Expression suite

Manufactured by Thermo Fisher Scientific

Sourced in United States

The Expression Suite is a comprehensive software platform designed to facilitate the analysis and visualization of gene expression data. It provides a robust set of tools for managing, analyzing, and interpreting complex gene expression datasets, enabling researchers to gain valuable insights into biological processes and pathways.

Automatically generated - may contain errors

Lab products found in correlation

Close spelling variants of this product

Gene Expression Suite™ software Expression Suite software Expression Suite Software v1.0.3 Expression Suite Software 1.0.3

16 protocols using expression suite

Rodent MicroRNA Expression Profiling

Check if the same lab product or an alternative is used in the 5 most similar protocols

Identical amounts of total RNAs extracted from animals belonging to the same experimental group were pooled together and subjected (700 ng per RNAs’ pool) to RT-PCR by using the TaqMan MicroRNA reverse transcription kit and the Megaplex RT primer pool (Life Technologies). Subsequently, microfluidic Rodent MicroRNA arrays v3.0 (Life Technologies) were used, according to the manufacturer’s instructions. Three replicates for each pooled sample were analyzed. MicroRNAs’ expression levels were evaluated by comparative assay. Samples were analyzed on a ViiA7 instrument (Life Technologies) and data were processed by ViiA7 software (Life Technologies). ΔΔCt method was used to determine the relative miRNAs’ expression levels. Mamm U6 was used as endogenous control. Global normalization analysis was also performed (Expression Suite, Life Technologies). Some specific MicroRNA Assays (Life Technologies) were performed on each single sample (3 replicates) in order to assess the miRNAs’ expression at the individual level. Further data analysis was carried out by using Expression Suite (Life Technologies) or GraphPad Prism (GraphPad software).

Tessitore A., Cicciarelli G., Del Vecchio F., Gaggiano A., Verzella D., Fischietti M., Mastroiaco V., Vetuschi A., Sferra R., Barnabei R., Capece D., Zazzeroni F, & Alesse E. (2016). MicroRNA expression analysis in high fat diet-induced NAFLD-NASH-HCC progression: study on C57BL/6J mice. BMC Cancer, 16, 3.

+ Open protocol

+ Expand

Quantitative Real-Time PCR Assay

Check if the same lab product or an alternative is used in the 5 most similar protocols

In all, 2.5 × 10⁵ cells were plated onto a 6-well plate. The day after, cells were washed in PBS and then RNA was extracted using RNeasy kit (Qiagen) following the manufacturer’s protocol. RNA was eluted in water and then quantified using Nanodrop (Thermo Fisher). 500 ng of RNA was reverse- transcribed using Quantitect Reverse Transcription kit. For real-time qPCR, cDNA was run using TaqMan™ Gene Expression Assay (FAM) (Thermo Scientific, catalog n. 4331182 250 μl, 20x: Hs00607978_s1 CXCR4; Hs03046964_s1 VHL; Hs01597989_g1 ASS1; Hs00427620_m1 TBP; Hs01001189_m1 SLC7A5) and Taqman Fast 2X master mix (Thermo Scientific). TATA-Box Binding Protein (TBP) was used as the endogenous control. Data and biological replicates were analyzed using Expression Suite (Thermo Scientific). Results were obtained from three independent experiments and presented as Relative quantification (RQ), with RQ max and RQ min calculated using SD1 algorithm. p-values were calculated by Expression Suite software.

Sciacovelli M., Dugourd A., Jimenez L.V., Yang M., Nikitopoulou E., Costa A.S., Tronci L., Caraffini V., Rodrigues P., Schmidt C., Ryan D.G., Young T., Zecchini V.R., Rossi S.H., Massie C., Lohoff C., Masid M., Hatzimanikatis V., Kuppe C., Von Kriegsheim A., Kramann R., Gnanapragasam V., Warren A.Y., Stewart G.D., Erez A., Vanharanta S., Saez-Rodriguez J, & Frezza C. (2022). Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression. Nature Communications, 13, 7830.

+ Open protocol

+ Expand

Sensitive RNA Analysis via RT-qPCR

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

RNA isolation, RT reactions, and real-time quantitative PCR analysis were performed essentially as described previously (Chu et al., 2011 (link), 2016 (link)). Briefly, cells were lysed in 350 uL of RLT plus buffer, and the total RNA were purified using RNeasy kits with either on-column DNase treatment or genomic DNA removal columns under the guidance of the user manual (QIAGEN). Between 100 ng to 500 ng of purified RNA were reverse transcribed with SuperScript IV VILO Master mix (Thermo Fisher Scientific, Cat. No. 11756050). To perform TaqMan qPCR reactions (10 μL total volumes), 1 μL of the diluted cDNA was subsequently used in each of the triplicate qPCR reactions with individual 1 × TaqMan Gene Expression assays and 1 × TaqMan Universal PCR Master Mix II (Thermo Fisher Scientific). The ViiA 7 System was used to perform qPDR, and ExpressionSuite was used to perform data analysis (all from Thermo Fisher Scientific). All TaqMan Gene Expression assays are from Thermo Fisher Scientific and are listed in the Key Resources Table.

Chu L.F., Mamott D., Ni Z., Bacher R., Liu C., Swanson S., Kendziorski C., Stewart R, & Thomson J.A. (2019). An In Vitro Human Segmentation Clock Model Derived from Embryonic Stem Cells. Cell reports, 28(9), 2247-2255.e5.

+ Open protocol

+ Expand

Robust Experimental Validation Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols

Graphs were generated using Graphpad Prism 8–9. The statistical analysis was performed using Prism software through either unpaired/paired t-test or one-way ANOVA using Dunnets’s, Sidak’s or Tukey’s tests for multiple comparisons. For the one-way ANOVA analysis, gaussian distribution and equal SD were assumed. For real-time qPCR, the statistical analysis was performed using Expression Suite software (Thermo Scientific) using SD algorithm on three independent experiments. The reproducibility of the experimental findings was supported by performing independent experiments (usually n = 3) or by having several independent culture replicates (replicate wells/dishes) as reported in the figure legends. Furthermore, additional experiments were conducted in other relevant cell lines to validate the main findings of the study. Western blot experiments were repeated more than once or validated with other techniques (qPCR or multi-omic analysis).

+ Open protocol

+ Expand

Quantitative Gene Expression Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols

Tissue homogenisation, RNA extraction, reverse transcription (RT) and quantitative polymerase chain reaction (qPCR) were carried out as described [35] , on the same biopsies analyzed for DNA methylation (see above). Primers for detection of PLAGL1 expression have been reported before [34] . TaqMan R qPCR assays (Applied Biosystems, CA, USA) used for all other markers are listed in Table 3. RPL19 and SDHA were used as reference genes [34, 39] .
Expression suite (Thermo Fisher Scientific, MA, USA) was used to calculate Ct values with respect to the average of the cycle threshold (Ct) values of the RPL19 and SDHA reference genes. Data were further recalculated as 2-Ct, with respect to the mean Ct value of the samples in the control group as described [40] . The resulting numbers are listed in the Figures and represent fold change in expression.

Schoorlemmer J., Macías-Redondo S., Strunk M., Ramos-Ruíz R., Calvo P., Benito R., Paules C, & Oros D. (2020). Altered DNA methylation in human placenta after (suspected) preterm labor. Epigenomics, 12(20).

+ Open protocol

+ Expand

Analyzing Colon Expression Profiles

Check if the same lab product or an alternative is used in the 5 most similar protocols

Data from qPCR were analyzed using ExpressionSuite (Thermo Fisher Scientific, Walton, MA, United States) software using the ΔΔCt method and expressed as fold-changes comparative to the control group. The qPCR data and those from the immunohistochemistry/immunofluorescence experiments were analyzed using student’s t-tests to compare between age groups for each region of colon. Proprietary software (GraphPad Prism v8.0, San Diego, CA, United States) was used for all statistical tests. A P-value of ≤0.05 indicated statistical significance.

Palmer A., Epton S., Crawley E., Straface M., Gammon L., Edgar M.M., Xu Y., Elahi S., Chin-Aleong J., Martin J.E., Bishop C.L., Knowles C.H, & Sanger G.J. (2021). Expression of p16 Within Myenteric Neurons of the Aged Colon: A Potential Marker of Declining Function. Frontiers in Neuroscience, 15, 747067.

+ Open protocol

+ Expand

miRNA expression profiling in pancreatic cancer

Check if the same lab product or an alternative is used in the 5 most similar protocols

RNA was extracted from fresh-frozen LCM samples using the RNAqueous-Micro Total RNA Isolation Kit (Thermo Fisher Scientific), quantified with a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific), and converted to cDNA using the TaqMan MicroRNA Reverse Transcription Kit (Thermo Fisher Scientific) with Megaplex RT Primers Rodent Pool A and B (Thermo Fisher Scientific). cDNA was preamplified 18 cycles using the TaqMan PreAmp Master Mix (Thermo Fisher Scientific) and Megaplex PreAmp Primers Rodent Pool A and B (Thermo Fisher Scientific). miRNA microarray was performed by the Johns Hopkins School of Medicine Genetic Resources Core Facility using the TaqMan OpenArray Rodent MicroRNA Panel (Thermo Fisher Scientific) and TaqMan OpenArray Real-Time PCR Master Mix (Thermo Fisher Scientific). All Ct values were normalized to endogenous levels of U6 snRNA. Fold changes were quantified utilizing the ΔΔCt method in which all PanIN groups were normalized to the normal group (normal ducts isolated from WT C57BL/6 mice). P-values for differential expression statistics were generated and adjusted for multiple hypothesis testing using ExpressionSuite (Thermo Fisher Scientific).

Chu N.J., Anders R.A., Fertig E.J., Cao M., Hopkins A.C., Keenan B.P., Popovic A., Armstrong T.D., Jaffee E.M, & Zimmerman J.W. (2020). Inhibition of miR-21 regulates mutant KRAS effector pathways and intercepts pancreatic ductal adenocarcinoma development. Cancer prevention research (Philadelphia, Pa.), 13(7), 569-582.

+ Open protocol

+ Expand

Sensitive RNA Analysis via RT-qPCR

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

+ Open protocol

+ Expand

Molecular Subgrouping of Medulloblastoma

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

Codeset genes expression analysis was used to generate a pairwise distance matrix. Additionally, MB cell lines previously assigned to the SHH subgroup: DAOY, UW228, ONS-76 [9 (link), 18 (link), 29 (link), 30 (link)] and the UW402 and UW473 (no subgroup information) were included in the analysis.
For molecular subgroup assignment, unsupervised hierarchical clustering was performed by Pearson distance correlation followed by an average-linkage algorithm. Delta Ct values were used during analysis and a Heatmap was generated using the Expression Suite® software (Life Technologies). A total of 763 MB samples from the study of Cavalli and colleagues [1 (link)] (GSE85217) in the R environment were analyzed for algorithm validation and heatmap comparison.

Cruzeiro G.A., Salomão K.B., de Biagi Jr C.A., Baumgartner M., Sturm D., Lira R.C., de Almeida Magalhães T., Baroni Milan M., da Silva Silveira V., Saggioro F.P., de Oliveira R.S., dos Santos Klinger P.H., Seidinger A.L., Yunes J.A., de Paula Queiroz R.G., Oba-Shinjo S.M., Scrideli C.A., Nagahashi S.M., Tone L.G, & Valera E.T. (2019). A simplified approach using Taqman low-density array for medulloblastoma subgrouping. Acta Neuropathologica Communications, 7, 33.

+ Open protocol

+ Expand

Comparative qPCR Expression Estimation

Check if the same lab product or an alternative is used in the 5 most similar protocols

There are a wide variety of algorithms available to estimate expression from qPCR amplification curves. To facilitate comparisons between these algorithms, we have applied many of these algorithms to our benchmark data set. The resulting expression estimates and quality scores are available as data objects in the miRcomp package.
Specifically, we provide expression estimates from the following methods:

LifeTech ExpressionSuite

4 parameter sigmoidal model (b4)

5 parameter sigmoidal model (b5)

4 parameter log sigmoidal model (l4)

5 parameter log sigmoidal model (l5)

Linear exponential model (linexp)

Additionally, the raw amplification data are available in the miRcompData package allowing researchers to easily generate expression estimates using other current or future algorithms.

McCall M.N., Baras A.S., Crits-Christoph A., Ingersoll R., McAlexander M.A., Witwer K.W, & Halushka M.K. (2016). A benchmark for microRNA quantification algorithms using the OpenArray platform. BMC Bioinformatics, 17, 138.

+ 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?

Revolutionizing how scientists
search and build protocols!