Serum samples were collected from a commissioned bovine and two healthy bovines, ensuring they shared the same species, age and sex for miRNA comparison. Each sample was duplicated for statistical analysis. MiRNAs were extracted from the serum samples using miRNeasy serum/plasma kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol. Subsequently, cDNA synthesis was performed using the TaqMan® MicroRNA Reverse Transcription Kit (Applied Biosystems, CA, USA) as per the manufacturer’s instructions. After conducting quality-control measures, a comprehensive profiling of 783 bovine miRNAs was carried out using the Affymetrix GeneChip miRNA 4.0 array (Affymetrix, CA, USA), following the manufacturer’s guidelines at Macrogen (Guri, Republic of Korea).
Affymetrix genechip mirna 4.0 array
Manufactured by Thermo Fisher Scientific
Sourced in United States
The Affymetrix GeneChip miRNA 4.0 Array is a high-density microarray designed for the detection and quantification of microRNA (miRNA) expression. It is a tool for comprehensive miRNA profiling in a wide range of species.
Automatically generated - may contain errors
Lab products found in correlation
Genechip scanner 3000 7g, by Thermo Fisher Scientific (4 mentions)
Flashtag biotin hsr rna labeling kit, by Thermo Fisher Scientific (3 mentions)
Rneasy mini kit, by Qiagen (3 mentions)
Genechip fluidics station 450, by Thermo Fisher Scientific (3 mentions)
Genechip scanner 3000, by Thermo Fisher Scientific (2 mentions)
Nanodrop spectrophotometer, by Thermo Fisher Scientific (2 mentions)
2100 bioanalyzer, by Agilent Technologies (2 mentions)
Taqman microrna reverse transcription kit, by Thermo Fisher Scientific (1 mentions)
Mirneasy serum plasma kit, by Qiagen (1 mentions)
Mirna qc tool software, by Thermo Fisher Scientific (1 mentions)
Affymetrix fluidics station 450, by Thermo Fisher Scientific (1 mentions)
Genechip command console, by Thermo Fisher Scientific (1 mentions)
Transcriptome analysis console 4, by Thermo Fisher Scientific (1 mentions)
Genespring 13, by Agilent Technologies (1 mentions)
Nanodrop 2000, by Thermo Fisher Scientific (1 mentions)
Nanodrop one microvolume uv vis spectrophotometer, by Thermo Fisher Scientific (1 mentions)
Transcriptome analysis console software, by Thermo Fisher Scientific (1 mentions)
Mircury rna isolation kit biofluid, by Qiagen (1 mentions)
Genechip scanner 3000 7g system, by Thermo Fisher Scientific (1 mentions)
Flashtag biotin rna labeling kit, by Thermo Fisher Scientific (1 mentions)
18 protocols using affymetrix genechip mirna 4.0 array
1
Bovine Serum miRNA Profiling
2
Differential miRNA Expression Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Microarray analysis was performed to detect differentially expressed miRNAs using Affymetrix GeneChip miRNA 4.0 array (Affymetrix, Thermo Fisher Scientific, Inc.). GeneChip® Scanner 3000 7G (Affymetrix, Thermo Fisher Scientific, Inc.) was used to scan the arrays. CEL files obtained from the Affymetrix GeneChip were analyzed by the Gminix-Cloud Biotechnology Information (GCBI) platform (http://www.gcbi.com.cn ) using Affymetrix default analysis settings and global scaling as the normalization method. SAM method was used to analyze the difference (22 (link)). According to the filter condition |Fold Change|>2, the final difference results were obtained.
3
miRNA Profiling by Microarray
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
miRNAs were collected from ~1 × 107 cells by applying a miRNeasy Micro Kit following protocols. The miRNAs were labelled and hybridized in the Affymetrix GeneChip miRNA 4.0 Array (Affymetrix, Thermo Fisher Scientific), which included miRNAs in the miRBase v20 database (http://www.mirbase.org/ ). Affymetrix GeneChip Scanner 3000 was used to scan the microarray and miRNA QC Tool software (Affymetrix) was for analysis.
4
Microarray Analysis of miRNA Expression
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Microarray analysis was performed by Gminix Biotechnology Company (Shanghai, China) using Affymetrix GeneChip miRNA 4.0 array (Affymetrix, USA). Gene chips were then scanned using the GeneChip® Scanner 3000 7G (Affymetrix). CEL-les of the raw data were exported and then uploaded to the website, Gminix-Cloud Biotechnology Information (GCBI), of Genminix Informatics Co., Ltd. (Shanghai, China; http://www.gcbi.com.cn) for further analysis. The data were analyzed through the Robust Multichip Analysis algorithm (RMA) using Affymetrix default analysis settings and global scaling as a normalization method. Then we used the successive approximation method (SAM) for differentially expressed miRNAs analysis. According to the lter condition | Fold Change | >1.2 & P value <0.05, the nal differential result was obtained.
5
Affymetrix GeneChip miRNA 4.0 Array Protocol
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Microarray hybridization was performed using the Affymetrix GeneChip miRNA 4.0 Array (Thermofisher, MA, USA) according to the manufacturer’s protocol. Total RNA samples were labeled using FlashTag™ Biotin RNA Labeling Kit (Genisphere, PA, USA). The labeled RNA samples were then quantified, fractionated, and hybridized to the microarray according to the manufacturer’s protocol. RNA-array hybridization was performed on an Affymetrix® 450 Fluidics Station (Thermofisher, MA, USA). The arrays were stained using a GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA, USA) and scanned using an Affymetrix GCS 3000 scanner (Affymetrix, Santa Clara, CA, USA). The miRNA-mRNA hybridization signals were analyzed using the Affymetrix® GeneChip™ Command Console.
6
Genome-wide miRNA Expression Profiling
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
RNA synthesis and whole-genome microarray analysis were outsourced to Filgen (Nagoya, Japan). Microarray analysis of miRNAs was performed using the Affymetrix GeneChip miRNA 4.0 Array (Thermo Fisher Scientific) in conjugation with the FlashTag Biotin HSR RNA Labeling Kit (Thermo Fisher Scientific). All reactions and hybridizations were carried out according to the manufacturer’s protocol. These arrays were washed with the GeneChip Fluidics Station 450 (Thermo Fisher Scientific) and scanned with the GeneChip Scanner 3000 (Thermo Fisher Scientific). Differentially expressed miRNAs were analyzed using the Transcriptome Analysis Console 4.0.2 (Thermo Fisher Scientific). To identify differentially expressed genes (DEGs), one-way analysis of variance was conducted, and gene lists were generated by applying a threshold fold change cutoff value of >|2| with a Benjamini–Hochberg false discovery rate (FDR) of < 0.05. We present the differentially expressed transcripts (DETs) in a heatmap with a dendrogram, where the distance metric is Euclidean; the distances between clusters were computed using the complete linkage method to profile gene expression patterns between the tested groups.
7
miRNA Expression Profiling in Gastric Cancer
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
miRNAs from ~1×107 cells were extracted using the miRVana™ miRNA isolation kit (cat. no. AM1560, Ambion; Thermo Fisher Scientific, Inc.) according to the manufacturer's protocol. The miRNAs extracted from three matched pairs of SGC7901 and SGC7901/DDP cells were labeled and hybridized with an Affymetrix GeneChip miRNA 4.0 Array (Affymetrix; Thermo Fisher Scientific, Inc.), which contained miRNAs from the miRBase v20 database (http://www.mirbase.org/ ). The microarray was scanned by CapitalBio Technology Corporation. The data were normalized and analyzed using GeneSpring 13.0 software (Agilent Technologies, Inc.). Student's t-test was used for analysis between two groups of data. Differential expression of miRNA was defined as a difference of >2-fold in miRNA expression that was statistically significant at P<0.05. Cluster analysis and graphical presentation of the data were performed using Cluster 3.0 software (developed by Michael Eisen, updated by Michiel de Hoon, University of Tokyo, Human Genome Center).
8
Cardiac miRNA Profiling in Doxorubicin-Induced CHF
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA was extracted with the RNeasy mini kit (Cat No. 74104; Qiagen, Hilden, Germany) from the left ventricular myocardial tissue of five untreated DOX-induced CHF rats and five DOX-induced CHF rats treated with QL. RNA concentration and purity were determined by spectrophotometry (NanoDrop 2000TM; Thermo Fisher Scientific, Wilmington, DE). The miRNA-seq tests were run in triplicate using the Affymetrix GeneChip miRNA 4.0 Array (Thermo Fisher Scientific, Waltham, MA). Differentially expressing miRNAs (DEmiRs) between the untreated CHF group and the CHF group treated with QL were analysed with the Gene-Cloud of Biotechnology Information (GCBI) platform. DEmiRs targets were predicted by target scan and miRanda. A volcano plot was constructed in R v. 5.50 (Mathsoft Engineering and Education, Inc., Cambridge, MA). Hierarchical clustering was executed with Cluster v. 3.0 (http://bonsai.hgc.jp/∼mdehoon/software/cluster/software.htm ).
9
Profiling microRNA Expression in Extracellular Vesicles
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
RNA was extracted from EVs using miRCURY RNA Isolation Kit—Biofluids (Exiqon, Qiagen, Vedbæk, Denmark) following protocols provided by the manufacturer. The extracted RNA was evaluated for quality and concentration using the Nanodrop One Microvolume UV–Vis Spectrophotometer (Thermo Fisher Scientific) and stored at − 80 °C. For total miRNA expression profiling of EVs we used the Affymetrix GeneChip miRNA 4.0 Array (Thermo Fisher Scientific). This microarray allows for the evaluation of 2578 mature human miRNAs (miRBase version 20). Sample preparation, hybridization, staining and washing procedures followed the manufacturer’s instructions FlashTag Biotin HSR RNA Labeling Kit, (Thermo Fisher Scientific). Hybridization signals were detected using the GeneChip Scanner 3000 7G (Thermo Fisher Scientific) with Affymetrix GeneChip Command Console Software parameters recommended by the manufacturer. A probeset was considered to be expressed if 50% of the samples in the dataset have DABG (Detected Above Background) values below the DABG threshold (the default DABG was set to 0.05). Array data quality analysis, data summarization and normalization (RMA + DABG) were carried out with the Transcriptome Analysis Console software v. 4.0.1 (Thermo Fisher Scientific).
10
Analyzing Extracellular Vesicle miRNA Profiles
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA was extracted from EVs using the RNeasy Mini kit (Qiagen, Germany). The purity of the RNA was assessed using a Nanodrop spectrophotometer (ThermoFisher Scientific), and the miRNA analysis was performed by Biocore Co. (Seoul, Korea). EV RNA integrity was determined using an Agilent 2100 Bioanalyzer (Santa Clara, CA, USA). Human miRNA was analysed using an Affymetrix GeneChip miRNA 4.0 array (ThermoFisher Scientific). Specifically, total RNA (1 µg per sample) was labelled using the FlashTag™ Biotin RNA Labeling Kit (Thermo Fisher Scientific), and the samples were hybridized on the arrays for 18 h at 48°C. The arrays were washed to remove non-specifically bound nucleic acids, stained using a Fluidics Station 450, and scanned using the GeneChip Scanner 3000 7G system (Affymetrix). Finally, differentially expressed miRNA was automatically analysed using the Affymetrix Expression Console software, version 1.4.1. Functional analysis of the miRNA was performed using publicly available algorithms including Cluster, version 3.0; TreeView; GeneSpring, version 13.1.1; and TargetScan, version 6.2. The gene ontology biological process (GO-BP) terms and KEGG pathway terms that were enriched in the predicted target genes were determined using DAVID Bioinformatics Resources, version 6.7.
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?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!