Log In Sign up
The largest database of trusted experimental protocols

Aminoallyl messageamp 2 kit

Manufactured by Thermo Fisher Scientific
Visit Supplier
Sourced in Japan, United States

The AminoAllyl MessageAmp II kit is a laboratory equipment product that enables the synthesis of aminoallyl-modified RNA from DNA templates. It provides a method for the preparation of aminoallyl-modified RNA, which can then be used for various downstream applications.

Automatically generated - may contain errors

Lab products found in correlation

Feature extraction software, by Agilent Technologies (4 mentions) Rnaqueous micro kit, by Thermo Fisher Scientific (3 mentions) Alexa fluor 555 reactive dye, by Thermo Fisher Scientific (2 mentions) Agilent scanner, by Agilent Technologies (2 mentions) Sureprint mouse 8x60k gene expression microarrays, by Agilent Technologies (2 mentions) Rna lysis buffer, by Thermo Fisher Scientific (2 mentions) Taqman, by Thermo Fisher Scientific (2 mentions) 7500 real time pcr system, by Thermo Fisher Scientific (2 mentions) Sureprint g3 mouse gene expression 8x60k microarray, by Agilent Technologies (2 mentions) Cy3 dye, by GE Healthcare (2 mentions) Facsaria, by BD (2 mentions) Micro array scanner g2565ca, by Agilent Technologies (1 mentions) Agilent microarray scanner g2565ca, by Agilent Technologies (1 mentions) Cy5 mono reactive dye pack, by GE Healthcare (1 mentions) Isogen, by Nippon Gene (1 mentions) Bioanalyzer 2200, by Agilent Technologies (1 mentions) Genepix 4000b microarray scanner, by Molecular Devices (1 mentions) Custom designed microarrays, by Agilent Technologies (1 mentions)

10 protocols using aminoallyl messageamp 2 kit

1

One-Color Microarray Gene Expression Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
Microarrays using the isolated RNA were performed by the RCUG team of Hannover Medical School and as previously described in detail in Schwarzer et al. Briefly, when possible, 100 ng (or less if not available) of total RNA was used to prepare Aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp II Kit; Thermo Fisher Scientific), applying one round of amplification as directed by the company, except for a 2-fold downscaling of all reaction volumes. Before the reverse transcription reaction, 1 μL of 1:5,000 dilution of Agilent’s One-Color Spike-in Kit stock solution (Agilent Technologies) was added to the total RNA used for each sample. The labeling of aaUTP-cRNA was performed with Alexa Fluor 555 Reactive Dye (Thermo Fisher Scientific) following the manufacturer’s instructions with the Amino Allyl MessageAmp II Kit (2-fold downscaled reaction volumes). Afterward, cRNA fragmentation, hybridization, and washing steps were carried out as recommended in “One-Color Microarray-Based Gene Expression Analysis Protocol V5.7,” except that 500 ng of each fluorescently labeled cRNA population was used for hybridization. Slides were scanned using the Agilent Micro Array Scanner G2565CA (pixel resolution 3 μm, bit depth 20). Data extraction was performed with the “FeatureExtraction Software V10.7.3.1” using the extraction protocol file “GE1_107_Sep09.xml.”
Bastone A.L., Dziadek V., John-Neek P., Mansel F., Fleischauer J., Agyeman-Duah E., Schaudien D., Dittrich-Breiholz O., Schwarzer A., Schambach A, & Rothe M. (2023). Development of an in vitro genotoxicity assay to detect retroviral vector-induced lymphoid insertional mutants. Molecular Therapy. Methods & Clinical Development, 30, 515-533.
+ Open protocol
+ Expand
2

Mouse Genome Microarray Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
The microarray utilized in this study represents a refined version of the Whole Mouse Genome Oligo Microarray 4 × 44K v2 (Design ID 026655, Agilent Technologies, Santa Clara, California, USA). Microarray design was created at Agilent's eArray portal using a 4 × 180K design format for mRNA expression. 40 ng of total RNA were used to prepare aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp™ II Kit, Thermo Fisher Scientific). Prior to the reverse transcription, 1 μl of Agilent's One-Color spike-in Kit stock solution (1:100000) was added to each analyzed sample. The labeling of aaUTP-cRNA was performed with Alexa Fluor 555 Reactive Dye (Thermo Fisher Scientific). cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the “One-Color Microarray-Based Gene Expression Analysis Protocol V5.7.” Slides were scanned using the Agilent Micro Array Scanner G2565CA. Data extraction was performed with the “Feature Extraction Software V10.7.3.1” (protocol file “GE1_107_Sep09.xml”). Average expression intensities were row normalized for each experiment and from this heatmaps were constructed. Rows were clustered using the complete linkage method which finds similar clusters. All calculations were performed in the R software using the libraries “pheatmap” and “gplots.”
Skuljec J., Jirmo A.C., Habener A., Talbot S.R., Pul R., Grychtol R., Aydin M., Kleinschnitz C., Happle C, & Hansen G. (2018). Absence of Regulatory T Cells Causes Phenotypic and Functional Switch in Murine Peritoneal Macrophages. Frontiers in Immunology, 9, 2458.
+ Open protocol
+ Expand
3

Profiling Gene Expression in FGFRL1-deficient Cells

Check if the same lab product or an alternative is used in the 5 most similar protocols
Total RNA was extracted from 6×106 cells of wild-type and FGFRL1-deficient KYSE520 cells, respectively, with Isogen (Nippon gene, Inc., Japan). RNA was amplified with Amino Allyl MessageAMP II kit (Thermo Fisher Scientific, Inc.) and coupled with Cy5 dye with Cy5 Mono-Reactive Dye Pack (GE healthcare), and then hybridized to a human Oligo chip (25 k; Toray Industries, Inc., Tokyo, Japan) according to the manufacturers protocol.
Takei Y., Matsumura T., Watanabe K., Nakamine H., Sudo T., Shimizu K, & Shimada Y. (2018). FGFRL1 deficiency reduces motility and tumorigenic potential of cells derived from oesophageal squamous cell carcinomas. Oncology Letters, 16(1), 809-814.
+ Open protocol
+ Expand
4

Hippocampal Transcriptome Profiling in Rats

Check if the same lab product or an alternative is used in the 5 most similar protocols
3 SD rats in each group were used in microarray. Rat hippocampal tissue RNA samples were extracted using TRIzol reagent 7 days after operation. RNA integrity was evaluated by Agilent 2200 Bioanalyzer. The purity of RNA samples was evaluated by ultraviolet spectrophotometer K5500. Fluorescent complementary DNA (cDNA) was synthesized with Amino Allyl MessageAmp II Kit (Life Technologies, USA). RiboArray™lncDETECT™RAT Array 1*12 K (Riobio, China) was applied to detect the transcript profiles of the hippocampus. The slides were scanned and analyzed by GenePix 4000B Microarray Scanner (Molecular Devices, USA). The differentially expressed transcripts were calculated using the Limma package in Bioconductor.
Cheng X., Li H., Zhao H., Li W., Qin J, & Jin G. (2019). Function and mechanism of long non-coding RNA Gm21284 in the development of hippocampal cholinergic neurons. Cell & Bioscience, 9, 72.
+ Open protocol
+ Expand
5

Microarray and qPCR Analysis of Lung Macrophages

Check if the same lab product or an alternative is used in the 5 most similar protocols
For microarray, lung macrophages (10,000 cells) were directly sorted into RNA lysis buffer (Ambion RNAqueous Micro for RNA isolation) and frozen on dry ice. RNA was isolated, amplified using the AminoAllyl MessageAmp II kit (Life Technologies, Grand Island, NY), coupled to Cy3, and hybridized to SurePrint Mouse 8x60k gene expression microarrays (Agilent Technologies, Santa Clara CA) as per manufacturer recommendations. Microarrays were scanned on an Agilent scanner, and spot intensities extracted with Feature Extraction software (Agilent Technologies). Data were quantile normalized, and statistical analysis was performed using Significance Analysis of Microarrays52 (link). All microarray data are available from the NCBI Gene Expression Omnibus under accession number GSE46437. For qPCR, RNA was extracted from lung tissue or sorted macrophages, and then reverse transcribed to cDNA, as previously described53 (link),54 (link). qPCR was performed using Taqman® (Applied Biosystems, Foster City, CA) kits and the Applied Biosystems 7500 Real-Time PCR System. All data were normalized to 18S ribosomal values and the quantification of differences between treatment groups was calculated according to the manufacturer's instructions. Gene expression is presented as the fold increase over naive WT controls or other groups indicated in detail in legends.
Chen F., Wu W., Millman A., Craft J.F., Chen E., Patel N., Boucher J.L., Urban J.F., Kim C.C, & Gause W.C. (2014). Neutrophils prime a long-lived effector macrophage phenotype that mediates accelerated helminth expulsion. Nature immunology, 15(10), 938-946.
+ Open protocol
+ Expand
6

Antigen-experienced T cell transcriptional profiling

Check if the same lab product or an alternative is used in the 5 most similar protocols
Antigen-experienced T cells (S2A Fig, [42 ,43 ]) were isolated from wild-type mice 6 d.p.i. by double-sorting to high purity on a FACSAria (BD). RNA was isolated using the RNAqueous Micro kit (Ambion) and amplified (Amino Allyl MessageAmp II kit, Life Technologies) to generate amino allyl incorporated amplified RNA (aaRNA). aaRNA was coupled to Cy3 dye (GE Healthcare Life Sciences) and hybridized overnight to a SurePrint G3 Mouse Gene Expression 8x60K microarray (Agilent), which was washed and scanned per manufacturer’s instructions. Raw intensities were extracted using Feature Extraction software (Agilent) and quantile normalized using Limma [87 ]. Differentially expressed genes were identified using Significance Analysis for Microarrays (SAM) [88 (link)]. Complete microarray data can be accessed in the Gene Expression Omnibus database (GEO; http://www.ncbi.nlm.nih.gov/geo/) under accession GSE81196.
Fontana M.F., de Melo G.L., Anidi C., Hamburger R., Kim C.Y., Lee S.Y., Pham J, & Kim C.C. (2016). Macrophage Colony Stimulating Factor Derived from CD4+ T Cells Contributes to Control of a Blood-Borne Infection. PLoS Pathogens, 12(12), e1006046.
+ Open protocol
+ Expand
7

Microarray-Based Analysis of LPS-Induced Genes

Check if the same lab product or an alternative is used in the 5 most similar protocols
Following a 4 h LPS stimulation, RNA was isolated from BMDM using the RNaqueous Micro kit (Ambion). Purified RNA was amplified (Amino Allyl MessageAmp II kit, Life Technologies) with minor modifications to manufacturer’s instructions to generate amino allyl incorporated amplified RNA (aaRNA). aaRNA was coupled to Cy3 dye (GE Healthcare Life Sciences) and hybridized overnight to a SurePrint G3 Mouse Gene Expression 8x60K microarray, which was washed and scanned per manufacturer’s instructions (Agilent). Raw intensities were extracted using Feature Extraction software (Agilent) and quantile normalized using Limma (17 ). Differentially expressed genes were identified using Significance Analysis for Microarrays (SAM) (18 (link)), and data were visualized as heat maps using custom Perl scripts. Genes that were increased by at least twofold according to SAM (1% FDR) in LPS-treated Junbfl/fl BMDM were considered to be LPS-induced. JUNB-dependent genes were identified using SAM (10% FDR, 1.5-fold change threshold) to compare LPS-stimulated gene expression values, normalized to average baseline expression, between Junbfl/fl and JunbΔLyz2 macrophages. The set of genes regulated by JUNB in response to LPS was defined as the intersection of LPS-induced genes and JUNB-dependent genes. All data are available in GEO under accession number GSE50542.
Fontana M.F., Baccarella A., Pancholi N., Pufall M.A., Herbert D.R, & Kim C.C. (2014). JUNB is a Key Transcriptional Modulator of Macrophage Activation. Journal of immunology (Baltimore, Md. : 1950), 194(1), 177-186.
+ Open protocol
+ Expand
8

Microarray Analysis of C4da Neurons

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
Microarray analysis was performed using previously described procedures (Jiang et al., 2014 (link)) with minor modifications. Body wall filets of 3rd instar larvae were dissociated to single cell suspensions in PBS containing 1 mg/ml collagenase for 20min at 37° C with automated mixing at 1000 rpm (Eppendorf Thermomixer). Samples were triturated 10× through a P1000 pipette tip every 5min during the incubation. C4da neurons were isolated by flow cytometry into 300μl PBS using a FACSAria (BD Biosciences), and immediately re-sorted into 100μl RNAqueous Micro Lysis buffer (ThermoFisher). Samples were flick-mixed and immediately frozen on dry ice. RNA was isolated using the RNAqueous Micro kit (ThermoFisher) as per the manufacturer’s protocol, and RNA was amplified using two rounds of linear amplification using the Aminoallyl MessageAmp II kit (Life Technologies). Dye-coupled aRNA was fragmented and hybridized to custom-designed 8×60k gene expression microarrays as per the manufacturer recommen-dations (Agilent Technologies). The microarray design used in this study was previously described (Lin et al., 2015 (link)), and details of the platform are available in the NCBI Gene Expression Omnibus under Accession number GPL19582.
Hoyer N., Zielke P., Hu C., Petersen M., Sauter K., Scharrenberg R., Peng Y., Kim C.C., Han C., Parrish J.Z, & Soba P. (2018). Ret and Substrate-Derived TGF-β Maverick Regulate Space-Filling Dendrite Growth in Drosophila Sensory Neurons. Cell reports, 24(9), 2261-2272.e5.
+ Open protocol
+ Expand
9

RNA Isolation, Amplification, and Microarray Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
RNA was isolated from FACS-sorted samples using the RNAqueous-Micro kit and DNase treated as per the manufacturer’s recommendations. All RNA samples were subjected to two rounds of linear amplification using the Aminoallyl MessageAmp II kit (Life Technologies). Dye-coupled aRNA was fragmented and hybridized to custom-designed microarrays as per the manufacturer recommendations (Agilent Technologies).
Parrish J.Z., Kim C.C., Tang L., Bergquist S., Wang T., DeRisi J.L., Jan L.Y., Jan Y.N, & Davis G.W. (2014). Krüppel Mediates the Selective Rebalancing of Ion Channel Expression. Neuron, 82(3), 537-544.
+ Open protocol
+ Expand
10

Microarray and qPCR Analysis of Lung Macrophages

Check if the same lab product or an alternative is used in the 5 most similar protocols
For microarray, lung macrophages (10,000 cells) were directly sorted into RNA lysis buffer (Ambion RNAqueous Micro for RNA isolation) and frozen on dry ice. RNA was isolated, amplified using the AminoAllyl MessageAmp II kit (Life Technologies, Grand Island, NY), coupled to Cy3, and hybridized to SurePrint Mouse 8x60k gene expression microarrays (Agilent Technologies, Santa Clara CA) as per manufacturer recommendations. Microarrays were scanned on an Agilent scanner, and spot intensities extracted with Feature Extraction software (Agilent Technologies). Data were quantile normalized, and statistical analysis was performed using Significance Analysis of Microarrays52 (link). All microarray data are available from the NCBI Gene Expression Omnibus under accession number GSE46437. For qPCR, RNA was extracted from lung tissue or sorted macrophages, and then reverse transcribed to cDNA, as previously described53 (link),54 (link). qPCR was performed using Taqman® (Applied Biosystems, Foster City, CA) kits and the Applied Biosystems 7500 Real-Time PCR System. All data were normalized to 18S ribosomal values and the quantification of differences between treatment groups was calculated according to the manufacturer's instructions. Gene expression is presented as the fold increase over naive WT controls or other groups indicated in detail in legends.
Chen F., Wu W., Millman A., Craft J.F., Chen E., Patel N., Boucher J.L., Urban J.F., Kim C.C, & Gause W.C. (2014). Neutrophils prime a long-lived effector macrophage phenotype that mediates accelerated helminth expulsion. Nature immunology, 15(10), 938-946.
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

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

Sign up now

Revolutionizing how scientists
search and build protocols!