Transcriptome analysis console software

Manufactured by Thermo Fisher Scientific

Sourced in United States

The Transcriptome Analysis Console software is a bioinformatics tool designed for the analysis and visualization of transcriptome data. It provides a comprehensive platform for processing, analyzing, and interpreting RNA sequencing data.

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189 protocols using transcriptome analysis console software

Microarray-based Transcriptome Analysis

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Following quality control (Agilent RNA 6000 Nano LabChips), RNA samples were subjected to PrimeView microarray (Affymetrix) preparation and analysis per the manufacturer’s specifications and scanned using a GeneChip 3000 scanner (Affymetrix). Robust multiarray averaging (RMA), quantile normalization, and median polishing on logged probe set intensity values were performed using Affymetrix Transcriptome Analysis Console (TAC) software. Fold change of the probe set intensity values to the matched untreated controls were calculated and one-way analysis of variance (ANOVA) was performed using Transcriptome Analysis Console (TAC) software (Affymetrix). Normalization and probe set analysis were performed for each sample type independently. Where genes have multiple probe sets, only probe sets showing the greatest overall level of change were retained for subsequent analyses. For heatmap presentation, log₂ probe emission intensity of each replicate was obtained from CEL files, then the data from treated samples and their corresponding controls were zero-meaned. Such normalization unified the scale of gene expression change without negating the magnitude of change.

Mostafa M.M., Rider C.F., Shah S., Traves S.L., Gordon P.M., Miller-Larsson A., Leigh R, & Newton R. (2019). Glucocorticoid-driven transcriptomes in human airway epithelial cells: commonalities, differences and functional insight from cell lines and primary cells. BMC Medical Genomics, 12, 29.

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Transcriptomic Analysis of Human Samples

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RNA extraction and purification was done using Direct-zol RNA Miniprep Kit (Zymo Research). GeneChip® WT PLUS Reagent Kit (ThermoFisher Scientific) was used. RNA samples were checked for purity (OD260/OD280 ≥ 1.8, RIN ≥ 8), and hybridized to the human Clariom™ D Arrays (Thermo Fisher Scientific). Data were analyzed using the Transcriptome Analysis Console (TAC) software (Thermo Fisher Scientific), carried out at the Institute of Genetics and Genomics of Geneva (iGE3). Transcriptome Analysis Console (TAC) software (Thermo Fisher Scientific) was used for data processing and analysis. Gene classification was assessed using DAVID software and ENRICHR online software^{75 (link)}. In addition, Gene Set Enrichment Analysis (GSEA) was used for the analysis of global transcriptomic data using curated gene signatures obtained from the MSigDB v7.2 database (https://software.broadinstitute.org/cancer/software/gsea).

Mazzeo L., Ghosh S., Di Cicco E., Isma J., Tavernari D., Samarkina A., Ostano P., Youssef M.K., Simon C, & Dotto G.P. (2024). ANKRD1 is a mesenchymal-specific driver of cancer-associated fibroblast activation bridging androgen receptor loss to AP-1 activation. Nature Communications, 15, 1038.

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Arginine-induced Transcriptome Analysis

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After arginine-stimulation treatment, the total RNA was extracted from the CWR22Rv1 cells by the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Microarray gene expression profiling was performed by the Transcriptome Analysis Console software (Thermofisher, Version 4.0) with Affymetrix GeneChip Human Clariom™ S Assay. The gene expression changes were identified by pairwise comparison analyses (≥1.5-fold threshold), and expression patterns were analyzed by hierarchical clustering.

Chen C.L., Hsu S.C., Chung T.Y., Chu C.Y., Wang H.J., Hsiao P.W., Yeh S.D., Ann D.K., Yen Y, & Kung H.J. (2021). Arginine is an epigenetic regulator targeting TEAD4 to modulate OXPHOS in prostate cancer cells. Nature Communications, 12, 2398.

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Transcriptome Analysis of Gene Expression

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The statistical analysis was carried out using the Transcriptome Analysis Console Software (Thermo Fisher Scientific, Waltham, MA, USA) and the Statistica 13.0 PL (Kraków, Poland). The ANOVA and Tukey’s post hoc test were performed (p < 0.05). The changes in the gene expression are presented as a fold change (FC).

Czerwiński M., Bednarska-Czerwińska A., Zmarzły N., Boroń D., Oplawski M, & Grabarek B.O. (2021). Evaluation of the Differences in the Expression of Biogenic Amine-Related mRNAs and Proteins in Endometrioid Endometrial Cancer. Journal of Clinical Medicine, 10(21), 4872.

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RNA Extraction and Transcriptomic Analysis

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RNA was extracted from cells using Direct-zol RNA Microprep Kit (ZymoResearch) following the manufacturer's instruction and quantified with NanoDrop2000/2000c Spectrophotometers (Thermo Fisher).
For qPCR, RNA was reverse transcribed with SuperScript IV VILO Master Mix with exDNase Enzyme or with High-Capacity cDNA Reverse Transcription Kit. qPCR was performed with ABU Prism 7900 HT (AB) using the TaqMan Fast Advanced PCR MasterMix (Applied Biosystem). Gene expression levels were normalized with β-actin expression (see Supplementary Material and Methods for list of oligonucleotides).
Microarray analysis was performed with Clariom S Assay, mouse (Thermo Fisher). Raw data were preprocessed using the sst-RMA algorithm implemented in the Transcriptome Analysis Console software (Thermo Fisher) and analyzed using R software. Differentially expressed genes were identified using the limma package (17 (link)). P values were adjusted for multiple tests using the Benjamini–Hocheberg FDR. Functional overrepresentation analysis of differentially expressed genes was carried using the topGO package with Gene Ontology (GO) biological process terms, and Qiagen's Ingenuity Pathway Analysis (IPA, Qiagen).

Perrone M., Chiodoni C., Lecchi M., Botti L., Bassani B., Piva A., Jachetti E., Milani M., Lecis D., Tagliabue E., Verderio P., Sangaletti S, & Colombo M.P. (2022). ATF3 Reprograms the Bone Marrow Niche in Response to Early Breast Cancer Transformation. Cancer Research, 83(1), 117-129.

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Microarray Analysis of Mouse RNA

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Aliquots (250 ng) of total RNA obtained from 4 animals per group at 16.5 wks were individually converted to cDNA and labeled with Clariom™ S Assay, mouse (Thermo Fisher Scientific, Inc., cat.# 902930) and GeneChip™WT PLUS Reagent Kit (Thermo Fisher Scientific, Inc., cat.# 902281) according to the manufacturer’s instructions. Hybridization, washing, and staining were performed using the Hybridization, Wash, and Stain Kit (Thermo Fisher Scientific, Inc., cat.# 900720), GeneChip™ Hybridization Oven 645 (Thermo Fisher Scientific, Inc.), and GeneChip™ Fluidics Station 450 (Thermo Fisher Scientific, Inc.), according to the manufacturer’s protocols. After washing, Array Strips were analyzed using GeneChip™ Scanner 3000 7G (Thermo Fisher Scientific, Inc.). Data were validated using Expression Console™ and Transcriptome Analysis Console™ Software (Thermo Fisher Scientific, Inc.). A cut-off point of ≤-1.3 or ≥1.3 of the linear fold change and P-values was used. We submitted our microarray data, which was approved under the accession number GSE18830 to the GEO repository.

Suzuki M., Kohmura-Kobayashi Y., Ueda M., Furuta-Isomura N., Matsumoto M., Oda T., Kawai K., Itoh T., Matsuya M., Narumi M., Tamura N., Uchida T., Mochizuki K, & Itoh H. (2022). Comparative Analysis of Gene Expression Profiles in the Adipose Tissue of Obese Adult Mice With Rapid Infantile Growth After Undernourishment In Utero. Frontiers in Endocrinology, 13, 818064.

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Isolation and Transcriptome Analysis of Fetal Liver Endothelial Cells

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The total RNAs were isolated from CD31^highCD146^highLyve1⁺ cells in fatal liver (E12.5 and E17.5) by NucleoSpin RNA kit (MACHEREY-NAGEL GmBH & Co, Duren, Germany). mRNA expressions were analyzed by GeneChip Mouse Genome 430 2.0 Array (Thermo Fisher Scientific) and detected by GeneChip Scanner 3000 7G (Thermo Fisher Scientific). Transcriptome Analysis Console software (Thermo Fisher Scientific) was used for data analysis.

Hayakawa M., Sakata A., Hayakawa H., Matsumoto H., Hiramoto T., Kashiwakura Y., Baatartsogt N., Fukushima N., Sakata Y., Suzuki-Inoue K, & Ohmori T. (2021). Characterization and visualization of murine coagulation factor VIII-producing cells in vivo. Scientific Reports, 11, 14824.

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Targeted Gene Expression Analysis

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Targeted gene expression analysis was performed with a custom designed panel of relevant BCL-2, PI3K/AKT, and apoptotic pathway genes as previously described [3 (link)]. Expression values and fold change (FC) were calculated using the Transcriptome Analysis Console software (TAC, version 4.0.2, Thermo Fisher Scientific, Waltham, MA, USA). To optimally represent the FC in linear space, FC values between 0 and 1 were modified by the TAC software as follows: (−1/Fold change)).

Holz C., Lange S., Sekora A., Knuebel G., Krohn S., Murua Escobar H., Junghanss C, & Richter A. (2023). Combined BCL-2 and PI3K/AKT Pathway Inhibition in KMT2A-Rearranged Acute B-Lymphoblastic Leukemia Cells. International Journal of Molecular Sciences, 24(2), 1359.

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Transcriptome Analysis using Gene 2.1 ST Array

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For transcriptomics analyses, total RNA was isolated using the RNeasy system (QIAGEN, Hilden, Germany). Total RNA concentrations were determined by the NanoDrop-1000 spectrophotometer (PEQLAB, Erlangen, Germany), and RNA quality was assessed by the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) (Figure S5). Transcriptome profiling was carried out by the Genomics Core Facility at the Medical University of Vienna (Vienna, Austria) using the Human Gene 2.1 ST Array (Thermo Fisher Scientific). Transcriptome Analysis Console software (v.4.0; Thermo Fisher Scientific) was used for data analysis, for PCA, to determine DEGs, for hierarchical clustering, for scatterplots, and to identify pathways associated with DEGs. Gene lists of DEGs (more than 2-fold change of log2-transormed expression values, p values below 0.05) were analyzed by Cytoscape (v.3.8.5)⁵³ (link) using the ClueGO (v.2.5.7) plug-in.⁵⁴ (link) Biological process, immune system process, molecular function, and Kyoto Encyclopedia of Genes and Genomes (KEGG) were selected to identify pathways and ontologies.

Laggner M., Gugerell A., Copic D., Jeitler M., Springer M., Peterbauer A., Kremslehner C., Filzwieser-Narzt M., Gruber F., Madlener S., Erb M., Widder J., Lechner W., Georg D., Mildner M, & Ankersmit H.J. (2021). Comparing the efficacy of γ- and electron-irradiation of PBMCs to promote secretion of paracrine, regenerative factors. Molecular Therapy. Methods & Clinical Development, 21, 14-27.

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RNA Extraction and Microarray Analysis of B16-C10 Tumor Samples

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B16-C10 tumors were treated with PBS, oBHV or MMC + oBHV as described previously. Tumors were collected from mice on day 5 and homogenized in Trizol (Invitrogen, Life Technologies Corporation, Carlsbad, CA, USA). Following Trizol extraction, the RNA was further purified using the Qiagen RNA extraction kit (Cat #74004). Extracted RNA was diluted to a concentration of 100 ng/µL and underwent reverse transcription. sscDNA was purified using magnetic beads and fragmented using UDG. The fragmented sample was hybridized to the Affymetrix Clariom S mouse arrays, and the stained arrays were scanned to generate intensity data. All of the reagents for this assay were developed by and purchased from Thermo Fisher Scientific. Raw data were analyzed using the Thermo Fisher Transcriptome Analysis Console software, version 4.0.2.1.5. The complete dataset can be found in the GEO database, TBD.

Davola M.E., Cormier O., Vito A., El-Sayes N., Collins S., Salem O., Revill S., Ask K., Wan Y, & Mossman K. (2023). Oncolytic BHV-1 Is Sufficient to Induce Immunogenic Cell Death and Synergizes with Low-Dose Chemotherapy to Dampen Immunosuppressive T Regulatory Cells. Cancers, 15(4), 1295.

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