The CEL files obtained from microarrays was processed as reported previously [7 (link),24 (link)]. Briefly, probe level analysis of CEL files was performed using R and Bioconductor and a list of gene expressions in various granulomas was obtained. Raw intensities of perfectly matching (PM) probes expressed in each array were subjected to local background correction using Microarray Suite Version 5.0 software (MAS5; Affymetrix, Santa Clara, CA). The values from each sample (in triplicate) were log2-transformed and median-centered. A family-wise p-value of ≤ 0.05 was applied to select the list of significantly differentially expressed genes (SDEG) between lung granulomatous lesion and uninvolved (control) parenchyma from raw CHP files using Partek Genomics Suite Version 6.7 software (Partek, St. Louis, MO). The expression levels in various granulomas were normalized with the corresponding gene expression in the uninvolved parenchyma. Gene ontology analysis and intensity plots of SDEG expressed exclusively or commonly between different types of lung granulomas were generated using Partek Genomics Suite Version 6.7 software (Partek, St. Louis, MO) as described previously [25 (link)]. The SDEG were further analyzed to determine pathway/network significantly affected by SDEG using Ingenuity Pathway Analysis (IPA) software (Ingenuity Systems, Redwood City, CA).
Microarray suite version 5
Manufactured by Thermo Fisher Scientific
Sourced in United States
Microarray Suite version 5.0 is a software application designed for the analysis and management of microarray data. The software provides tools for data normalization, quality control, and statistical analysis of microarray experiments.
Automatically generated - may contain errors
Lab products found in correlation
Agilent 2100 bioanalyzer, by Agilent Technologies (4 mentions)
Genechip operating software, by Thermo Fisher Scientific (3 mentions)
Nanodrop nd 1000 uv vis spectrophotometer, by Thermo Fisher Scientific (3 mentions)
Trizol reagent, by Thermo Fisher Scientific (3 mentions)
Affymetrix genechip mouse 4302 arrays, by Thermo Fisher Scientific (2 mentions)
Rneasy mini kit, by Qiagen (2 mentions)
Messageamp premier rna amplification kit, by Thermo Fisher Scientific (2 mentions)
Rna 6000 nano kit, by Agilent Technologies (2 mentions)
Tri reagent, by Molecular Research Center (2 mentions)
Ingenuity pathway analysis software, by Qiagen (1 mentions)
Human genome u133 plus 2 gene chips, by Thermo Fisher Scientific (1 mentions)
Rna 6000 nano assay, by Agilent Technologies (1 mentions)
Tempus spin rna isolation kit, by Thermo Fisher Scientific (1 mentions)
Genechip wt plus reagent kit, by Thermo Fisher Scientific (1 mentions)
Bioanalyzer, by Agilent Technologies (1 mentions)
Genechip human genome u133a array, by Thermo Fisher Scientific (1 mentions)
Human genome u133 plus 2.0 array, by Thermo Fisher Scientific (1 mentions)
Rna 6000 nano labchip kit, by Agilent Technologies (1 mentions)
Affymetrix genechip scanner 3000 7g, by Thermo Fisher Scientific (1 mentions)
Genechip p aeruginosa genome array, by Thermo Fisher Scientific (1 mentions)
22 protocols using microarray suite version 5
1
Microarray Analysis of Lung Granulomas
2
Profiling Mouse Brain Transcriptome using Affymetrix Arrays
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Total RNA was isolated from brain samples stored in RNAlater® using Trizol Reagent (Invitrogen, Breda, The Netherlands) and the RNEasy Mini kit (Qiagen, Venlo, The Netherlands). RNA concentrations and OD 260/280 ratios were measured with the NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop Technologies, Wilmington, USA). Assessment of RNA quality and purity was performed with the RNA 6000 Nano kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). RNA (200 ng) was labeled using the MessageAmp Premier RNA Amplification kit (Applied Biosystems) and hybridized to Affymetrix GeneChip® Mouse 4302 Arrays (Affymetrix, ThermoFischer Scientific, Bleiswijk, The Netherlands), according to the manufacturer's recommendations. Image analysis was performed using GeneChip Operating Software (Affymetrix). Microarray Suite version 5.0 software (Affymetrix) was used to generate .dat and .cel files for each experiment. The raw data was deposited in ArrayExpress under access number E-MTAB-5832.
3
Whole Blood RNA Isolation and Microarray
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Blood was collected in Tempus Blood RNA tubes (ABI, Foster city, CA, USA). Total RNA was isolated from whole blood using the Tempus Spin RNA isolation kit (Applied Biosystems, Bleiswijk, The Netherlands). Globin RNA was removed from total RNA preparations using the Globiclear kit (Life Technologies). RNA concentrations and OD 260/280 ratios were measured with the NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop Technologies, Wilmington,USA). Assessment of RNA quality and purity was performed with the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). RNA (100 ng) was labelled using the MessageAmp Premier RNA Amplication kit (Applied Biosystems) and hybridized to Human Genome U133 plus 2 gene chips (Affymetrix), according to the manufacturer’s recommendations. Image analysis was performed using GeneChip Operating Software (Affymetrix). Microarray Suite version 5.0 software (Affymetrix) was used to generate .dat and .cel files for each experiment. The raw data has been deposited in the arrayExpress database under access number E-MTAB-3162.
4
Transcriptome Analysis of Mouse Brain
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Brains stored in RNA-later were homogenized in Trizol Reagent (Invitrogen, Breda, Netherlands), and subsequently total RNA was isolated and purified using the RNeasy Mini Kit (Qiagen, Hilden, Germany): 250 μl of ethanol was added to the upper aqueous phase of the processed Trizol samples and directly transferred to the RNeasy spin columns for purification. RNA concentrations and OD 260/280 ratios were measured with the NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop Technologies, Wilmington, United States). Assessment of RNA quality and purity was performed with the RNA 6000 Nano kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, United States). RNA (200 ng) was labeled using the MessageAmp Premier RNA Amplification kit (Applied Biosystems) and hybridized to Affymetrix GeneChip® Mouse 4302 Arrays (Affymetrix, Thermo Fisher Scientific, Bleiswijk, Netherlands), according to the manufacturer’s recommendations. Image analysis was performed using GeneChip Operating Software (Affymetrix). Microarray Suite version 5.0 software (Affymetrix) was used to generate .dat and .cel files for each experiment.
5
Affymetrix Microarray Gene Expression Analysis
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Gene expression profiles were analysed using an Affymetrix GeneChip human Clariom D array (PN 902923, Life Technologies). Briefly, total RNA from HCSCs after 2 days of culture in TC medium (with or without 20 μmol/L LPA) was isolated with the TRIzol Reagent (Invitrogen) according to the manufacturer's instructions. Isolated RNA was then purified using an RNeasy column, followed by quality monitoring using a Bioanalyzer (Agilent Technologies). Total RNA amplification, labelling and processing were performed according to the instructions in the Affymetrix user manual for the GeneChip WT PLUS Reagent Kit. After cDNA labelling and GeneChip hybridization, a GeneArray G7 scanner (Affymetrix) was used to scan the results, which were analysed using Microarray Suite Version 5 software (Affymetrix) and converted to gene expression levels (EScores) using the Probe Profiler software (Corimbia). The cytokine genes were further screened using DAVID.
6
Microarray Data Processing and Validation
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Microarray data were processed using the MAS5 algorithm (Affymetrix Microarray Suite Version 5 software) and GeneSpring software. Full details are available in Text S1 . The raw microarray data are publically available at the Gene Expression Omnibus (GEO) site (http://www.ncbi.nlm.nih.gov/geo/ ) under the accession number GSE43939. Changes in the expression of significant genes were confirmed with TaqMan PCR; full details are available in Text S1 .
7
Transcriptomic Analysis of IBV Infection
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Microarray hybridization and image analysis were carried out as previously described (Nasirudeen and Liu, 2009 (link); Zhong et al., 2012 (link)). Briefly, RNA was independently prepared from IBV-infected Vero cells harvested at 24 h post-infection and hybridized to GeneChip® Human Genome U133A Array (Affymetrix, USA), according to the manufacturer's instructions (Affymetrix). GeneChip arrays were scanned on an Affymetrix probe array scanner, and data were analyzed using the statistics software Microarray Suite version 5.0 (MAS5.0) from Affymetrix.
Transcriptomic analysis was carried out by the Biomarker Technologies Co, LTD, Beijing, China, as previously described (Yuan et al., 2022 (link)). Briefly, RNA was independently prepared from IBV-infected H1299 cells harvested at 20 h post-infection and sequenced using Illumina HiSeq sequencing technology platform to construct transcriptome libraries and obtain sequencing data.
Transcriptomic analysis was carried out by the Biomarker Technologies Co, LTD, Beijing, China, as previously described (Yuan et al., 2022 (link)). Briefly, RNA was independently prepared from IBV-infected H1299 cells harvested at 20 h post-infection and sequenced using Illumina HiSeq sequencing technology platform to construct transcriptome libraries and obtain sequencing data.
8
Gene Expression Profiling of ESCC Biopsies
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The RNAs of the biopsy samples were isolated by homogenizing them in an ISOGEN lysis buffer followed by phenol extraction and precipitation in isopropanol. The samples were treated with RNase-free DNase I in the presence of RNase inhibitor and re-isolated by the above procedure with ISOGEN lysis buffer. The RNA samples were finally subjected to microarray analysis after quality check by RNA 6000 nano LabChip kit (Agilent Technologies Ltd., CA, USA). Gene expression profiles were obtained from 185 samples: 60 biopsy samples from before and after CRT of 30 identical patients, and 121 before CRT from another ESCC patient set. Total RNAs extracted from the needle biopsy samples were biotin-labeled and hybridized to high-density oligonucleotide microarrays (Human Genome U133PLUS2.0 Array, Affymetrix, Santa Clara, CA, USA) in accordance with the manufacturer’s instructions. The scanned data of the arrays were processed by Affymetrix Microarray Suite version 5.0, which scaled the average intensity of all the genes on each array to a target signal of 1,000 to reliably compare variable multiple arrays. All the microarray data have been deposited in a MIAME compliant database, GEO; the accession number GSE69925.
9
Differential Gene Expression in P. aeruginosa Biofilm
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Differential gene expression of P. aeruginosa biofilm cells caused by 6-gingerol was analyzed using GeneChip P. aeruginosa Genome Array (900339, Affymetrix, CA, USA). A PAO1 chip has been used to analyze both PAO1 and PA14 transcriptome because of the high similarity of genomes between the two strains46 (link). All of the procedures followed the manufacturer's protocols (Affymetrix) and were conducted at Seoulin Bioscience (Seongnam, South Korea). Briefly, total RNA (10 μg) was converted into cDNA using random primers, and the cDNA was fragmented using DNase I and biotinylated using terminal transferase. Biotinylated cDNA (5 μg) was then hybridized for 16 hr at 45°C on the GeneChip. An Affymetrix Fluidics Station 450 (Affymetrix) was used to wash and stain the GeneChip, and Affymetrix GeneChip Scanner 3000 7G (Affymetrix) was used to read the hybridization signals of the GeneChip. The Robust Multi-chip Average (RMA) algorithm was used for normalizing probe-level intensity47 (link).
Microarray Suite version 5.0 (Affymetrix) was used to analyze GeneChip data using default analysis settings and global scaling. The differentially expressed genes were selected based on greater than 1.5-fold repression or induction by 6-gingerol.
Microarray Suite version 5.0 (Affymetrix) was used to analyze GeneChip data using default analysis settings and global scaling. The differentially expressed genes were selected based on greater than 1.5-fold repression or induction by 6-gingerol.
10
Microarray Gene Expression Analysis
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Total RNA (10 μg) was hybridized to the HG-U133A 2.0 microarray (54675 human genes; Affymetrix, Santa Clara, CA) following the manufacturer's standard protocol for sample preparation and microarray processing. Expression data were analyzed using Microarray Suite version 5.0 (Affymetrix) and GenPlex v2.4 software (ISTECH Inc., Seoul, Republic of Korea).
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