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Rictor mediates eIF4E binding to mRNA translational repressor, 4E-BP1. (a): Equivalent amounts of cell lysates were analyzed for known downstream targets of Rictor, HIF-2alpha, pAkt (S473) by Western blot analysis in RCC 786-O cells silenced of Rictor using small inhibitory <t>RNA</t> (siRNA) or scrambled control (scr) as described in materials and methods. Total Akt and GAPDH were used as loading controls. (b): Steady state levels of HIF-2alpha mRNA levels were examined in RCC 786-O cells silenced of Rictor (siRictor) or scrambled control (scr). (c): eIF4E association with 4E-BP1 was examined as outlined in Fig. 1C using 7-methyl-GTP sepharose beads from RCC 786-O cells silenced for Rictor using siRNA (siRictor) or scrambled control (scr). The data are representative of at least three independent experiments. (d): Polysomal fractions were prepared by passing cytosolic lysates from RCC 786-O cells silenced of Rictor (siRictor) or scrambled control (scr), over sucrose gradients as described in experimental methods. HIF-2alpha and GAPDH mRNAs were detected in each fraction by <t>RT-PCR</t> on RNA extracted from each fraction. (e): Quantitative RT-PCR was performed as outlined in materials and methods to examine the mRNA expression levels HIF-responsive genes (VEGF and TGF-alpha) after siRNA down-regulation of Rictor or scrambled control. The data is representative of three independent experiments and are expressed as fold control where the ratio of the scrambled control was defined as 1. Values are the means +/− S.E, ** p
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1) Product Images from "Stabilization of HIF-2alpha through redox regulation of mTORC2 activation and initiation of mRNA translation"

Article Title: Stabilization of HIF-2alpha through redox regulation of mTORC2 activation and initiation of mRNA translation

Journal: Oncogene

doi: 10.1038/onc.2012.333

Rictor mediates eIF4E binding to mRNA translational repressor, 4E-BP1. (a): Equivalent amounts of cell lysates were analyzed for known downstream targets of Rictor, HIF-2alpha, pAkt (S473) by Western blot analysis in RCC 786-O cells silenced of Rictor using small inhibitory RNA (siRNA) or scrambled control (scr) as described in materials and methods. Total Akt and GAPDH were used as loading controls. (b): Steady state levels of HIF-2alpha mRNA levels were examined in RCC 786-O cells silenced of Rictor (siRictor) or scrambled control (scr). (c): eIF4E association with 4E-BP1 was examined as outlined in Fig. 1C using 7-methyl-GTP sepharose beads from RCC 786-O cells silenced for Rictor using siRNA (siRictor) or scrambled control (scr). The data are representative of at least three independent experiments. (d): Polysomal fractions were prepared by passing cytosolic lysates from RCC 786-O cells silenced of Rictor (siRictor) or scrambled control (scr), over sucrose gradients as described in experimental methods. HIF-2alpha and GAPDH mRNAs were detected in each fraction by RT-PCR on RNA extracted from each fraction. (e): Quantitative RT-PCR was performed as outlined in materials and methods to examine the mRNA expression levels HIF-responsive genes (VEGF and TGF-alpha) after siRNA down-regulation of Rictor or scrambled control. The data is representative of three independent experiments and are expressed as fold control where the ratio of the scrambled control was defined as 1. Values are the means +/− S.E, ** p
Figure Legend Snippet: Rictor mediates eIF4E binding to mRNA translational repressor, 4E-BP1. (a): Equivalent amounts of cell lysates were analyzed for known downstream targets of Rictor, HIF-2alpha, pAkt (S473) by Western blot analysis in RCC 786-O cells silenced of Rictor using small inhibitory RNA (siRNA) or scrambled control (scr) as described in materials and methods. Total Akt and GAPDH were used as loading controls. (b): Steady state levels of HIF-2alpha mRNA levels were examined in RCC 786-O cells silenced of Rictor (siRictor) or scrambled control (scr). (c): eIF4E association with 4E-BP1 was examined as outlined in Fig. 1C using 7-methyl-GTP sepharose beads from RCC 786-O cells silenced for Rictor using siRNA (siRictor) or scrambled control (scr). The data are representative of at least three independent experiments. (d): Polysomal fractions were prepared by passing cytosolic lysates from RCC 786-O cells silenced of Rictor (siRictor) or scrambled control (scr), over sucrose gradients as described in experimental methods. HIF-2alpha and GAPDH mRNAs were detected in each fraction by RT-PCR on RNA extracted from each fraction. (e): Quantitative RT-PCR was performed as outlined in materials and methods to examine the mRNA expression levels HIF-responsive genes (VEGF and TGF-alpha) after siRNA down-regulation of Rictor or scrambled control. The data is representative of three independent experiments and are expressed as fold control where the ratio of the scrambled control was defined as 1. Values are the means +/− S.E, ** p

Techniques Used: Binding Assay, Western Blot, Reverse Transcription Polymerase Chain Reaction, Quantitative RT-PCR, Expressing

Effects of p22 phox inhibition on eIF4E-dependent mRNA translation. (a): p22 phox was stably knocked down using lentiviral short hairpin loop RNA (shp22 phox ) or vector control (shVector) as described in materials and methods. Western blot analysis (left panel) was carried out to confirm p22 phox downregulation in indicated independent single cell shp22 phox clones. GAPDH was used as loading control and quantitative RT-PCR (right panel) was carried out to confirm p22 phox mRNA down regulation (b): NADPH oxidase activity was measured in parallel. (c): eIF4E association with 4E-BP1 was examined as outlined in Fig. 1C using 7-methyl-GTP sepharose beads from RCC 786-O cells stably silenced for p22phox (shp22 phox ) or Vector control (shVector). The data are representative of at least three independent experiments. (d): Polysomal analysis was performed from RCC 786-O cells stably silenced for p22phox (shp22 phox ) or Vector control (shVector) as outlined in 2 D and as described in experimental methods.
Figure Legend Snippet: Effects of p22 phox inhibition on eIF4E-dependent mRNA translation. (a): p22 phox was stably knocked down using lentiviral short hairpin loop RNA (shp22 phox ) or vector control (shVector) as described in materials and methods. Western blot analysis (left panel) was carried out to confirm p22 phox downregulation in indicated independent single cell shp22 phox clones. GAPDH was used as loading control and quantitative RT-PCR (right panel) was carried out to confirm p22 phox mRNA down regulation (b): NADPH oxidase activity was measured in parallel. (c): eIF4E association with 4E-BP1 was examined as outlined in Fig. 1C using 7-methyl-GTP sepharose beads from RCC 786-O cells stably silenced for p22phox (shp22 phox ) or Vector control (shVector). The data are representative of at least three independent experiments. (d): Polysomal analysis was performed from RCC 786-O cells stably silenced for p22phox (shp22 phox ) or Vector control (shVector) as outlined in 2 D and as described in experimental methods.

Techniques Used: Inhibition, Stable Transfection, Plasmid Preparation, Western Blot, Clone Assay, Quantitative RT-PCR, Activity Assay

Effects of mTORC1 and mTORC2 inhibition on eIF4E binding to mRNA repressor, 4E-BP1. (a): VHL-deficient RCC 786-O cells were incubated with buffer alone (−), mTORC1 inhibitor (CCI-779), or the mTORC1/mTORC2 inhibitor (pp242) for 24 hours. Cellular lysates were analyzed by Western blot analysis for HIF-2alpha expression. GAPDH was used as a loading control. (b): In parallel to A, RNA was extracted and HIF-2alpha mRNA was examined by quantitative RT-PCR. (c): Cellular lysates were prepared as described in materials and methods from RCC 786-O cells treated with buffer alone (−), CCI-779, or pp242 for 24 hrs and eIF4E and its associated proteins were affinity purified using 7-methyl-GTP sepharose beads followed by Western blot analysis for total eIF4E and 4E-BP1. The data are representative of three independent experiments. (d): Polysomal fractions were prepared by passing cytosolic lysates from RCC 786-O cells treated with buffer treated (−), CCI-779, or pp242, over sucrose gradients as described in experimental methods. HIF-2alpha and GAPDH mRNAs were detected in each fraction by RT-PCR on RNA extracted from each fraction. Sedimentation analysis was examined in parallel of RCC 786-O cells by measuring optical density at 254 nm. (e): Quantitative RT-PCR was performed as outlined in materials and methods to examine the mRNA expression levels HIF-responsive genes (VEGF and TGF-alpha) in RCC 786-O cells treated with buffer alone (−), CCI-779, and pp242. The data is representative of three independent experiments and are expressed as fold control where the ratio of the buffer treated control cells was defined as 1. Values are the means +/− S.E, * p
Figure Legend Snippet: Effects of mTORC1 and mTORC2 inhibition on eIF4E binding to mRNA repressor, 4E-BP1. (a): VHL-deficient RCC 786-O cells were incubated with buffer alone (−), mTORC1 inhibitor (CCI-779), or the mTORC1/mTORC2 inhibitor (pp242) for 24 hours. Cellular lysates were analyzed by Western blot analysis for HIF-2alpha expression. GAPDH was used as a loading control. (b): In parallel to A, RNA was extracted and HIF-2alpha mRNA was examined by quantitative RT-PCR. (c): Cellular lysates were prepared as described in materials and methods from RCC 786-O cells treated with buffer alone (−), CCI-779, or pp242 for 24 hrs and eIF4E and its associated proteins were affinity purified using 7-methyl-GTP sepharose beads followed by Western blot analysis for total eIF4E and 4E-BP1. The data are representative of three independent experiments. (d): Polysomal fractions were prepared by passing cytosolic lysates from RCC 786-O cells treated with buffer treated (−), CCI-779, or pp242, over sucrose gradients as described in experimental methods. HIF-2alpha and GAPDH mRNAs were detected in each fraction by RT-PCR on RNA extracted from each fraction. Sedimentation analysis was examined in parallel of RCC 786-O cells by measuring optical density at 254 nm. (e): Quantitative RT-PCR was performed as outlined in materials and methods to examine the mRNA expression levels HIF-responsive genes (VEGF and TGF-alpha) in RCC 786-O cells treated with buffer alone (−), CCI-779, and pp242. The data is representative of three independent experiments and are expressed as fold control where the ratio of the buffer treated control cells was defined as 1. Values are the means +/− S.E, * p

Techniques Used: Inhibition, Binding Assay, Incubation, Western Blot, Expressing, Quantitative RT-PCR, Affinity Purification, Reverse Transcription Polymerase Chain Reaction, Sedimentation

2) Product Images from "Suppression of the NF-\u03baB Pathway by Diesel Exhaust Particles Impairs Human Antimycobacterial Immunity"

Article Title: Suppression of the NF-\u03baB Pathway by Diesel Exhaust Particles Impairs Human Antimycobacterial Immunity

Journal: Journal of Immunology (Baltimore, Md. : 1950)

doi: 10.4049/jimmunol.1101380

DEP Effects on M.tb -Induced Th1-Th2-Th3 Pathway-specific mRNA Expression
Figure Legend Snippet: DEP Effects on M.tb -Induced Th1-Th2-Th3 Pathway-specific mRNA Expression

Techniques Used: Expressing

3) Product Images from "Induction of multiple matrix metalloproteinases in human dermal and synovial fibroblasts by Staphylococcus aureus: implications in the pathogenesis of septic arthritis and other soft tissue infections"

Article Title: Induction of multiple matrix metalloproteinases in human dermal and synovial fibroblasts by Staphylococcus aureus: implications in the pathogenesis of septic arthritis and other soft tissue infections

Journal: Arthritis Research & Therapy

doi: 10.1186/ar2086

Mitogen-activated protein kinase (MAPK) family mRNA expression profile in human dermal fibroblasts (a) and human synovial fibroblasts (b) exposed to Staphylococcus aureus whole cell lysate and filtered culture supernatant. Confluent monolayers of de-identified human dermal fibroblasts from normal volunteer and synovial fibroblasts from a patient with rheumatoid arthritis were treated with 25 μg/ml per well of S. aureus whole lysate, filtered culture supernatant, and a combination of rhIL-1β and TNF-α (10 ng/ml each) for 8 hours. Cells were harvested and total cellular RNA was isolated and reverse-transcribed. The MAPK family gene expression was analyzed using the Human MAPK Gene Family I Multigene-12 reverse transcription-polymerase chain reaction (PCR) profiling kit. The semiquantitative values were generated by determining the ratios of the band intensities of respective PCR products to that of housekeeping gene GAPDH (glyceraldehyde phosphate dehydrogenase) in each sample. The experiments were repeated three times. The band densities were determined using three-dimensional densitometric scanning software from Alpha Innotech Corporation (San Leandro, CA, USA). Of the 11 tested Human MAPK Family I genes (ERK1, ERK2, MAPK2/4, ERK3, ERK5, JNK1, JNK2, JNK3, p38b MAPK, p38g MAPK, and p38delta), ERK1, ERK2, JNK1, JNK2, MAPK4, and p38b were elevated significantly in both dermal and synovial fibroblasts upon exposure to S. aureus components ( p
Figure Legend Snippet: Mitogen-activated protein kinase (MAPK) family mRNA expression profile in human dermal fibroblasts (a) and human synovial fibroblasts (b) exposed to Staphylococcus aureus whole cell lysate and filtered culture supernatant. Confluent monolayers of de-identified human dermal fibroblasts from normal volunteer and synovial fibroblasts from a patient with rheumatoid arthritis were treated with 25 μg/ml per well of S. aureus whole lysate, filtered culture supernatant, and a combination of rhIL-1β and TNF-α (10 ng/ml each) for 8 hours. Cells were harvested and total cellular RNA was isolated and reverse-transcribed. The MAPK family gene expression was analyzed using the Human MAPK Gene Family I Multigene-12 reverse transcription-polymerase chain reaction (PCR) profiling kit. The semiquantitative values were generated by determining the ratios of the band intensities of respective PCR products to that of housekeeping gene GAPDH (glyceraldehyde phosphate dehydrogenase) in each sample. The experiments were repeated three times. The band densities were determined using three-dimensional densitometric scanning software from Alpha Innotech Corporation (San Leandro, CA, USA). Of the 11 tested Human MAPK Family I genes (ERK1, ERK2, MAPK2/4, ERK3, ERK5, JNK1, JNK2, JNK3, p38b MAPK, p38g MAPK, and p38delta), ERK1, ERK2, JNK1, JNK2, MAPK4, and p38b were elevated significantly in both dermal and synovial fibroblasts upon exposure to S. aureus components ( p

Techniques Used: Expressing, Isolation, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Generated, Software

4) Product Images from "GENDER-SPECIFIC EXPRESSION OF ?1 INTEGRIN OF VERY-LATE ANTIGEN-4 IN MYELIN BASIC PROTEIN-PRIMED T CELLS: IMPLICATIONS FOR GENDER BIAS IN MULTIPLE SCLEROSIS"

Article Title: GENDER-SPECIFIC EXPRESSION OF ?1 INTEGRIN OF VERY-LATE ANTIGEN-4 IN MYELIN BASIC PROTEIN-PRIMED T CELLS: IMPLICATIONS FOR GENDER BIAS IN MULTIPLE SCLEROSIS

Journal: Journal of immunology (Baltimore, Md. : 1950)

doi: 10.4049/jimmunol.0804356

Gene array analysis of mouse integrin α and β gene families A, MBP-primed T cells of female and male mice were analyzed for α and β integrin gene families by Multigene-12™ PCR (SuperArray) as described under “Materials and Methods”. B, densitometric analysis was performed to show comparative expressions of α and β integrin genes between female and male MBP-primed T cells relative to GAPDH. Data are mean ± S.D. of three different experiments.
Figure Legend Snippet: Gene array analysis of mouse integrin α and β gene families A, MBP-primed T cells of female and male mice were analyzed for α and β integrin gene families by Multigene-12™ PCR (SuperArray) as described under “Materials and Methods”. B, densitometric analysis was performed to show comparative expressions of α and β integrin genes between female and male MBP-primed T cells relative to GAPDH. Data are mean ± S.D. of three different experiments.

Techniques Used: Mouse Assay, Polymerase Chain Reaction

5) Product Images from "Induction of multiple matrix metalloproteinases in human dermal and synovial fibroblasts by Staphylococcus aureus: implications in the pathogenesis of septic arthritis and other soft tissue infections"

Article Title: Induction of multiple matrix metalloproteinases in human dermal and synovial fibroblasts by Staphylococcus aureus: implications in the pathogenesis of septic arthritis and other soft tissue infections

Journal: Arthritis Research & Therapy

doi: 10.1186/ar2086

Mitogen-activated protein kinase (MAPK) family mRNA expression profile in human dermal fibroblasts (a) and human synovial fibroblasts (b) exposed to Staphylococcus aureus whole cell lysate and filtered culture supernatant. Confluent monolayers of de-identified human dermal fibroblasts from normal volunteer and synovial fibroblasts from a patient with rheumatoid arthritis were treated with 25 μg/ml per well of S. aureus whole lysate, filtered culture supernatant, and a combination of rhIL-1β and TNF-α (10 ng/ml each) for 8 hours. Cells were harvested and total cellular RNA was isolated and reverse-transcribed. The MAPK family gene expression was analyzed using the Human MAPK Gene Family I Multigene-12 reverse transcription-polymerase chain reaction (PCR) profiling kit. The semiquantitative values were generated by determining the ratios of the band intensities of respective PCR products to that of housekeeping gene GAPDH (glyceraldehyde phosphate dehydrogenase) in each sample. The experiments were repeated three times. The band densities were determined using three-dimensional densitometric scanning software from Alpha Innotech Corporation (San Leandro, CA, USA). Of the 11 tested Human MAPK Family I genes (ERK1, ERK2, MAPK2/4, ERK3, ERK5, JNK1, JNK2, JNK3, p38b MAPK, p38g MAPK, and p38delta), ERK1, ERK2, JNK1, JNK2, MAPK4, and p38b were elevated significantly in both dermal and synovial fibroblasts upon exposure to S. aureus components ( p
Figure Legend Snippet: Mitogen-activated protein kinase (MAPK) family mRNA expression profile in human dermal fibroblasts (a) and human synovial fibroblasts (b) exposed to Staphylococcus aureus whole cell lysate and filtered culture supernatant. Confluent monolayers of de-identified human dermal fibroblasts from normal volunteer and synovial fibroblasts from a patient with rheumatoid arthritis were treated with 25 μg/ml per well of S. aureus whole lysate, filtered culture supernatant, and a combination of rhIL-1β and TNF-α (10 ng/ml each) for 8 hours. Cells were harvested and total cellular RNA was isolated and reverse-transcribed. The MAPK family gene expression was analyzed using the Human MAPK Gene Family I Multigene-12 reverse transcription-polymerase chain reaction (PCR) profiling kit. The semiquantitative values were generated by determining the ratios of the band intensities of respective PCR products to that of housekeeping gene GAPDH (glyceraldehyde phosphate dehydrogenase) in each sample. The experiments were repeated three times. The band densities were determined using three-dimensional densitometric scanning software from Alpha Innotech Corporation (San Leandro, CA, USA). Of the 11 tested Human MAPK Family I genes (ERK1, ERK2, MAPK2/4, ERK3, ERK5, JNK1, JNK2, JNK3, p38b MAPK, p38g MAPK, and p38delta), ERK1, ERK2, JNK1, JNK2, MAPK4, and p38b were elevated significantly in both dermal and synovial fibroblasts upon exposure to S. aureus components ( p

Techniques Used: Expressing, Isolation, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Generated, Software

6) Product Images from "Induction of multiple matrix metalloproteinases in human dermal and synovial fibroblasts by Staphylococcus aureus: implications in the pathogenesis of septic arthritis and other soft tissue infections"

Article Title: Induction of multiple matrix metalloproteinases in human dermal and synovial fibroblasts by Staphylococcus aureus: implications in the pathogenesis of septic arthritis and other soft tissue infections

Journal: Arthritis Research & Therapy

doi: 10.1186/ar2086

Mitogen-activated protein kinase (MAPK) family mRNA expression profile in human dermal fibroblasts (a) and human synovial fibroblasts (b) exposed to Staphylococcus aureus whole cell lysate and filtered culture supernatant. Confluent monolayers of de-identified human dermal fibroblasts from normal volunteer and synovial fibroblasts from a patient with rheumatoid arthritis were treated with 25 μg/ml per well of S. aureus whole lysate, filtered culture supernatant, and a combination of rhIL-1β and TNF-α (10 ng/ml each) for 8 hours. Cells were harvested and total cellular RNA was isolated and reverse-transcribed. The MAPK family gene expression was analyzed using the Human MAPK Gene Family I Multigene-12 reverse transcription-polymerase chain reaction (PCR) profiling kit. The semiquantitative values were generated by determining the ratios of the band intensities of respective PCR products to that of housekeeping gene GAPDH (glyceraldehyde phosphate dehydrogenase) in each sample. The experiments were repeated three times. The band densities were determined using three-dimensional densitometric scanning software from Alpha Innotech Corporation (San Leandro, CA, USA). Of the 11 tested Human MAPK Family I genes (ERK1, ERK2, MAPK2/4, ERK3, ERK5, JNK1, JNK2, JNK3, p38b MAPK, p38g MAPK, and p38delta), ERK1, ERK2, JNK1, JNK2, MAPK4, and p38b were elevated significantly in both dermal and synovial fibroblasts upon exposure to S. aureus components ( p
Figure Legend Snippet: Mitogen-activated protein kinase (MAPK) family mRNA expression profile in human dermal fibroblasts (a) and human synovial fibroblasts (b) exposed to Staphylococcus aureus whole cell lysate and filtered culture supernatant. Confluent monolayers of de-identified human dermal fibroblasts from normal volunteer and synovial fibroblasts from a patient with rheumatoid arthritis were treated with 25 μg/ml per well of S. aureus whole lysate, filtered culture supernatant, and a combination of rhIL-1β and TNF-α (10 ng/ml each) for 8 hours. Cells were harvested and total cellular RNA was isolated and reverse-transcribed. The MAPK family gene expression was analyzed using the Human MAPK Gene Family I Multigene-12 reverse transcription-polymerase chain reaction (PCR) profiling kit. The semiquantitative values were generated by determining the ratios of the band intensities of respective PCR products to that of housekeeping gene GAPDH (glyceraldehyde phosphate dehydrogenase) in each sample. The experiments were repeated three times. The band densities were determined using three-dimensional densitometric scanning software from Alpha Innotech Corporation (San Leandro, CA, USA). Of the 11 tested Human MAPK Family I genes (ERK1, ERK2, MAPK2/4, ERK3, ERK5, JNK1, JNK2, JNK3, p38b MAPK, p38g MAPK, and p38delta), ERK1, ERK2, JNK1, JNK2, MAPK4, and p38b were elevated significantly in both dermal and synovial fibroblasts upon exposure to S. aureus components ( p

Techniques Used: Expressing, Isolation, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Generated, Software

7) Product Images from "Induction of multiple matrix metalloproteinases in human dermal and synovial fibroblasts by Staphylococcus aureus: implications in the pathogenesis of septic arthritis and other soft tissue infections"

Article Title: Induction of multiple matrix metalloproteinases in human dermal and synovial fibroblasts by Staphylococcus aureus: implications in the pathogenesis of septic arthritis and other soft tissue infections

Journal: Arthritis Research & Therapy

doi: 10.1186/ar2086

Mitogen-activated protein kinase (MAPK) family mRNA expression profile in human dermal fibroblasts (a) and human synovial fibroblasts (b) exposed to Staphylococcus aureus whole cell lysate and filtered culture supernatant. Confluent monolayers of de-identified human dermal fibroblasts from normal volunteer and synovial fibroblasts from a patient with rheumatoid arthritis were treated with 25 μg/ml per well of S. aureus whole lysate, filtered culture supernatant, and a combination of rhIL-1β and TNF-α (10 ng/ml each) for 8 hours. Cells were harvested and total cellular RNA was isolated and reverse-transcribed. The MAPK family gene expression was analyzed using the Human MAPK Gene Family I Multigene-12 reverse transcription-polymerase chain reaction (PCR) profiling kit. The semiquantitative values were generated by determining the ratios of the band intensities of respective PCR products to that of housekeeping gene GAPDH (glyceraldehyde phosphate dehydrogenase) in each sample. The experiments were repeated three times. The band densities were determined using three-dimensional densitometric scanning software from Alpha Innotech Corporation (San Leandro, CA, USA). Of the 11 tested Human MAPK Family I genes (ERK1, ERK2, MAPK2/4, ERK3, ERK5, JNK1, JNK2, JNK3, p38b MAPK, p38g MAPK, and p38delta), ERK1, ERK2, JNK1, JNK2, MAPK4, and p38b were elevated significantly in both dermal and synovial fibroblasts upon exposure to S. aureus components ( p
Figure Legend Snippet: Mitogen-activated protein kinase (MAPK) family mRNA expression profile in human dermal fibroblasts (a) and human synovial fibroblasts (b) exposed to Staphylococcus aureus whole cell lysate and filtered culture supernatant. Confluent monolayers of de-identified human dermal fibroblasts from normal volunteer and synovial fibroblasts from a patient with rheumatoid arthritis were treated with 25 μg/ml per well of S. aureus whole lysate, filtered culture supernatant, and a combination of rhIL-1β and TNF-α (10 ng/ml each) for 8 hours. Cells were harvested and total cellular RNA was isolated and reverse-transcribed. The MAPK family gene expression was analyzed using the Human MAPK Gene Family I Multigene-12 reverse transcription-polymerase chain reaction (PCR) profiling kit. The semiquantitative values were generated by determining the ratios of the band intensities of respective PCR products to that of housekeeping gene GAPDH (glyceraldehyde phosphate dehydrogenase) in each sample. The experiments were repeated three times. The band densities were determined using three-dimensional densitometric scanning software from Alpha Innotech Corporation (San Leandro, CA, USA). Of the 11 tested Human MAPK Family I genes (ERK1, ERK2, MAPK2/4, ERK3, ERK5, JNK1, JNK2, JNK3, p38b MAPK, p38g MAPK, and p38delta), ERK1, ERK2, JNK1, JNK2, MAPK4, and p38b were elevated significantly in both dermal and synovial fibroblasts upon exposure to S. aureus components ( p

Techniques Used: Expressing, Isolation, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Generated, Software

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Amplification:

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Positive Control:

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Synthesized:

Article Title: Chemical Genetics Identifies c-Src as an Activator of Primitive Ectoderm Formation in Murine Embryonic Stem Cells #
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Quantitative RT-PCR:

Article Title: Suppression of the NF-\u03baB Pathway by Diesel Exhaust Particles Impairs Human Antimycobacterial Immunity
Article Snippet: .. Reagents were obtained from the following sources: ELISPOT assays : capture and biotinylated detection antibodies for IL-1β and IL-6 (Cell sciences, Inc., Canton, MA), IFN-γ, TNF-α (Endogen Pierce, Rockford, IL), IL-10, IL-4 (BD Pharmingen, San Diego, CA), Streptavidin-peroxidase (Sigma, St. Louis, MO), chromogen 1% 3-amino-9-ethylcarbazole (AEC, Pierce, Rockford, IL), MultiscreenHTS high protein binding 96-well plates (Millipore Bedford, MA); PBMC isolation, culture and stimulation: phytohemagglutinin (PHA, Sigma), lipopolysaccharide (LPS, E.coli 026:B6, Sigma) and PPD (Statens Serum Institute, Kopenhagen, Denmark), RPMI-1640 (BioWhittaker, Walkersville, MO), L-glutamine (Cellgro, Manassas, VA), pooled human AB serum (Gemini Bioproducts, Woodland, CA), Ficoll-Paque (GE Healthcare Biosciences, Pittsburgh, PA); RNA extraction and qRT-PCR : RNeasy mini kit (Qiagen, Germantown, MD), RNase-free DNase set (Qiagen), RT2 First Strand kit, RT2 qPCR master mix (SuperArray Bioscience Corporation, Frederick, MD), Power SYBR green PCR master mix (Applied Biosystems, Foster city, CA), Taqman reverse transcription reagents (Applied biosystems); pathway-specific gene expression arrays: Human Th1-Th2-Th3 (PAHS-34E) and TLR (PAHS-18E) (SuperArray Bioscience Corporation); M.tb culture : H37Ra (ATCC # 25177, Manassas, VA), Middlebrook 7H9 broth medium (Difco Laboratories, Detroit, MI) supplemented with 10% albumin dextrose catalase (Difco Laboratories), 7H10 solid agar plates (Becton, Dickinson, Sparks, MD). .. Flowcytometry : Annexin V/PI apoptosis detection assay (BD Biosciences, San José, CA).

Article Title: Stabilization of HIF-2alpha through redox regulation of mTORC2 activation and initiation of mRNA translation
Article Snippet: Real-time (RT-PCR) amplification was performed in polyribosomal fractions using the Superscript One-Step RT-PCR kit from Invitrogen. .. Real Time-PCR Sybr Green was performed on 50 ng of RNA using the SuperArray kit (SuperArray Bioscience Corporation) and the Eppendorf realplex machine.

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SYBR Green Assay:

Article Title: Suppression of the NF-\u03baB Pathway by Diesel Exhaust Particles Impairs Human Antimycobacterial Immunity
Article Snippet: .. Reagents were obtained from the following sources: ELISPOT assays : capture and biotinylated detection antibodies for IL-1β and IL-6 (Cell sciences, Inc., Canton, MA), IFN-γ, TNF-α (Endogen Pierce, Rockford, IL), IL-10, IL-4 (BD Pharmingen, San Diego, CA), Streptavidin-peroxidase (Sigma, St. Louis, MO), chromogen 1% 3-amino-9-ethylcarbazole (AEC, Pierce, Rockford, IL), MultiscreenHTS high protein binding 96-well plates (Millipore Bedford, MA); PBMC isolation, culture and stimulation: phytohemagglutinin (PHA, Sigma), lipopolysaccharide (LPS, E.coli 026:B6, Sigma) and PPD (Statens Serum Institute, Kopenhagen, Denmark), RPMI-1640 (BioWhittaker, Walkersville, MO), L-glutamine (Cellgro, Manassas, VA), pooled human AB serum (Gemini Bioproducts, Woodland, CA), Ficoll-Paque (GE Healthcare Biosciences, Pittsburgh, PA); RNA extraction and qRT-PCR : RNeasy mini kit (Qiagen, Germantown, MD), RNase-free DNase set (Qiagen), RT2 First Strand kit, RT2 qPCR master mix (SuperArray Bioscience Corporation, Frederick, MD), Power SYBR green PCR master mix (Applied Biosystems, Foster city, CA), Taqman reverse transcription reagents (Applied biosystems); pathway-specific gene expression arrays: Human Th1-Th2-Th3 (PAHS-34E) and TLR (PAHS-18E) (SuperArray Bioscience Corporation); M.tb culture : H37Ra (ATCC # 25177, Manassas, VA), Middlebrook 7H9 broth medium (Difco Laboratories, Detroit, MI) supplemented with 10% albumin dextrose catalase (Difco Laboratories), 7H10 solid agar plates (Becton, Dickinson, Sparks, MD). .. Flowcytometry : Annexin V/PI apoptosis detection assay (BD Biosciences, San José, CA).

Article Title: Stabilization of HIF-2alpha through redox regulation of mTORC2 activation and initiation of mRNA translation
Article Snippet: .. Real Time-PCR Sybr Green was performed on 50 ng of RNA using the SuperArray kit (SuperArray Bioscience Corporation) and the Eppendorf realplex machine. ..

Article Title: Burn Injury Triggered Dysfunction in Dendritic Cell Response to TLR9 Activation and Resulted in Skewed T Cell Functions
Article Snippet: The expression of genes related to TLR-mediated signal transduction was examined by real-time PCR Array using a SuperArray real-time PCR Kit (SuperArray Bioscience Corp., MD). .. Transcript levels of TLR9 was evaluated by qPCR, performed using a SYBR@Green ERTM qPCR SuperMix Kit (Invitrogen) using the forward primer 5′-CGT TTC TCG GTG CTG GAC CTA AGC G-3′ and the reverse primer 5′-CTG AAA GGC ATT GGT GTG GTT G-3′.

Microarray:

Article Title: Prostaglandin E2 modulates dendritic cell function during chlamydial genital infection
Article Snippet: .. The RNA (5–10 lg) was sent to SuperArray Bioscience Corp. for performance of a non-rad-GEArray microarray analysis which contains oligo DNAs dotted on a membrane that represent 96 genes specific for mouse dendritic and antigen-presenting cells and controls. .. The hybridization is described in the SuperArray Analysis section of the Materials and methods.

Infection:

Article Title: Prostaglandin E2 modulates dendritic cell function during chlamydial genital infection
Article Snippet: We puri-fied RNA from infected or mock-infected BMDCs treated with PGE2 or DMSO control. .. The RNA (5–10 lg) was sent to SuperArray Bioscience Corp. for performance of a non-rad-GEArray microarray analysis which contains oligo DNAs dotted on a membrane that represent 96 genes specific for mouse dendritic and antigen-presenting cells and controls.

Expressing:

Article Title: High-Fat Diet Induces Apoptosis of Hypothalamic Neurons
Article Snippet: Samples obtained from three hypothalami from control and HF diet fed rats and Swiss mice were analyzed using a real-time PCR array (RT2 profiler PCR array rat apoptosis - SuperArray Bioscience Corp., Frederick, MD, USA) containing 84 apoptosis related genes, as shown in www.superarray.com/rt_pcr_product/HTML/PARN-012A.html . .. Real-time PCR analysis of gene expression was carried out in an ABI Prism 7500 sequence detection system (Applied Biosystems).

Article Title: Increasing the relative expression of endogenous non-coding Steroid Receptor RNA Activator (SRA) in human breast cancer cells using modified oligonucleotides
Article Snippet: Real-time PCR-array Half a microgram of RNA was reverse transcribed using ReactionReady™ First Strand cDNA synthesis Kit (SuperArray Bioscience Corp., Frederick, MD) and applied to Breast Cancer and Estrogen Receptor RT2 Profiler™ PCR arrays (SuperArray Bioscience Corp., Frederick, MD) as detailed by the manufacturer ( and ). .. Differences between gene expression upon SRA–AS and βgl–AS treatments were tested using the Student's t -test (two-sided).

Article Title: A gastrin precursor, gastrin-gly, upregulates VEGF expression in colonic epithelial cells through an HIF-1-independent mechanism
Article Snippet: Gastrin mRNA expression was controlled 48, 72 and 96 hr after transfection using real time PCR as described above. .. HT29 cells were stably transfected using a shRNA plasmid for Human gastrin (SuperArray Bioscience Corporation) according to manufacturer’s instructions.

Article Title: Suppression of the NF-\u03baB Pathway by Diesel Exhaust Particles Impairs Human Antimycobacterial Immunity
Article Snippet: .. Reagents were obtained from the following sources: ELISPOT assays : capture and biotinylated detection antibodies for IL-1β and IL-6 (Cell sciences, Inc., Canton, MA), IFN-γ, TNF-α (Endogen Pierce, Rockford, IL), IL-10, IL-4 (BD Pharmingen, San Diego, CA), Streptavidin-peroxidase (Sigma, St. Louis, MO), chromogen 1% 3-amino-9-ethylcarbazole (AEC, Pierce, Rockford, IL), MultiscreenHTS high protein binding 96-well plates (Millipore Bedford, MA); PBMC isolation, culture and stimulation: phytohemagglutinin (PHA, Sigma), lipopolysaccharide (LPS, E.coli 026:B6, Sigma) and PPD (Statens Serum Institute, Kopenhagen, Denmark), RPMI-1640 (BioWhittaker, Walkersville, MO), L-glutamine (Cellgro, Manassas, VA), pooled human AB serum (Gemini Bioproducts, Woodland, CA), Ficoll-Paque (GE Healthcare Biosciences, Pittsburgh, PA); RNA extraction and qRT-PCR : RNeasy mini kit (Qiagen, Germantown, MD), RNase-free DNase set (Qiagen), RT2 First Strand kit, RT2 qPCR master mix (SuperArray Bioscience Corporation, Frederick, MD), Power SYBR green PCR master mix (Applied Biosystems, Foster city, CA), Taqman reverse transcription reagents (Applied biosystems); pathway-specific gene expression arrays: Human Th1-Th2-Th3 (PAHS-34E) and TLR (PAHS-18E) (SuperArray Bioscience Corporation); M.tb culture : H37Ra (ATCC # 25177, Manassas, VA), Middlebrook 7H9 broth medium (Difco Laboratories, Detroit, MI) supplemented with 10% albumin dextrose catalase (Difco Laboratories), 7H10 solid agar plates (Becton, Dickinson, Sparks, MD). .. Flowcytometry : Annexin V/PI apoptosis detection assay (BD Biosciences, San José, CA).

Article Title: Burn Injury Triggered Dysfunction in Dendritic Cell Response to TLR9 Activation and Resulted in Skewed T Cell Functions
Article Snippet: .. The expression of genes related to TLR-mediated signal transduction was examined by real-time PCR Array using a SuperArray real-time PCR Kit (SuperArray Bioscience Corp., MD). .. Fold changes of transcript levels of genes in DCs of burn mice were calculated relative to those in the sham group.

Article Title: Interleukin-6 Released from Fibroblasts Is Essential for Up-regulation of Matrix Metalloproteinase-1 Expression by U937 Macrophages in Coculture
Article Snippet: PCR Array —The first strand cDNA was synthesized from RNA using the RT2 First Strand Kit (SuperArray Bioscience Corp., Frederick, MD). .. Human inflammatory cytokines and receptor PCR array (catalog number PAHS-011, SuperArray Bioscience Corp.) was used to profile the cytokine expression by fibroblasts in the coculture by following the instructions from the manufacturer.

Article Title: Induction of multiple matrix metalloproteinases in human dermal and synovial fibroblasts by Staphylococcus aureus: implications in the pathogenesis of septic arthritis and other soft tissue infections
Article Snippet: .. We therefore analyzed the mRNA expression levels of 12 members of the MAPK family using the MultiGene-12 RT-PCR profiling kit from Superarray Bioscience Corporation. .. Synovial fibroblasts obtained from patients with RA and OA were exposed to 25 μg of total proteins from bacterial culture supernatant or cell lysate, and total RNA was isolated 6 hours later, reverse-transcribed, and assayed for mRNA of 12 MAPK genes.

Hybridization:

Article Title: Prostaglandin E2 modulates dendritic cell function during chlamydial genital infection
Article Snippet: The RNA (5–10 lg) was sent to SuperArray Bioscience Corp. for performance of a non-rad-GEArray microarray analysis which contains oligo DNAs dotted on a membrane that represent 96 genes specific for mouse dendritic and antigen-presenting cells and controls. .. The hybridization is described in the SuperArray Analysis section of the Materials and methods.

Transfection:

Article Title: A gastrin precursor, gastrin-gly, upregulates VEGF expression in colonic epithelial cells through an HIF-1-independent mechanism
Article Snippet: .. HT29 cells were stably transfected using a shRNA plasmid for Human gastrin (SuperArray Bioscience Corporation) according to manufacturer’s instructions. ..

Article Title: Interleukin-6 Released from Fibroblasts Is Essential for Up-regulation of Matrix Metalloproteinase-1 Expression by U937 Macrophages in Coculture
Article Snippet: After the transfection for 24 h, cells were cultured independently or cocultured with U937 cells in the presence or absence of LPS. .. PCR Array —The first strand cDNA was synthesized from RNA using the RT2 First Strand Kit (SuperArray Bioscience Corp., Frederick, MD).

Stable Transfection:

Article Title: A gastrin precursor, gastrin-gly, upregulates VEGF expression in colonic epithelial cells through an HIF-1-independent mechanism
Article Snippet: .. HT29 cells were stably transfected using a shRNA plasmid for Human gastrin (SuperArray Bioscience Corporation) according to manufacturer’s instructions. ..

Concentration Assay:

Article Title: High-Fat Diet Induces Apoptosis of Hypothalamic Neurons
Article Snippet: Samples obtained from three hypothalami from control and HF diet fed rats and Swiss mice were analyzed using a real-time PCR array (RT2 profiler PCR array rat apoptosis - SuperArray Bioscience Corp., Frederick, MD, USA) containing 84 apoptosis related genes, as shown in www.superarray.com/rt_pcr_product/HTML/PARN-012A.html . .. The optimal concentration of cDNA and primers, as well as the maximum efficiency of amplification, were obtained through seven-point, 3-fold dilution curve analysis for each gene.

Article Title: Interleukin-6 Released from Fibroblasts Is Essential for Up-regulation of Matrix Metalloproteinase-1 Expression by U937 Macrophages in Coculture
Article Snippet: PCR Array —The first strand cDNA was synthesized from RNA using the RT2 First Strand Kit (SuperArray Bioscience Corp., Frederick, MD). .. The concentration of protein was determined using a protein assay kit (Bio-Rad).

Cell Culture:

Article Title: Interleukin-6 Released from Fibroblasts Is Essential for Up-regulation of Matrix Metalloproteinase-1 Expression by U937 Macrophages in Coculture
Article Snippet: After the transfection for 24 h, cells were cultured independently or cocultured with U937 cells in the presence or absence of LPS. .. PCR Array —The first strand cDNA was synthesized from RNA using the RT2 First Strand Kit (SuperArray Bioscience Corp., Frederick, MD).

Sedimentation:

Article Title: Stabilization of HIF-2alpha through redox regulation of mTORC2 activation and initiation of mRNA translation
Article Snippet: Real Time-PCR Sybr Green was performed on 50 ng of RNA using the SuperArray kit (SuperArray Bioscience Corporation) and the Eppendorf realplex machine. .. Sedimentation analysis was examined in parallel of RCC 786-O cells by measuring optical density at 254 nm.

Generated:

Article Title: Chemical Genetics Identifies c-Src as an Activator of Primitive Ectoderm Formation in Murine Embryonic Stem Cells #
Article Snippet: .. For quantitative PCR analysis, cDNA was generated from 1 µg of total RNA using the RT2 First Strand Kit from SuperArray Bioscience Corporation. .. PCR reactions were performed using the RT2 SYBR/Rox Master Mix from SuperArray using 1 µl of a 1:100 dilution of the cDNA reaction.

Polymerase Chain Reaction:

Article Title: High-Fat Diet Induces Apoptosis of Hypothalamic Neurons
Article Snippet: .. Samples obtained from three hypothalami from control and HF diet fed rats and Swiss mice were analyzed using a real-time PCR array (RT2 profiler PCR array rat apoptosis - SuperArray Bioscience Corp., Frederick, MD, USA) containing 84 apoptosis related genes, as shown in www.superarray.com/rt_pcr_product/HTML/PARN-012A.html . .. Real-time PCR analysis of gene expression was carried out in an ABI Prism 7500 sequence detection system (Applied Biosystems).

Article Title: Increasing the relative expression of endogenous non-coding Steroid Receptor RNA Activator (SRA) in human breast cancer cells using modified oligonucleotides
Article Snippet: .. Real-time PCR-array Half a microgram of RNA was reverse transcribed using ReactionReady™ First Strand cDNA synthesis Kit (SuperArray Bioscience Corp., Frederick, MD) and applied to Breast Cancer and Estrogen Receptor RT2 Profiler™ PCR arrays (SuperArray Bioscience Corp., Frederick, MD) as detailed by the manufacturer ( and ). ..

Article Title: Chemical Genetics Identifies c-Src as an Activator of Primitive Ectoderm Formation in Murine Embryonic Stem Cells #
Article Snippet: One-fifteenth of each RT reaction was then used in 50 µl PCR reactions. .. For quantitative PCR analysis, cDNA was generated from 1 µg of total RNA using the RT2 First Strand Kit from SuperArray Bioscience Corporation.

Article Title: Suppression of the NF-\u03baB Pathway by Diesel Exhaust Particles Impairs Human Antimycobacterial Immunity
Article Snippet: .. Reagents were obtained from the following sources: ELISPOT assays : capture and biotinylated detection antibodies for IL-1β and IL-6 (Cell sciences, Inc., Canton, MA), IFN-γ, TNF-α (Endogen Pierce, Rockford, IL), IL-10, IL-4 (BD Pharmingen, San Diego, CA), Streptavidin-peroxidase (Sigma, St. Louis, MO), chromogen 1% 3-amino-9-ethylcarbazole (AEC, Pierce, Rockford, IL), MultiscreenHTS high protein binding 96-well plates (Millipore Bedford, MA); PBMC isolation, culture and stimulation: phytohemagglutinin (PHA, Sigma), lipopolysaccharide (LPS, E.coli 026:B6, Sigma) and PPD (Statens Serum Institute, Kopenhagen, Denmark), RPMI-1640 (BioWhittaker, Walkersville, MO), L-glutamine (Cellgro, Manassas, VA), pooled human AB serum (Gemini Bioproducts, Woodland, CA), Ficoll-Paque (GE Healthcare Biosciences, Pittsburgh, PA); RNA extraction and qRT-PCR : RNeasy mini kit (Qiagen, Germantown, MD), RNase-free DNase set (Qiagen), RT2 First Strand kit, RT2 qPCR master mix (SuperArray Bioscience Corporation, Frederick, MD), Power SYBR green PCR master mix (Applied Biosystems, Foster city, CA), Taqman reverse transcription reagents (Applied biosystems); pathway-specific gene expression arrays: Human Th1-Th2-Th3 (PAHS-34E) and TLR (PAHS-18E) (SuperArray Bioscience Corporation); M.tb culture : H37Ra (ATCC # 25177, Manassas, VA), Middlebrook 7H9 broth medium (Difco Laboratories, Detroit, MI) supplemented with 10% albumin dextrose catalase (Difco Laboratories), 7H10 solid agar plates (Becton, Dickinson, Sparks, MD). .. Flowcytometry : Annexin V/PI apoptosis detection assay (BD Biosciences, San José, CA).

Article Title: Interleukin-6 Released from Fibroblasts Is Essential for Up-regulation of Matrix Metalloproteinase-1 Expression by U937 Macrophages in Coculture
Article Snippet: .. PCR Array —The first strand cDNA was synthesized from RNA using the RT2 First Strand Kit (SuperArray Bioscience Corp., Frederick, MD). .. Human inflammatory cytokines and receptor PCR array (catalog number PAHS-011, SuperArray Bioscience Corp.) was used to profile the cytokine expression by fibroblasts in the coculture by following the instructions from the manufacturer.

Negative Control:

Article Title: A gastrin precursor, gastrin-gly, upregulates VEGF expression in colonic epithelial cells through an HIF-1-independent mechanism
Article Snippet: Lovo cells (1 × 105 cells ml−1 in 6-well plates) were transiently transfected with 60 nM of Silencer Negative control siRNA or Gastrin silencer pre-designed siRNA (from Ambion) using the transfection agent siPORT NeoFX according to the manufacturer protocol. .. HT29 cells were stably transfected using a shRNA plasmid for Human gastrin (SuperArray Bioscience Corporation) according to manufacturer’s instructions.

Sequencing:

Article Title: High-Fat Diet Induces Apoptosis of Hypothalamic Neurons
Article Snippet: Samples obtained from three hypothalami from control and HF diet fed rats and Swiss mice were analyzed using a real-time PCR array (RT2 profiler PCR array rat apoptosis - SuperArray Bioscience Corp., Frederick, MD, USA) containing 84 apoptosis related genes, as shown in www.superarray.com/rt_pcr_product/HTML/PARN-012A.html . .. Real-time PCR analysis of gene expression was carried out in an ABI Prism 7500 sequence detection system (Applied Biosystems).

Isolation:

Article Title: Chemical Genetics Identifies c-Src as an Activator of Primitive Ectoderm Formation in Murine Embryonic Stem Cells #
Article Snippet: Total RNA was isolated using the RNAeasy kit in conjunction with QiaShredder columns (Qiagen). .. For quantitative PCR analysis, cDNA was generated from 1 µg of total RNA using the RT2 First Strand Kit from SuperArray Bioscience Corporation.

Article Title: Suppression of the NF-\u03baB Pathway by Diesel Exhaust Particles Impairs Human Antimycobacterial Immunity
Article Snippet: .. Reagents were obtained from the following sources: ELISPOT assays : capture and biotinylated detection antibodies for IL-1β and IL-6 (Cell sciences, Inc., Canton, MA), IFN-γ, TNF-α (Endogen Pierce, Rockford, IL), IL-10, IL-4 (BD Pharmingen, San Diego, CA), Streptavidin-peroxidase (Sigma, St. Louis, MO), chromogen 1% 3-amino-9-ethylcarbazole (AEC, Pierce, Rockford, IL), MultiscreenHTS high protein binding 96-well plates (Millipore Bedford, MA); PBMC isolation, culture and stimulation: phytohemagglutinin (PHA, Sigma), lipopolysaccharide (LPS, E.coli 026:B6, Sigma) and PPD (Statens Serum Institute, Kopenhagen, Denmark), RPMI-1640 (BioWhittaker, Walkersville, MO), L-glutamine (Cellgro, Manassas, VA), pooled human AB serum (Gemini Bioproducts, Woodland, CA), Ficoll-Paque (GE Healthcare Biosciences, Pittsburgh, PA); RNA extraction and qRT-PCR : RNeasy mini kit (Qiagen, Germantown, MD), RNase-free DNase set (Qiagen), RT2 First Strand kit, RT2 qPCR master mix (SuperArray Bioscience Corporation, Frederick, MD), Power SYBR green PCR master mix (Applied Biosystems, Foster city, CA), Taqman reverse transcription reagents (Applied biosystems); pathway-specific gene expression arrays: Human Th1-Th2-Th3 (PAHS-34E) and TLR (PAHS-18E) (SuperArray Bioscience Corporation); M.tb culture : H37Ra (ATCC # 25177, Manassas, VA), Middlebrook 7H9 broth medium (Difco Laboratories, Detroit, MI) supplemented with 10% albumin dextrose catalase (Difco Laboratories), 7H10 solid agar plates (Becton, Dickinson, Sparks, MD). .. Flowcytometry : Annexin V/PI apoptosis detection assay (BD Biosciences, San José, CA).

Article Title: Stabilization of HIF-2alpha through redox regulation of mTORC2 activation and initiation of mRNA translation
Article Snippet: Paragraph title: Polysome isolation and fractionation and Quantitative Real time PCR ... Real Time-PCR Sybr Green was performed on 50 ng of RNA using the SuperArray kit (SuperArray Bioscience Corporation) and the Eppendorf realplex machine.

Article Title: Burn Injury Triggered Dysfunction in Dendritic Cell Response to TLR9 Activation and Resulted in Skewed T Cell Functions
Article Snippet: Paragraph title: RNA Isolation and qRT/PCR ... The expression of genes related to TLR-mediated signal transduction was examined by real-time PCR Array using a SuperArray real-time PCR Kit (SuperArray Bioscience Corp., MD).

Article Title: Induction of multiple matrix metalloproteinases in human dermal and synovial fibroblasts by Staphylococcus aureus: implications in the pathogenesis of septic arthritis and other soft tissue infections
Article Snippet: We therefore analyzed the mRNA expression levels of 12 members of the MAPK family using the MultiGene-12 RT-PCR profiling kit from Superarray Bioscience Corporation. .. Synovial fibroblasts obtained from patients with RA and OA were exposed to 25 μg of total proteins from bacterial culture supernatant or cell lysate, and total RNA was isolated 6 hours later, reverse-transcribed, and assayed for mRNA of 12 MAPK genes.

Detection Assay:

Article Title: Suppression of the NF-\u03baB Pathway by Diesel Exhaust Particles Impairs Human Antimycobacterial Immunity
Article Snippet: Reagents were obtained from the following sources: ELISPOT assays : capture and biotinylated detection antibodies for IL-1β and IL-6 (Cell sciences, Inc., Canton, MA), IFN-γ, TNF-α (Endogen Pierce, Rockford, IL), IL-10, IL-4 (BD Pharmingen, San Diego, CA), Streptavidin-peroxidase (Sigma, St. Louis, MO), chromogen 1% 3-amino-9-ethylcarbazole (AEC, Pierce, Rockford, IL), MultiscreenHTS high protein binding 96-well plates (Millipore Bedford, MA); PBMC isolation, culture and stimulation: phytohemagglutinin (PHA, Sigma), lipopolysaccharide (LPS, E.coli 026:B6, Sigma) and PPD (Statens Serum Institute, Kopenhagen, Denmark), RPMI-1640 (BioWhittaker, Walkersville, MO), L-glutamine (Cellgro, Manassas, VA), pooled human AB serum (Gemini Bioproducts, Woodland, CA), Ficoll-Paque (GE Healthcare Biosciences, Pittsburgh, PA); RNA extraction and qRT-PCR : RNeasy mini kit (Qiagen, Germantown, MD), RNase-free DNase set (Qiagen), RT2 First Strand kit, RT2 qPCR master mix (SuperArray Bioscience Corporation, Frederick, MD), Power SYBR green PCR master mix (Applied Biosystems, Foster city, CA), Taqman reverse transcription reagents (Applied biosystems); pathway-specific gene expression arrays: Human Th1-Th2-Th3 (PAHS-34E) and TLR (PAHS-18E) (SuperArray Bioscience Corporation); M.tb culture : H37Ra (ATCC # 25177, Manassas, VA), Middlebrook 7H9 broth medium (Difco Laboratories, Detroit, MI) supplemented with 10% albumin dextrose catalase (Difco Laboratories), 7H10 solid agar plates (Becton, Dickinson, Sparks, MD). .. Flowcytometry : Annexin V/PI apoptosis detection assay (BD Biosciences, San José, CA).

RNA Extraction:

Article Title: Suppression of the NF-\u03baB Pathway by Diesel Exhaust Particles Impairs Human Antimycobacterial Immunity
Article Snippet: .. Reagents were obtained from the following sources: ELISPOT assays : capture and biotinylated detection antibodies for IL-1β and IL-6 (Cell sciences, Inc., Canton, MA), IFN-γ, TNF-α (Endogen Pierce, Rockford, IL), IL-10, IL-4 (BD Pharmingen, San Diego, CA), Streptavidin-peroxidase (Sigma, St. Louis, MO), chromogen 1% 3-amino-9-ethylcarbazole (AEC, Pierce, Rockford, IL), MultiscreenHTS high protein binding 96-well plates (Millipore Bedford, MA); PBMC isolation, culture and stimulation: phytohemagglutinin (PHA, Sigma), lipopolysaccharide (LPS, E.coli 026:B6, Sigma) and PPD (Statens Serum Institute, Kopenhagen, Denmark), RPMI-1640 (BioWhittaker, Walkersville, MO), L-glutamine (Cellgro, Manassas, VA), pooled human AB serum (Gemini Bioproducts, Woodland, CA), Ficoll-Paque (GE Healthcare Biosciences, Pittsburgh, PA); RNA extraction and qRT-PCR : RNeasy mini kit (Qiagen, Germantown, MD), RNase-free DNase set (Qiagen), RT2 First Strand kit, RT2 qPCR master mix (SuperArray Bioscience Corporation, Frederick, MD), Power SYBR green PCR master mix (Applied Biosystems, Foster city, CA), Taqman reverse transcription reagents (Applied biosystems); pathway-specific gene expression arrays: Human Th1-Th2-Th3 (PAHS-34E) and TLR (PAHS-18E) (SuperArray Bioscience Corporation); M.tb culture : H37Ra (ATCC # 25177, Manassas, VA), Middlebrook 7H9 broth medium (Difco Laboratories, Detroit, MI) supplemented with 10% albumin dextrose catalase (Difco Laboratories), 7H10 solid agar plates (Becton, Dickinson, Sparks, MD). .. Flowcytometry : Annexin V/PI apoptosis detection assay (BD Biosciences, San José, CA).

Mouse Assay:

Article Title: High-Fat Diet Induces Apoptosis of Hypothalamic Neurons
Article Snippet: .. Samples obtained from three hypothalami from control and HF diet fed rats and Swiss mice were analyzed using a real-time PCR array (RT2 profiler PCR array rat apoptosis - SuperArray Bioscience Corp., Frederick, MD, USA) containing 84 apoptosis related genes, as shown in www.superarray.com/rt_pcr_product/HTML/PARN-012A.html . .. Real-time PCR analysis of gene expression was carried out in an ABI Prism 7500 sequence detection system (Applied Biosystems).

Article Title: Burn Injury Triggered Dysfunction in Dendritic Cell Response to TLR9 Activation and Resulted in Skewed T Cell Functions
Article Snippet: The expression of genes related to TLR-mediated signal transduction was examined by real-time PCR Array using a SuperArray real-time PCR Kit (SuperArray Bioscience Corp., MD). .. Fold changes of transcript levels of genes in DCs of burn mice were calculated relative to those in the sham group.

Reverse Transcription Polymerase Chain Reaction:

Article Title: Chemical Genetics Identifies c-Src as an Activator of Primitive Ectoderm Formation in Murine Embryonic Stem Cells #
Article Snippet: Paragraph title: RT-PCR ... For quantitative PCR analysis, cDNA was generated from 1 µg of total RNA using the RT2 First Strand Kit from SuperArray Bioscience Corporation.

Article Title: Stabilization of HIF-2alpha through redox regulation of mTORC2 activation and initiation of mRNA translation
Article Snippet: Real-time (RT-PCR) amplification was performed in polyribosomal fractions using the Superscript One-Step RT-PCR kit from Invitrogen. .. Real Time-PCR Sybr Green was performed on 50 ng of RNA using the SuperArray kit (SuperArray Bioscience Corporation) and the Eppendorf realplex machine.

Article Title: GENDER-SPECIFIC EXPRESSION OF ?1 INTEGRIN OF VERY-LATE ANTIGEN-4 IN MYELIN BASIC PROTEIN-PRIMED T CELLS: IMPLICATIONS FOR GENDER BIAS IN MULTIPLE SCLEROSIS
Article Snippet: .. Multigene-12 RT-PCR profiling kits for mouse integrin gene family I & II were purchased from SuperArray Bioscience Corporation. .. Annexin V-PE apoptosis detection kit was obtained from Biovision. β-estradiol, progesterone, testosterone and dihydrotestosterone (5α-androstan-17β-ol-3-one) were purchased from Sigma.

Article Title: Induction of multiple matrix metalloproteinases in human dermal and synovial fibroblasts by Staphylococcus aureus: implications in the pathogenesis of septic arthritis and other soft tissue infections
Article Snippet: .. We therefore analyzed the mRNA expression levels of 12 members of the MAPK family using the MultiGene-12 RT-PCR profiling kit from Superarray Bioscience Corporation. .. Synovial fibroblasts obtained from patients with RA and OA were exposed to 25 μg of total proteins from bacterial culture supernatant or cell lysate, and total RNA was isolated 6 hours later, reverse-transcribed, and assayed for mRNA of 12 MAPK genes.

Blocking Assay:

Article Title: GENDER-SPECIFIC EXPRESSION OF ?1 INTEGRIN OF VERY-LATE ANTIGEN-4 IN MYELIN BASIC PROTEIN-PRIMED T CELLS: IMPLICATIONS FOR GENDER BIAS IN MULTIPLE SCLEROSIS
Article Snippet: Functional blocking antibodies and FITC-labeled antibodies to CD49d (the α4 chain of VLA-4) and CD29 (the β1 chain of VLA-4) were obtained from Pharmingen. .. Multigene-12 RT-PCR profiling kits for mouse integrin gene family I & II were purchased from SuperArray Bioscience Corporation.

Purification:

Article Title: Burn Injury Triggered Dysfunction in Dendritic Cell Response to TLR9 Activation and Resulted in Skewed T Cell Functions
Article Snippet: RNA Isolation and qRT/PCR Three days after burn injury, splenic cDCs and pDCs were purified to a purity of > 98%, as described above, and were stored in TriZol (invitrogen) until further processing. .. The expression of genes related to TLR-mediated signal transduction was examined by real-time PCR Array using a SuperArray real-time PCR Kit (SuperArray Bioscience Corp., MD).

Plasmid Preparation:

Article Title: A gastrin precursor, gastrin-gly, upregulates VEGF expression in colonic epithelial cells through an HIF-1-independent mechanism
Article Snippet: .. HT29 cells were stably transfected using a shRNA plasmid for Human gastrin (SuperArray Bioscience Corporation) according to manufacturer’s instructions. ..

Software:

Article Title: Interleukin-6 Released from Fibroblasts Is Essential for Up-regulation of Matrix Metalloproteinase-1 Expression by U937 Macrophages in Coculture
Article Snippet: Data were analyzed with the iCycler iQ™ software. .. PCR Array —The first strand cDNA was synthesized from RNA using the RT2 First Strand Kit (SuperArray Bioscience Corp., Frederick, MD).

Article Title: Prostaglandin E2 modulates dendritic cell function during chlamydial genital infection
Article Snippet: The RNA (5–10 lg) was sent to SuperArray Bioscience Corp. for performance of a non-rad-GEArray microarray analysis which contains oligo DNAs dotted on a membrane that represent 96 genes specific for mouse dendritic and antigen-presenting cells and controls. .. Data were quantified using a laser densitometer and IMAGEQUANT software (Molecular Dynamics, Sunnyvale, CA) to calculate the average integrated volumes of spots.

Real-time Polymerase Chain Reaction:

Article Title: High-Fat Diet Induces Apoptosis of Hypothalamic Neurons
Article Snippet: .. Samples obtained from three hypothalami from control and HF diet fed rats and Swiss mice were analyzed using a real-time PCR array (RT2 profiler PCR array rat apoptosis - SuperArray Bioscience Corp., Frederick, MD, USA) containing 84 apoptosis related genes, as shown in www.superarray.com/rt_pcr_product/HTML/PARN-012A.html . .. Real-time PCR analysis of gene expression was carried out in an ABI Prism 7500 sequence detection system (Applied Biosystems).

Article Title: A gastrin precursor, gastrin-gly, upregulates VEGF expression in colonic epithelial cells through an HIF-1-independent mechanism
Article Snippet: Gastrin mRNA expression was controlled 48, 72 and 96 hr after transfection using real time PCR as described above. .. HT29 cells were stably transfected using a shRNA plasmid for Human gastrin (SuperArray Bioscience Corporation) according to manufacturer’s instructions.

Article Title: Chemical Genetics Identifies c-Src as an Activator of Primitive Ectoderm Formation in Murine Embryonic Stem Cells #
Article Snippet: .. For quantitative PCR analysis, cDNA was generated from 1 µg of total RNA using the RT2 First Strand Kit from SuperArray Bioscience Corporation. .. PCR reactions were performed using the RT2 SYBR/Rox Master Mix from SuperArray using 1 µl of a 1:100 dilution of the cDNA reaction.

Article Title: Suppression of the NF-\u03baB Pathway by Diesel Exhaust Particles Impairs Human Antimycobacterial Immunity
Article Snippet: .. Reagents were obtained from the following sources: ELISPOT assays : capture and biotinylated detection antibodies for IL-1β and IL-6 (Cell sciences, Inc., Canton, MA), IFN-γ, TNF-α (Endogen Pierce, Rockford, IL), IL-10, IL-4 (BD Pharmingen, San Diego, CA), Streptavidin-peroxidase (Sigma, St. Louis, MO), chromogen 1% 3-amino-9-ethylcarbazole (AEC, Pierce, Rockford, IL), MultiscreenHTS high protein binding 96-well plates (Millipore Bedford, MA); PBMC isolation, culture and stimulation: phytohemagglutinin (PHA, Sigma), lipopolysaccharide (LPS, E.coli 026:B6, Sigma) and PPD (Statens Serum Institute, Kopenhagen, Denmark), RPMI-1640 (BioWhittaker, Walkersville, MO), L-glutamine (Cellgro, Manassas, VA), pooled human AB serum (Gemini Bioproducts, Woodland, CA), Ficoll-Paque (GE Healthcare Biosciences, Pittsburgh, PA); RNA extraction and qRT-PCR : RNeasy mini kit (Qiagen, Germantown, MD), RNase-free DNase set (Qiagen), RT2 First Strand kit, RT2 qPCR master mix (SuperArray Bioscience Corporation, Frederick, MD), Power SYBR green PCR master mix (Applied Biosystems, Foster city, CA), Taqman reverse transcription reagents (Applied biosystems); pathway-specific gene expression arrays: Human Th1-Th2-Th3 (PAHS-34E) and TLR (PAHS-18E) (SuperArray Bioscience Corporation); M.tb culture : H37Ra (ATCC # 25177, Manassas, VA), Middlebrook 7H9 broth medium (Difco Laboratories, Detroit, MI) supplemented with 10% albumin dextrose catalase (Difco Laboratories), 7H10 solid agar plates (Becton, Dickinson, Sparks, MD). .. Flowcytometry : Annexin V/PI apoptosis detection assay (BD Biosciences, San José, CA).

Article Title: Stabilization of HIF-2alpha through redox regulation of mTORC2 activation and initiation of mRNA translation
Article Snippet: .. Real Time-PCR Sybr Green was performed on 50 ng of RNA using the SuperArray kit (SuperArray Bioscience Corporation) and the Eppendorf realplex machine. ..

Article Title: Burn Injury Triggered Dysfunction in Dendritic Cell Response to TLR9 Activation and Resulted in Skewed T Cell Functions
Article Snippet: .. The expression of genes related to TLR-mediated signal transduction was examined by real-time PCR Array using a SuperArray real-time PCR Kit (SuperArray Bioscience Corp., MD). .. Fold changes of transcript levels of genes in DCs of burn mice were calculated relative to those in the sham group.

Functional Assay:

Article Title: GENDER-SPECIFIC EXPRESSION OF ?1 INTEGRIN OF VERY-LATE ANTIGEN-4 IN MYELIN BASIC PROTEIN-PRIMED T CELLS: IMPLICATIONS FOR GENDER BIAS IN MULTIPLE SCLEROSIS
Article Snippet: Functional blocking antibodies and FITC-labeled antibodies to CD49d (the α4 chain of VLA-4) and CD29 (the β1 chain of VLA-4) were obtained from Pharmingen. .. Multigene-12 RT-PCR profiling kits for mouse integrin gene family I & II were purchased from SuperArray Bioscience Corporation.

shRNA:

Article Title: A gastrin precursor, gastrin-gly, upregulates VEGF expression in colonic epithelial cells through an HIF-1-independent mechanism
Article Snippet: .. HT29 cells were stably transfected using a shRNA plasmid for Human gastrin (SuperArray Bioscience Corporation) according to manufacturer’s instructions. ..

Protein Binding:

Article Title: Suppression of the NF-\u03baB Pathway by Diesel Exhaust Particles Impairs Human Antimycobacterial Immunity
Article Snippet: .. Reagents were obtained from the following sources: ELISPOT assays : capture and biotinylated detection antibodies for IL-1β and IL-6 (Cell sciences, Inc., Canton, MA), IFN-γ, TNF-α (Endogen Pierce, Rockford, IL), IL-10, IL-4 (BD Pharmingen, San Diego, CA), Streptavidin-peroxidase (Sigma, St. Louis, MO), chromogen 1% 3-amino-9-ethylcarbazole (AEC, Pierce, Rockford, IL), MultiscreenHTS high protein binding 96-well plates (Millipore Bedford, MA); PBMC isolation, culture and stimulation: phytohemagglutinin (PHA, Sigma), lipopolysaccharide (LPS, E.coli 026:B6, Sigma) and PPD (Statens Serum Institute, Kopenhagen, Denmark), RPMI-1640 (BioWhittaker, Walkersville, MO), L-glutamine (Cellgro, Manassas, VA), pooled human AB serum (Gemini Bioproducts, Woodland, CA), Ficoll-Paque (GE Healthcare Biosciences, Pittsburgh, PA); RNA extraction and qRT-PCR : RNeasy mini kit (Qiagen, Germantown, MD), RNase-free DNase set (Qiagen), RT2 First Strand kit, RT2 qPCR master mix (SuperArray Bioscience Corporation, Frederick, MD), Power SYBR green PCR master mix (Applied Biosystems, Foster city, CA), Taqman reverse transcription reagents (Applied biosystems); pathway-specific gene expression arrays: Human Th1-Th2-Th3 (PAHS-34E) and TLR (PAHS-18E) (SuperArray Bioscience Corporation); M.tb culture : H37Ra (ATCC # 25177, Manassas, VA), Middlebrook 7H9 broth medium (Difco Laboratories, Detroit, MI) supplemented with 10% albumin dextrose catalase (Difco Laboratories), 7H10 solid agar plates (Becton, Dickinson, Sparks, MD). .. Flowcytometry : Annexin V/PI apoptosis detection assay (BD Biosciences, San José, CA).

Activation Assay:

Article Title: Induction of multiple matrix metalloproteinases in human dermal and synovial fibroblasts by Staphylococcus aureus: implications in the pathogenesis of septic arthritis and other soft tissue infections
Article Snippet: MAPK gene expression in synovial fibroblasts from patients with RA and OA Members of the MAPK gene family (such as ERK1/2 and p38MAPK) are involved in the induction of MMPs through activation protein (AP-1) transcription factors. .. We therefore analyzed the mRNA expression levels of 12 members of the MAPK family using the MultiGene-12 RT-PCR profiling kit from Superarray Bioscience Corporation.

Enzyme-linked Immunospot:

Article Title: Suppression of the NF-\u03baB Pathway by Diesel Exhaust Particles Impairs Human Antimycobacterial Immunity
Article Snippet: .. Reagents were obtained from the following sources: ELISPOT assays : capture and biotinylated detection antibodies for IL-1β and IL-6 (Cell sciences, Inc., Canton, MA), IFN-γ, TNF-α (Endogen Pierce, Rockford, IL), IL-10, IL-4 (BD Pharmingen, San Diego, CA), Streptavidin-peroxidase (Sigma, St. Louis, MO), chromogen 1% 3-amino-9-ethylcarbazole (AEC, Pierce, Rockford, IL), MultiscreenHTS high protein binding 96-well plates (Millipore Bedford, MA); PBMC isolation, culture and stimulation: phytohemagglutinin (PHA, Sigma), lipopolysaccharide (LPS, E.coli 026:B6, Sigma) and PPD (Statens Serum Institute, Kopenhagen, Denmark), RPMI-1640 (BioWhittaker, Walkersville, MO), L-glutamine (Cellgro, Manassas, VA), pooled human AB serum (Gemini Bioproducts, Woodland, CA), Ficoll-Paque (GE Healthcare Biosciences, Pittsburgh, PA); RNA extraction and qRT-PCR : RNeasy mini kit (Qiagen, Germantown, MD), RNase-free DNase set (Qiagen), RT2 First Strand kit, RT2 qPCR master mix (SuperArray Bioscience Corporation, Frederick, MD), Power SYBR green PCR master mix (Applied Biosystems, Foster city, CA), Taqman reverse transcription reagents (Applied biosystems); pathway-specific gene expression arrays: Human Th1-Th2-Th3 (PAHS-34E) and TLR (PAHS-18E) (SuperArray Bioscience Corporation); M.tb culture : H37Ra (ATCC # 25177, Manassas, VA), Middlebrook 7H9 broth medium (Difco Laboratories, Detroit, MI) supplemented with 10% albumin dextrose catalase (Difco Laboratories), 7H10 solid agar plates (Becton, Dickinson, Sparks, MD). .. Flowcytometry : Annexin V/PI apoptosis detection assay (BD Biosciences, San José, CA).

Fractionation:

Article Title: Stabilization of HIF-2alpha through redox regulation of mTORC2 activation and initiation of mRNA translation
Article Snippet: Paragraph title: Polysome isolation and fractionation and Quantitative Real time PCR ... Real Time-PCR Sybr Green was performed on 50 ng of RNA using the SuperArray kit (SuperArray Bioscience Corporation) and the Eppendorf realplex machine.

CTG Assay:

Article Title: Burn Injury Triggered Dysfunction in Dendritic Cell Response to TLR9 Activation and Resulted in Skewed T Cell Functions
Article Snippet: The expression of genes related to TLR-mediated signal transduction was examined by real-time PCR Array using a SuperArray real-time PCR Kit (SuperArray Bioscience Corp., MD). .. Transcript levels of TLR9 was evaluated by qPCR, performed using a SYBR@Green ERTM qPCR SuperMix Kit (Invitrogen) using the forward primer 5′-CGT TTC TCG GTG CTG GAC CTA AGC G-3′ and the reverse primer 5′-CTG AAA GGC ATT GGT GTG GTT G-3′.

Staining:

Article Title: Chemical Genetics Identifies c-Src as an Activator of Primitive Ectoderm Formation in Murine Embryonic Stem Cells #
Article Snippet: Aliquots (5 µl) of each reaction were run on 2% agarose gels and stained with ethidium bromide. .. For quantitative PCR analysis, cDNA was generated from 1 µg of total RNA using the RT2 First Strand Kit from SuperArray Bioscience Corporation.

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    SuperArray Bioscience Corporation transcription rt polymerase chain reaction polymerase chain reaction pcr kit
    Transcription Rt Polymerase Chain Reaction Polymerase Chain Reaction Pcr Kit, supplied by SuperArray Bioscience Corporation, used in various techniques. Bioz Stars score: 94/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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