BrightStar Biotinylated RNA Century Plus Markers ladder (Ambion) were each brought to a final total volume of 40 μL using gel loading buffer II (Ambion) and boiled for 5 min at 95°C.

    Techniques: Reverse Transcription Polymerase Chain Reaction, Produced, Transfection

    Purification and in vitro cleavage assay of Synechocystis WT Cas6-1 and mutated Cas6-1 proteins. (A) Coomassie-stained 15% SDS-PAGE of heterologously overexpressed and purified Cas6-1 protein variants. The expected molecular weight of Cas6-1_6xHis is ∼ 30 kDa. 66.67 pmol recombinant enzyme was loaded on each lane and PageRuler™ Prestained Protein Ladder (Thermo Fisher Scientific) served for protein size estimation. (B, C) In in vitro cleavage assays both the (B) CRISPR1 RNA oligo repeat sequence and the (C) pre-acrRNA cassette is processed with variable efficiency by the purified Cas6-1 protein variants shown in (A). After incubation at 30°C the RNA fragments were electrophoretically size separated on a 15% PAA sequencing gel and visualized with SYBR® Gold Nucleic Acid Gel Stain. The processing results in a pattern of RNA fragments of distinct lengths. Cleavage assays were conducted with a three-fold excess (B) or a 1:1 ratio (C) of protein to RNA-substrate in cleavage buffer and incubated at 30°C for the indicated time. Expected RNA fragments and their corresponding sizes are illustrated by cartoons. Another Cas6-1 WT protein sample, which was overexpressed and purified independently, is indicated by an asterisk. Negative controls were complemented with 1 μL of H 2 O or 1 μL eluate of a mock control. Two additional nucleotides resulting from in vitro transcription were added to the 215 nt long acrRNA yielding a 217 nt long pre-acrRNA. For RNA size estimation a CRISPR1 repeat oligo ladder (C1L), RiboRuler low range RNA ladder (Thermo Fisher Scientific), low range ssRNA ladder or microRNA marker (both from New England Biolabs) were used.

    Journal: RNA Biology

    Article Title: Biochemical analysis of the Cas6-1 RNA endonuclease associated with the subtype I-D CRISPR-Cas system in Synechocystis sp. PCC 6803

    doi: 10.1080/15476286.2018.1447742

    Figure Lengend Snippet: Purification and in vitro cleavage assay of Synechocystis WT Cas6-1 and mutated Cas6-1 proteins. (A) Coomassie-stained 15% SDS-PAGE of heterologously overexpressed and purified Cas6-1 protein variants. The expected molecular weight of Cas6-1_6xHis is ∼ 30 kDa. 66.67 pmol recombinant enzyme was loaded on each lane and PageRuler™ Prestained Protein Ladder (Thermo Fisher Scientific) served for protein size estimation. (B, C) In in vitro cleavage assays both the (B) CRISPR1 RNA oligo repeat sequence and the (C) pre-acrRNA cassette is processed with variable efficiency by the purified Cas6-1 protein variants shown in (A). After incubation at 30°C the RNA fragments were electrophoretically size separated on a 15% PAA sequencing gel and visualized with SYBR® Gold Nucleic Acid Gel Stain. The processing results in a pattern of RNA fragments of distinct lengths. Cleavage assays were conducted with a three-fold excess (B) or a 1:1 ratio (C) of protein to RNA-substrate in cleavage buffer and incubated at 30°C for the indicated time. Expected RNA fragments and their corresponding sizes are illustrated by cartoons. Another Cas6-1 WT protein sample, which was overexpressed and purified independently, is indicated by an asterisk. Negative controls were complemented with 1 μL of H 2 O or 1 μL eluate of a mock control. Two additional nucleotides resulting from in vitro transcription were added to the 215 nt long acrRNA yielding a 217 nt long pre-acrRNA. For RNA size estimation a CRISPR1 repeat oligo ladder (C1L), RiboRuler low range RNA ladder (Thermo Fisher Scientific), low range ssRNA ladder or microRNA marker (both from New England Biolabs) were used.

    Article Snippet: The low range ssRNA ladder (ssRNA marker) (New England Biolabs), the RiboRuler low range RNA ladder (Thermo Fisher Scientific) and the microRNA marker (New England Biolabs) served as RNA ladders for size estimation.

    Techniques: Purification, In Vitro, Cleavage Assay, Staining, SDS Page, Molecular Weight, Recombinant, Sequencing, Incubation, Marker

    In vitro cleavage assays of Cas6-1 WT reveals a single turnover mechanism. In vitro cleavage assays with varying enzyme to substrate (CRISPR1 repeat RNA oligo) ratios revealed a single turnover mechanism for the WT Cas6-1. Protein to RNA ratios were applied as indicated above the respective image. RNA cleavage was visualized on a SYBR® Gold stained 15% PAA gel and analyzed with Quantity One software (BIO-RAD). Negative controls were complemented with 1 μL of H 2 O or 1 μL eluate of a mock control. The low molecular weight band of ∼20 nt visible in all lanes is a synthesis by-product. The microRNA marker (New England Biolabs) served for RNA size estimation. (B) ImageJ was used to calculate the percentage of cleaved RNA from the gel images by the amount of product divided by the sum of the amount of product and substrate multiplied by 100 and plotted against time. Standard errors of the mean (SEM) are indicated by vertical bars. A representative of three independent replicates is shown.

    Journal: RNA Biology

    Article Title: Biochemical analysis of the Cas6-1 RNA endonuclease associated with the subtype I-D CRISPR-Cas system in Synechocystis sp. PCC 6803

    doi: 10.1080/15476286.2018.1447742

    Figure Lengend Snippet: In vitro cleavage assays of Cas6-1 WT reveals a single turnover mechanism. In vitro cleavage assays with varying enzyme to substrate (CRISPR1 repeat RNA oligo) ratios revealed a single turnover mechanism for the WT Cas6-1. Protein to RNA ratios were applied as indicated above the respective image. RNA cleavage was visualized on a SYBR® Gold stained 15% PAA gel and analyzed with Quantity One software (BIO-RAD). Negative controls were complemented with 1 μL of H 2 O or 1 μL eluate of a mock control. The low molecular weight band of ∼20 nt visible in all lanes is a synthesis by-product. The microRNA marker (New England Biolabs) served for RNA size estimation. (B) ImageJ was used to calculate the percentage of cleaved RNA from the gel images by the amount of product divided by the sum of the amount of product and substrate multiplied by 100 and plotted against time. Standard errors of the mean (SEM) are indicated by vertical bars. A representative of three independent replicates is shown.

    Article Snippet: The low range ssRNA ladder (ssRNA marker) (New England Biolabs), the RiboRuler low range RNA ladder (Thermo Fisher Scientific) and the microRNA marker (New England Biolabs) served as RNA ladders for size estimation.

    Techniques: In Vitro, Staining, Software, Molecular Weight, Marker

    Northern blot detection of small RNA in BC-Actin dsRNA-fed psyllids. Teneral adult psyllids were allowed to feed for 72h on artificial diet containing 700 ng/µL of BC-Actin , BC-ATPase or GFP dsRNAs. Subsequently, small RNAs were isolated from group of ∼80 individuals, and 1 µg small RNA was separated on a 15% PAGE gel containing 8M Urea and transferred to a nylon membrane. 32 P-UTP-l abeled negative strand BC-Actin (A), BC-ATPase (B) or GFP (C) RNA transcripts were used as a probe for the corresponding blot. MicroRNA markers were analyzed on the same gel and sizes are indicated to the right of each blot. As a positive control, a TMV vector pJL36 containing BC-Actin, BC-ATPase or GFP fragment was agro-infiltrated into N. benthamiana and siRNAs were isolated after 2 weeks. (A) Lane 1, pJL36- BC-Actin -infected N. benthamiana ; Lane 2, BC-Actin dsRNA-fed psyllids; Lane 3, GFP dsRNA-fed psyllids; Lane 4, sucrose-fed psyllids. The arrow on the left indicates the position of the siRNAs. (B) Lane 1, pJL36- BC-ATPase -infected N. benthamiana ; Lane 2, BC-ATPase dsRNA-fed psyllids; Lane 3, GFP dsRNA-fed psyllids; Lane 4, sucrose-fed psyllids. (C) Lane 1, pJL36-GFP-infected N. benthamiana ; Lane 2, GFP dsRNA-fed psyllids; Lane 3, GFP dsRNA-fed psyllids were transferred to and fed on tomato seedling for 48h; Lane 4, GFP dsRNA-fed psyllids were transferred to and fed on tomato seedling for 96h; Lane 5, sucrose-fed psyllids. The panels at the bottom show ethidium bromide stained rRNA as a loading control. The exposure times for BC-Actin , BC-ATPase and GFP were 15 h, 19 h and 8 h, respectively.

    Journal: PLoS ONE

    Article Title: Oral Delivery of Double-Stranded RNAs and siRNAs Induces RNAi Effects in the Potato/Tomato Psyllid, Bactericerca cockerelli

    doi: 10.1371/journal.pone.0027736

    Figure Lengend Snippet: Northern blot detection of small RNA in BC-Actin dsRNA-fed psyllids. Teneral adult psyllids were allowed to feed for 72h on artificial diet containing 700 ng/µL of BC-Actin , BC-ATPase or GFP dsRNAs. Subsequently, small RNAs were isolated from group of ∼80 individuals, and 1 µg small RNA was separated on a 15% PAGE gel containing 8M Urea and transferred to a nylon membrane. 32 P-UTP-l abeled negative strand BC-Actin (A), BC-ATPase (B) or GFP (C) RNA transcripts were used as a probe for the corresponding blot. MicroRNA markers were analyzed on the same gel and sizes are indicated to the right of each blot. As a positive control, a TMV vector pJL36 containing BC-Actin, BC-ATPase or GFP fragment was agro-infiltrated into N. benthamiana and siRNAs were isolated after 2 weeks. (A) Lane 1, pJL36- BC-Actin -infected N. benthamiana ; Lane 2, BC-Actin dsRNA-fed psyllids; Lane 3, GFP dsRNA-fed psyllids; Lane 4, sucrose-fed psyllids. The arrow on the left indicates the position of the siRNAs. (B) Lane 1, pJL36- BC-ATPase -infected N. benthamiana ; Lane 2, BC-ATPase dsRNA-fed psyllids; Lane 3, GFP dsRNA-fed psyllids; Lane 4, sucrose-fed psyllids. (C) Lane 1, pJL36-GFP-infected N. benthamiana ; Lane 2, GFP dsRNA-fed psyllids; Lane 3, GFP dsRNA-fed psyllids were transferred to and fed on tomato seedling for 48h; Lane 4, GFP dsRNA-fed psyllids were transferred to and fed on tomato seedling for 96h; Lane 5, sucrose-fed psyllids. The panels at the bottom show ethidium bromide stained rRNA as a loading control. The exposure times for BC-Actin , BC-ATPase and GFP were 15 h, 19 h and 8 h, respectively.

    Article Snippet: MicroRNA Marker (New England Biolabs; catalog NO. N2102S) was used on the same gel to estimate RNA sizes.

    Techniques: Northern Blot, Isolation, Polyacrylamide Gel Electrophoresis, Positive Control, Plasmid Preparation, Infection, Staining