Expression levels of miRNAs in the discovery study samples were assessed using GeneChip® microarray and Flashtag™ Bundle (Affymetrix, CA, USA). Labeling for miRNAs with FlashTag Biotin HSR was performed with samples containing 130ng of total RNA in 8μl of nuclease free water according to the manufacturer’s instructions. Samples were then hybridized to GeneChipTM miRNA 4.0 microarrays. Afterwards the miRNA microarray chips were washed and stained using the Genechip Fluidics Station 450. Subsequently miRNA microarray chips were scanned using an Affymetrix GeneChip 7G scanner.
Genechip microarray
Manufactured by Thermo Fisher Scientific
Sourced in United States, China
GeneChip microarrays are high-density oligonucleotide arrays used for genome-wide expression analysis. They contain thousands of probes designed to measure the expression levels of genes and transcripts in a biological sample.
Automatically generated - may contain errors
Lab products found in correlation
Agilent 2100 bioanalyzer, by Agilent Technologies (3 mentions)
Bioconductor2 suite, by Thermo Fisher Scientific (2 mentions)
Rneasy mini kit, by Qiagen (2 mentions)
Genechip scanner 3000, by Thermo Fisher Scientific (2 mentions)
Nanodrop 1000 spectrophotometer, by Thermo Fisher Scientific (2 mentions)
Nanodrop 2000, by Thermo Fisher Scientific (2 mentions)
Genechip scanner 7g, by Thermo Fisher Scientific (1 mentions)
Genechip expression analysis technical manual, by Thermo Fisher Scientific (1 mentions)
Human transcriptome 2.0 array, by Thermo Fisher Scientific (1 mentions)
Genechip operating software, by Thermo Fisher Scientific (1 mentions)
Rnalater, by Thermo Fisher Scientific (1 mentions)
2100 bioanalyzer, by Agilent Technologies (1 mentions)
Mirneasy mini kit, by Qiagen (1 mentions)
Expression console, by Thermo Fisher Scientific (1 mentions)
Rneasy isolation kit, by Qiagen (1 mentions)
Human gene 2.0 st array, by Thermo Fisher Scientific (1 mentions)
Genechip wt plus kit, by Thermo Fisher Scientific (1 mentions)
Mirneasy isolation kit, by Qiagen (1 mentions)
Rna 6000 nano, by Agilent Technologies (1 mentions)
Agilent bioanalyzer, by Agilent Technologies (1 mentions)
21 protocols using genechip microarray
1
Profiling miRNA Expression with Microarray
2
Differential Gene Expression Analysis
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Affymetrix Gene Chip microarray data underwent strict quality control processing using the simpleaffy package in the Bioconductor2 suite from the R statistical programming environment. Log-scale Robust Multiarray Analysis (RMA) from the affy package was used to normalize the data and eliminate systematic differences across the arrays. Differential expression of genes across the conditions was identified from a moderated test statistic employed by the limma package. The False Discovery Rate (FDR) method was used to correct for multiple hypothesis testing. Gene set enrichment analysis was performed to identify differentially regulated pathways and gene ontology terms for each of the comparisons performed. Heatmap of the differentially expressed genes (FDR ≤ 0.05) for each < Ctrl > versus < EGF > comparison. Gene expression has been z-score normalized and the samples and genes are clustered by correlation distance with complete linkage. The heatmap shows all genes that were identified as significant in at least one of the comparisons. Heatmaps only include genes that had an FDR ≤ 0.05 and a log2FC > 5 or < −5. Hierarchical clustering plot of all of the samples based on expression of all genes on the arrays were shown. The samples are clustered using a correlation distance with complete linkage. Samples are colored by their condition.
3
Affymetrix GeneChip Microarray Protocol for Dehalococcoides
4
Differential Gene Expression Analysis
5
Microarray Analysis of MG-Treated Rice Seedlings
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IR64 rice cultivar was chosen for microarray analysis. Seven day old seedlings were treated with 10 mM MG for 16 h in hydroponics. Shoot tissue was harvested and total RNA was isolated from the control and MG-treated samples as described previously (Kaur et al., 2013 (link)). RNA samples were used for Affymetrix rice chip hybridization experiment and data analysis. A total of four hybridizations were carried out as two biological replicates for each condition (control and MG treatment). Single color Affymetrix rice chip was used, where only one dye (Cy3 dye) was used per sample/per hybridization and the arrays were processed further as per the GeneChip microarray (Affymetrix) manufacturer's protocol. Quality control analysis was carried out prior to cDNA synthesis followed by its labeling and hybridization and the expression data of 57,381 probe sets was generated. Overall quality of the prepared hybridized chip was assessed using sample correlation and principle component analysis (PCA) (Table S1 and Figure S1 ).
6
Identifying MELK Downstream Targets
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To identify the downstream targets of MELK, we performed Affymetrix Genechip microarray using parental, Cas9-p15 control, and two MELK KO (C3 and C28) MDA-MB-231 cells. In brief, the cells (1 × 106 cells) were cultured in 10-cm plates for 48 hours, followed by RNA extraction using the Invitrogen PureLink RNA Mini Kit (Thermo Fisher Scientific). RNA expression was measured using Human Transcriptome 2.0 Array (Affymetrix Inc) at the Sequencing and Microarray Facility at MD Anderson according to standard Affymetrix protocols. Differential gene expression profile analysis was performed (see Supplementary Methods and Materials for details).
7
miRNA Expression Profiling Protocol
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MiRNA expression profile microarrays of these specimens were performed by CapitalBio. Procedures are described in detail on the CapitalBio website (http://www.capitalbio.com ). Briefly, the procedure included total RNA extraction, quality control, miRNA isolation, FlashTag biotin labeling of miRNAs, hybridization to an Affymetrix GeneChip microarray (Affymetrix miRNA 4.0), and microarray washing, staining, and scanning. If the miRNAs expression changed by at least ±2.5-fold (p < 0.05), this was considered a significant difference.
8
Profiling SIRT1 Knockdown in NHEK Cells
9
Transcriptomic Analysis of Rhodobacter sphaeroides
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RNA was isolated from exponential phase cultures of R. sphaeroides strains that were grown photosynthetically in 16 mL screw cap tubes or 500 ml cultures in roux bottles with bubbling (95% N2, 5% CO2) [11] (link),[78] (link). RNA isolation and subsequent cDNA synthesis, labeling and hybridization to R. sphaeroides GeneChip microarrays (Affymetrix, Santa Clara, CA) were performed as previously described [82] (link). Microarray datasets were normalized by Robust Multichip Average (RMA) to log2 scale with background adjustment and quantile normalization [83] (link). Statistical analysis of normalized data to identify differentially expressed genes was done using the limma package [84] . Correction for multiple testing was done using Benjamini-Hochberg correction [85] . All analyses were conducted in the R statistical programming environment (http://www.R-project.org ).
10
Differential miRNA Profiles in Mannose-Induced ADSCs
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MicroRNA expression profiles in G-ADSCs and M-ADSCs were checked using microarray analysis. ADSCs were cultured in glucose-free DMEM culture medium (10% FBS, 5% Pen/Strep, and 5% glutamine) supplemented with 25 mM D-mannose (M-ADSCs) or in the high-glucose (25 mM) DMEM culture medium with 10% FBS, 5% Pen/Strep, and 5% glutamine (G-ADSCs). Cells were harvested three days later and stored in RNAlater (Ambion) and shipped for microarray analysis. RNA was isolated using the RNeasy Mini kit (Qiagen) and quantified in a NanoDrop spectrophotometer. RNA sample purity ratios were more than 1.8 for ratios of 260/280 nm and 260/230 nm and RIN (RNA Integrity Number) values were greater than 7.8 as evaluated on Bioanalyzer 2100 (Agilent Technologies). For the microarray assay, samples were loaded in Affymetrix GeneChip® Microarrays and proceeded in GeneChip platform stations, and data were analyzed by using Affymetrix GeneChip Operating Software and RStudio.
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