AffymetrixClariom™ S Arrays (mouse) interrogate more than 22,100 genes in around 800,000 probes. The generated data (expression values of genes) were analyzed using the Transcriptome Analysis Console (TAC) version 4.0.2.15 (Thermo Fisher Scientific) with the SST-RMA normalization algorithm (robust multi-array average, improved by “signal space transformation”). Technical replicate groups were summarized using LIMMA (linear models for microarray data) statistics. Differentially expressed genes (DEG) were identified using filter parameters, fold change >2 or ≤2, old-change > 2 or ≤ 2, LIMMA p value < 0.05, and FDR q value < 0.05. For the comparative analysis, we always compared groups of infected (M, F, or MF) mice to the group of uninfected mice (naive). Multivariate analysis was carried out by principal component analysis (PCA), also using Transcriptome Analysis Console (TAC) version 4.0.2.15 (Thermo Fisher Scientific). Differential gene expression levels were visualized using TAC version 4.0.2.15 to prepare volcano plots. ShinyGO (version 0.61; Ge et al., 2020 (link)) was used to classify genes according to Gene Ontology (GO) categories and analyze them for enrichment. Further, expression levels of chosen genes linked to the host’s immune response were grouped according to their function and visualized using Origin (version 2021; OriginLab) to create a heat map.
Transcriptome analysis console tac
Manufactured by Thermo Fisher Scientific
Sourced in United States
The Transcriptome Analysis Console (TAC) is a software application designed for the analysis of gene expression data from high-throughput sequencing experiments. It provides a comprehensive suite of tools for the processing, normalization, and statistical analysis of transcriptome data.
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Lab products found in correlation
Mirneasy kit, by Qiagen (2 mentions)
Rneasy mini kit, by Qiagen (2 mentions)
Clariom s human array, by Thermo Fisher Scientific (1 mentions)
Human genome u133 plus 2.0 array, by Thermo Fisher Scientific (1 mentions)
Genechip wt pico reagent kit, by Thermo Fisher Scientific (1 mentions)
Genechip 3 ivt plus reagent kit, by Thermo Fisher Scientific (1 mentions)
Agilent bioanalyzer rna nano kit, by Agilent Technologies (1 mentions)
Genechip human genome u133 plus 2.0 array, by Thermo Fisher Scientific (1 mentions)
Nanodrop 1000, by Agilent Technologies (1 mentions)
Wt plus reagent kit, by Thermo Fisher Scientific (1 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions)
Qiaamp rneasy mini kit, by Qiagen (1 mentions)
Ingenuity pathway analysis ipa, by Qiagen (1 mentions)
Genechip mouse gene 1.0 st array, by Thermo Fisher Scientific (1 mentions)
Genechip analysis suite software, by Thermo Fisher Scientific (1 mentions)
Genechip scanner 3000, by Thermo Fisher Scientific (1 mentions)
Dnase treatment, by Qiagen (1 mentions)
Rneasy micro kit, by Qiagen (1 mentions)
20 protocols using transcriptome analysis console tac
1
Transcriptomic Analysis of Host Immune Response
2
Skeletal Muscle Biopsy and Gene Expression
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Skeletal muscle biopsies were obtained from the lateral part of vastus lateralis muscle using a Bergström needle as previously described (10 (link)). Biopsies were taken 8 days before (baseline) and 5 days after the intervention in a resting state 60 minutes after the end of an OGTT. Gene expression was performed as previously described (10 (link)). In brief, total RNA was isolated from vastus lateralis biopsies using a miRNeasy Kit (Qiagen). Gene expression levels were determined using the Human Clariom S array (Thermo Fisher Scientific). Transcriptome Analysis Console (TAC; version 4.0.0.25; Thermo Fisher) was used for quality control and to obtain annotated normalized SST-RMA (signal space transformation-robust multichip analysis) gene-level data. Data are available from the GEO database at NCBI with the accession numbers GSE161749 (10 (link)) and GSE161750 (10 (link)). As outlined in the study design, 25 samples from 7 individuals (50, 58, 61, 62, 66, 67, and 72) were not included in this analysis.
3
Lung mononuclear cells miRNA analysis
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miRNA analysis was carried out as described previously (Alharris et al., 2018 (link); Neamah et al., 2019 (link)). Briefly, total RNA, including miRNA, was isolated from lung mononuclear cells using the miRNeasy kit from QIAGEN and following the protocol of the company. Microarray was performed using Affymetrix miRNA Array (version 4.1). Raw files generated from the miRNA microarray were uploaded to Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo ) and deposited under accession number GSE220159 . By using Transcriptome Analysis Console (TAC, ThermoFisher, United States), Log2 fold change of more than 3,000 miRNAs was detected from the raw array data, and only those miRNAs that were altered more than 2-fold were considered for further analysis. Filtered miRNAs were analyzed for their role in various biological pathways using Ingenuity Pathway Analysis (IPA) software http://www.ingenuity.com (Qiagen, Germany). Also, microRNA.org database was used to examine the sequence alignment regions between miR-100-5p and its targeted genes.
4
Transcriptomic Analysis of Liver Stress
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Affymetrix gene expression data were pre-processed using Transcriptome Analysis Console (TAC) (v4.0, ThermoFisher Scientific). Custom mouse Brainarray chip definition (v22) was used to further annotate the DE files with Entrez and gene symbol IDs. For further analysis, just gene transcript with FDR (a = 0.05) correction and 1.5 > fold change was considerated. For pathway enrichment analysis, data obtained from untreated wild type or IRE1αcKO after poly I:C treatment liver mice tissues were used as reference for tunicamycin (Tm) and etoposide (Eto) treatment comparisons, to further input them in ClueGO (v2.3.2) software using Reactome pathway enrichment database (v09.11.2016). In addition, to visualize patterns in the gene expression and pathway enrichment scores for specific ontologies, heatmaps were generated using RStudio (v0.99.489, R 3.4.1) based on KEGG pathway database gene lists. Genes which show change of the ratios higher (or lower) than 1.5-fold in the arrays at any comparison have been considered as up or downregulated and subjected for functional enrichment analysis. The Bioconductor package ‘clusterProfiler’ was applied to perform functional enrichment analysis using the following repositories: GO (Gene Ontology), KEGG (Kyoto Encyclopedia of Genes and Genomes), and Reactome Pathways. GEO Dataset ID: GSE130952.
5
Transcriptome Analysis of Polycystic Kidneys
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The original human microarray dataset was identified and downloaded from the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/ ) (ID: GSE7869) as raw CEL files. The array was performed using GPL570 (Affymetrix Human Genome U133 Plus 2.0 Array). The kidney samples included 5 polycystic kidneys and 3 non-cancerous cortical tissue samples from kidneys removed for renal cell carcinoma as described by Song et al.46 (link). The 5 polycystic kidney samples were separated into minimally cystic tissue (MCT) (n = 5) and small (<1 ml, n = 5), medium (10–20 ml, n = 5) and large cysts (>50 ml, n = 3)46 (link). For cystic cell micro array expression analysis, a previous dataset was identified and downloaded from the ArrayExpress data base (https://www.ebi.ac.uk/arrayexpress/ ) (ID: E-MTAB-4189). The cell culture micro arrays are derived from two non-cystic cell cultures and three cystic cell cultures as outlined by Streets et al.45 (link). Individual gene expression analysis was performed using Transcriptome Analysis Console (TAC), Thermo Fisher Scientific. Where multiple probes targeted the same gene, the sum of probe intensities was used for analysis.
6
Gene Expression Profiling of Macrodissected Tissues
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Samples were provided by NI Biobank. In brief, total RNA was extracted from macrodissected tissue and amplified using the GeneChip WT Pico Reagent Kit (Thermo Fisher Scientific, Wilmington, NC, USA). The biotinylated sense-stranded DNA was hybridized to the ClariomTM D Human array (Thermo Fisher Scientific, Wilmington, NC, USA) and profiled. Transcriptome Analysis Console (TAC; Thermo Fisher Scientific) software was used to conduct quality control (QC) assessments and data summarization prior to further analysis (see Supplementary Materials for details).
7
Transcriptome Analysis Console Protocol
8
Transcriptome Profiling of Cell Types
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Quality and quantity of the 60 nucleic acid samples were established using the Agilent Bioanalyzer RNA Nano kit and the Nanodrop 1000, respectively. GeneChip 3′ IVT PLUS Reagent Kit (Thermo Scientific) provided sufficient amplified double-stranded cDNA for each holoclone, meroclone, or paraclone total RNA sample, letting to in vitro transcribe it to labeled cRNA, that could be fragmented and therefore hybridized onto single GeneChip™ Human Genome U133 Plus 2.0 Array (ThermoScientific), following the manufacturer’s indications. To avoid batch effect among samples, i.e. no technical sources of variation added to the samples during handling, samples were randomized during RNA isolation, sample preparation, and hybridization/scanning working sessions. All samples were processed with the same reagents lot number, when available. Sample and hybridization quality controls were carried out with Transcriptome Analysis Console (TAC, ThermoScientific) to verify complete and unbiased coverage of the transcriptome.
9
Identifying ZEB1-regulated Genes in Breast Cancer
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First, microarray data from Lehmann et al. were processed and analyzed for differential expression using the Transcriptome Analysis Console (TAC) from ThermoFisher. The set of significantly downregulated genes (FDR < 0.05, log(Fold change) <−2) was obtained. Next, genes which were significantly (Spearman r >0.5) correlated with ZEB1 in the breast cancer TCGA dataset were identified and downloaded. The two gene sets were compared for intersection, with 186 genes contained in both sets. Finally, the BRCA-TCGA expression data for these genes in the breast cancer dataset was downloaded. The partial correlation for each gene with ZEB1 was computed, adjusting for the stromal cell content using the ppcor package. The overlap between ZEB1-regulated and -correlated genes was tested for significance using the hypergeometric test.
10
Transcriptome analysis of NEN and domperidone
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For the transcriptome analysis, HCT116 cells were treated with vehicle control, 1.2 µM NEN, 30 µM domperidone, and NEN + domperidone. Cells were harvested after 16 h, before the occurrence of major cell death. Total RNA was isolated employing the RNeasy Mini kit (Qiagen) including on‐column DNase digestion. The Agilent 2100 Bioanalyzer was used to assess RNA quality, and only high‐quality RNA (RIN > 7) was used for microarray analysis. 3 out of 5 replicates were chosen for the microarray analysis. Total RNA (150 ng) was amplified using the WT PLUS Reagent Kit (Affymetrix, Santa Clara, US). Amplified cDNA was hybridized on Human Clariom S HT arrays (Affymetrix). Staining and scanning was done according to the Affymetrix expression protocol. Transcriptome Analysis Console (TAC; version 4.0.0.25; Thermo Fisher Scientific) was used for quality control. Array data have been submitted to the GEO database (https://www.ncbi.nlm.nih.gov/geo/ ) at NCBI (accession: GSE148682).
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