Structured Review

Horizon Discovery rna sequence
IRF4 and AhR drive activin-A–induced human Tr1 cell differentiation. ( A ) Tconv or act-A–iTr1 cells were stimulated with APCs and allergen, and transduced with <t>shRNA</t> against human IRF4 (sh- IRF4 ) or a scrambled nontargeting control <t>RNA</t> sequence
Rna Sequence, supplied by Horizon Discovery, used in various techniques. Bioz Stars score: 90/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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1) Product Images from "Activin-A co-opts IRF4 and AhR signaling to induce human regulatory T cells that restrain asthmatic responses"

Article Title: Activin-A co-opts IRF4 and AhR signaling to induce human regulatory T cells that restrain asthmatic responses

Journal: Proceedings of the National Academy of Sciences of the United States of America

doi: 10.1073/pnas.1616942114

IRF4 and AhR drive activin-A–induced human Tr1 cell differentiation. ( A ) Tconv or act-A–iTr1 cells were stimulated with APCs and allergen, and transduced with shRNA against human IRF4 (sh- IRF4 ) or a scrambled nontargeting control RNA sequence
Figure Legend Snippet: IRF4 and AhR drive activin-A–induced human Tr1 cell differentiation. ( A ) Tconv or act-A–iTr1 cells were stimulated with APCs and allergen, and transduced with shRNA against human IRF4 (sh- IRF4 ) or a scrambled nontargeting control RNA sequence

Techniques Used: Cell Differentiation, Activated Clotting Time Assay, Transduction, shRNA, Sequencing

2) Product Images from "Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides"

Article Title: Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides

Journal: Nucleic Acids Research

doi: 10.1093/nar/gks058

Binding analysis of αCP1–KH domains of αCP1 to target RNA and DNA using SPR. Sensorgrams of αCP1–KH1 binding to a series of biotinylated DNA sequences, designed to test the preferential binding of cytosine at each of the four nucleotide binding positions. The sequences are shown above each set of sensorgrams with the binding tetrad underlined. Five adenines were used as a spacer between the biotin and the oligonucleotide binding site. Oligonucletides were captured on SA-coated sensor chips at a range of protein concentrations. Binding curves, derived from the approximated steady state binding of the proteins, were used to determine equilibrum dissociation constants ( K D s). Errors are standard errors arising from fits.
Figure Legend Snippet: Binding analysis of αCP1–KH domains of αCP1 to target RNA and DNA using SPR. Sensorgrams of αCP1–KH1 binding to a series of biotinylated DNA sequences, designed to test the preferential binding of cytosine at each of the four nucleotide binding positions. The sequences are shown above each set of sensorgrams with the binding tetrad underlined. Five adenines were used as a spacer between the biotin and the oligonucleotide binding site. Oligonucletides were captured on SA-coated sensor chips at a range of protein concentrations. Binding curves, derived from the approximated steady state binding of the proteins, were used to determine equilibrum dissociation constants ( K D s). Errors are standard errors arising from fits.

Techniques Used: Binding Assay, SPR Assay, Derivative Assay

Binding analysis of separate KH domains of αCP1 to target RNA and DNA using SPR. Sensorgrams of αCP1 KH1, KH2 and KH3 binding to biotinylated mRNA (5′-CUCUCCUUUCUUUUUCUUCUUCCCUCCCUA-3′) representing nucleotides 3296–3325 of androgen receptor mRNA (flow cell 2) and biotinylated DNA (5′-CTCTCCTTTCTTTTTCTTCTTCCCTCCCTA-3′) analogous to the above RNA sequence (flow cell 3) captured on SA-coated sensor chips at a range of protein concentrations are shown. Binding curves, derived from the approximated steady state binding of the proteins, were used to determine equilibrum dissociation constants ( K D s). Errors are standard errors arising from fits.
Figure Legend Snippet: Binding analysis of separate KH domains of αCP1 to target RNA and DNA using SPR. Sensorgrams of αCP1 KH1, KH2 and KH3 binding to biotinylated mRNA (5′-CUCUCCUUUCUUUUUCUUCUUCCCUCCCUA-3′) representing nucleotides 3296–3325 of androgen receptor mRNA (flow cell 2) and biotinylated DNA (5′-CTCTCCTTTCTTTTTCTTCTTCCCTCCCTA-3′) analogous to the above RNA sequence (flow cell 3) captured on SA-coated sensor chips at a range of protein concentrations are shown. Binding curves, derived from the approximated steady state binding of the proteins, were used to determine equilibrum dissociation constants ( K D s). Errors are standard errors arising from fits.

Techniques Used: Binding Assay, SPR Assay, Flow Cytometry, Sequencing, Derivative Assay

Binding of αCP1 and αCP1–KH1 to oligonucleotides representing the UC-rich region of androgen receptor 3′-UTR. ( A ) A mobility shift assay, run on a 5% PAA/0.5 × TBE gel is shown. 5′-end labelled RNA was incubated either alone (−) or in the presence of purified αCP1 or αCP1–KH1 as indicated above the gel. The probe comprises a total of 107-nt RNA containing vector sequences and nucleotides 3275–3325 of the androgen receptor mRNA. Increasing protein concentrations are indicated by a wedge and are, from the left: 1 × 10 −8 M, 2 × 10 −8 M, 5 × 10 −8 M, 1 × 10 −7 M, 2 × 10 −7 M, 5 × 10 −7 M or 1 × 10 −6 M for both proteins. In all cases, RNA concentration is 1 × 10 −8 M. All lanes also contained 1 μg yeast tRNA added as a non-specific competitor. ( B ) A mobility shift assay, run on a 10% PAA/0.5 × TBE gel is shown. 5′ = -end labelled 11-mer RNA or DNA was incubated either alone (−) or in the presence of purified αCP1 or αCP1–KH1 as indicated above the gel. Probe sequences are: RNA: 5′-UUCCCUCCCUA; DNA: 5′-TTCCCTCCCTA. Increasing protein concentrations are indicated by a wedge and are, from the left: for αCP 1, 1 × 10 −7 M, 3 × 10 −7 M and 1 × 10 −6 M; for αCP1–KH1, 1 × 10 −6 M, 3 × 10 −6 M and 1 × 10 −5 M. In all cases, RNA or DNA concentration is 1 × 10 −7 M. All lanes also contained 1 μg yeast tRNA added as a non-specific competitor.
Figure Legend Snippet: Binding of αCP1 and αCP1–KH1 to oligonucleotides representing the UC-rich region of androgen receptor 3′-UTR. ( A ) A mobility shift assay, run on a 5% PAA/0.5 × TBE gel is shown. 5′-end labelled RNA was incubated either alone (−) or in the presence of purified αCP1 or αCP1–KH1 as indicated above the gel. The probe comprises a total of 107-nt RNA containing vector sequences and nucleotides 3275–3325 of the androgen receptor mRNA. Increasing protein concentrations are indicated by a wedge and are, from the left: 1 × 10 −8 M, 2 × 10 −8 M, 5 × 10 −8 M, 1 × 10 −7 M, 2 × 10 −7 M, 5 × 10 −7 M or 1 × 10 −6 M for both proteins. In all cases, RNA concentration is 1 × 10 −8 M. All lanes also contained 1 μg yeast tRNA added as a non-specific competitor. ( B ) A mobility shift assay, run on a 10% PAA/0.5 × TBE gel is shown. 5′ = -end labelled 11-mer RNA or DNA was incubated either alone (−) or in the presence of purified αCP1 or αCP1–KH1 as indicated above the gel. Probe sequences are: RNA: 5′-UUCCCUCCCUA; DNA: 5′-TTCCCTCCCTA. Increasing protein concentrations are indicated by a wedge and are, from the left: for αCP 1, 1 × 10 −7 M, 3 × 10 −7 M and 1 × 10 −6 M; for αCP1–KH1, 1 × 10 −6 M, 3 × 10 −6 M and 1 × 10 −5 M. In all cases, RNA or DNA concentration is 1 × 10 −7 M. All lanes also contained 1 μg yeast tRNA added as a non-specific competitor.

Techniques Used: Binding Assay, Mobility Shift, Incubation, Purification, Plasmid Preparation, Concentration Assay

Related Articles

Nucleic Acid Electrophoresis:

Article Title: Characterization of a native hammerhead ribozyme derived from schistosomes
Article Snippet: .. RNA sequences in Figure 1B,C were purchased from Dharmacon, purified by denaturing gel electrophoresis on 20%/7 M urea polyacrylamide gels, and electroeluted from the gel slice. .. Sequences corresponding to P1 and P2 (5′ and 3′-OH) were also purchased from Dharmacon.

Flow Cytometry:

Article Title: Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides
Article Snippet: .. 5′-biotinylated DNA (5′-CTCTCCTTTCTTTTTCTTCTTCCCTCCCTA-3′) analogous to the above RNA sequence was also obtained from Dharmacon and immobilized on flow cell 3 as the captured molecule. .. For comparison of αCP1–KH1 binding to a series of tetrad DNA target sites, the following 5′-biotinylated sequences were purchased from Geneworks Australia: (5′-AAAAAATCCA-3′; 5′-AAAAAACTCA-3′; 5′-AAAAAACCTA-3′; 5′-AAAAAACCCA-3′; 5′-AAAAACCCCA-3′).

shRNA:

Article Title: Activin-A co-opts IRF4 and AhR signaling to induce human regulatory T cells that restrain asthmatic responses
Article Snippet: .. Naive CD4+ T cells (2 × 104 cells) were activated with allergen-loaded APCs (2 × 104 cells) or anti-CD3/CD28 antibodies with or without activin-A for 2.5 d. Cells were spun with lentivirus containing GFP-expressing shRNA against human AHR , IRF4 , or a scrambled RNA sequence (Dharmacon) and 8 μg/mL polybrene (Sigma–Aldrich). ..

Methylation:

Article Title: A piRNA utilizes HILI and HIWI2 mediated pathway to down-regulate ferritin heavy chain 1 mRNA in human somatic cells
Article Snippet: .. The 3′-end 2′- O -methylated RNA sequences (piR-FTH1 and scramble piR-FTH1) were purchased from Dharmacon, Inc. .. The non-methylated RNA sequences (piR-FTH1(NM) and scramble piR-FTH1(NM)) sequences were in vitro transcribed ( ).

Article Title: A piRNA utilizes HILI and HIWI2 mediated pathway to down-regulate ferritin heavy chain 1 mRNA in human somatic cells
Article Snippet: .. Preparation of oligonucleotide sequences The 3′-end 2′-O -methylated RNA sequences (piR-FTH1 and scramble piR-FTH1) were purchased from Dharmacon, Inc. .. The non-methylated RNA sequences (piR-FTH1(NM) and scramble piR-FTH1(NM)) sequences were in vitro transcribed ( ).

Synthesized:

Article Title: Evidence That Antibiotics Bind to Human Mitochondrial Ribosomal RNA Has Implications for Aminoglycoside Toxicity *
Article Snippet: .. RNA sequences corresponding to the H69 and H44 species (see ) were chemically synthesized (Dharmacon). .. Because the presence of pseudouridine-modified residues in H69 does not considerably affect aminoglycoside binding affinity, as well as the native structure or stability, the H69 constructs did not include pseudouridine modifications ( , ).

Negative Control:

Article Title: STAT5-dependent regulation of CDC25A by miR-16 controls proliferation and differentiation in FLT3-ITD acute myeloid leukemia
Article Snippet: .. RNA sequences were: specific STAT5A and STAT5B siRNA (ON-TARGETplus SMARTpool, human STAT5A and STAT5B, Dharmacon, Lafayette, CO, USA) or siRNA control (sigenome control pool non targeting #2, or ON-TARGETplus control pool, Dharmacon, Lafayette, CO, USA), anti-miR control or anti-miR-16 (Life Technologies, Carlsbad, CA, USA), and pre-microRNA negative control or pre-microRNA-16 (Life Technologies, Carlsbad, CA, USA). .. Cells were then transfected with the nucleofector device (program 5 for MOLM14, MV4-11 and OCI-AML3 cell lines, custom program for the HEL cell line), and subsequently re-suspended in normal culture medium at a concentration of 1 × 106 cells/ml.

Purification:

Article Title: Characterization of a native hammerhead ribozyme derived from schistosomes
Article Snippet: .. RNA sequences in Figure 1B,C were purchased from Dharmacon, purified by denaturing gel electrophoresis on 20%/7 M urea polyacrylamide gels, and electroeluted from the gel slice. .. Sequences corresponding to P1 and P2 (5′ and 3′-OH) were also purchased from Dharmacon.

Article Title: A simple ligand that selectively targets CUG trinucleotide repeats and inhibits MBNL protein binding
Article Snippet: .. Purified RNA sequences were obtained from Dharmacon Research. .. Yeast tRNA was purchased from Sigma-Aldrich.

Sequencing:

Article Title: Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides
Article Snippet: .. 5′-biotinylated DNA (5′-CTCTCCTTTCTTTTTCTTCTTCCCTCCCTA-3′) analogous to the above RNA sequence was also obtained from Dharmacon and immobilized on flow cell 3 as the captured molecule. .. For comparison of αCP1–KH1 binding to a series of tetrad DNA target sites, the following 5′-biotinylated sequences were purchased from Geneworks Australia: (5′-AAAAAATCCA-3′; 5′-AAAAAACTCA-3′; 5′-AAAAAACCTA-3′; 5′-AAAAAACCCA-3′; 5′-AAAAACCCCA-3′).

Article Title: Activin-A co-opts IRF4 and AhR signaling to induce human regulatory T cells that restrain asthmatic responses
Article Snippet: .. Naive CD4+ T cells (2 × 104 cells) were activated with allergen-loaded APCs (2 × 104 cells) or anti-CD3/CD28 antibodies with or without activin-A for 2.5 d. Cells were spun with lentivirus containing GFP-expressing shRNA against human AHR , IRF4 , or a scrambled RNA sequence (Dharmacon) and 8 μg/mL polybrene (Sigma–Aldrich). ..

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    Horizon Discovery genomic dna sequencing hap 1 wild type wt
    Mitochondrial gene expression is not different between WT and LRRC8A‐KO <t>HAP‐1</t> cells. NADH‐ubiquinone oxidoreductase (NDUFS) complex I (a), Succinate dehydrogenase (SDH) complex II (b), Cytochrome b (cytb) Complex III (c), Cytochrome Oxidase (MT‐CO1) complex IV (d), and mitochondrial encoded ATP synthase membrane subunit 6 (MT‐ATP6) complex V (e) levels in WT and LRRC8A‐KO cells were not significantly different. Mitochondrial <t>DNA</t> (f) and mitochondrial transcription factor A (TFAM) expression (g) were also not significantly different between the two groups ( n = 3)
    Genomic Dna Sequencing Hap 1 Wild Type Wt, supplied by Horizon Discovery, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/genomic dna sequencing hap 1 wild type wt/product/Horizon Discovery
    Average 93 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    genomic dna sequencing hap 1 wild type wt - by Bioz Stars, 2020-09
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    Mitochondrial gene expression is not different between WT and LRRC8A‐KO HAP‐1 cells. NADH‐ubiquinone oxidoreductase (NDUFS) complex I (a), Succinate dehydrogenase (SDH) complex II (b), Cytochrome b (cytb) Complex III (c), Cytochrome Oxidase (MT‐CO1) complex IV (d), and mitochondrial encoded ATP synthase membrane subunit 6 (MT‐ATP6) complex V (e) levels in WT and LRRC8A‐KO cells were not significantly different. Mitochondrial DNA (f) and mitochondrial transcription factor A (TFAM) expression (g) were also not significantly different between the two groups ( n = 3)

    Journal: Physiological Reports

    Article Title: The LRRC8 volume‐regulated anion channel inhibitor, DCPIB, inhibits mitochondrial respiration independently of the channel, et al. The LRRC8 volume‐regulated anion channel inhibitor, DCPIB, inhibits mitochondrial respiration independently of the channel

    doi: 10.14814/phy2.14303

    Figure Lengend Snippet: Mitochondrial gene expression is not different between WT and LRRC8A‐KO HAP‐1 cells. NADH‐ubiquinone oxidoreductase (NDUFS) complex I (a), Succinate dehydrogenase (SDH) complex II (b), Cytochrome b (cytb) Complex III (c), Cytochrome Oxidase (MT‐CO1) complex IV (d), and mitochondrial encoded ATP synthase membrane subunit 6 (MT‐ATP6) complex V (e) levels in WT and LRRC8A‐KO cells were not significantly different. Mitochondrial DNA (f) and mitochondrial transcription factor A (TFAM) expression (g) were also not significantly different between the two groups ( n = 3)

    Article Snippet: 2.2 HAP‐1 cell culture and genomic DNA sequencing HAP‐1 wild type (WT) and LRRC8A‐knockout (KO) cells were purchased from Horizon Discovery and cultured at 37°C in a 5% CO2 incubator in Iscove's modified medium supplemented with 10% FBS.

    Techniques: Expressing