Using 250 ng of total RNA, the labeling process was initiated with poly-A tailing of each RNA strand with poly-A polymerase, followed by the ligation of biotin-labeled 3DNA dendrimer. Biotinylated RNA strands were hybridized at 48 °C for 18 h on an Affymetrix GeneChip miRNA 4.0 Array (Affymetrix, Hatfield, PA, USA). The GeneChip miRNA 4.0 Array was washed and stained in Affymetrix Fluidics Station 450. The fluorescence signals amplified by the branched structure of the 3DNA dendrimer were scanned by using an Affymetrix GeneChip Scanner. 3000 7G. The arrays were analyzed by using an Agilent scanner and the associated software. miRNA expression levels were calculated by using Expression Console 1.4 (Affymetrix, Hatfield, PA, USA). The relative signal intensities for each miRNA were generated by using the Robust Multi-Array Average algorithm. The target predictions were computed and analyzed by using TargetScan and microRNA.org databases.
Genechip mirna 4.0 array
Manufactured by Thermo Fisher Scientific
Sourced in United States
The GeneChip miRNA 4.0 Array is a high-density microarray designed for comprehensive analysis of small non-coding RNAs, including miRNA, small nuclear RNA, small nucleolar RNA, and other short transcripts. The array provides coverage for multiple species and enables the simultaneous detection and quantification of thousands of small RNA molecules from a single sample.
Automatically generated - may contain errors
Lab products found in correlation
Flashtag biotin hsr rna labeling kit, by Thermo Fisher Scientific (23 mentions)
Genechip scanner 3000 7g, by Thermo Fisher Scientific (21 mentions)
Fluidics station 450, by Thermo Fisher Scientific (20 mentions)
Mirneasy mini kit, by Qiagen (16 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (15 mentions)
Expression console software, by Thermo Fisher Scientific (9 mentions)
Genechip fluidics station 450, by Thermo Fisher Scientific (9 mentions)
2100 bioanalyzer, by Agilent Technologies (8 mentions)
Genechip command console software, by Thermo Fisher Scientific (8 mentions)
Trizol reagent, by Thermo Fisher Scientific (7 mentions)
Mirneasy kit, by Qiagen (5 mentions)
Mirneasy micro kit, by Qiagen (4 mentions)
Genechip scanner 3000, by Thermo Fisher Scientific (4 mentions)
Genechip hybridization oven 645, by Thermo Fisher Scientific (4 mentions)
Nanodrop spectrophotometer, by Thermo Fisher Scientific (4 mentions)
Flashtag biotin hsr labeling kit, by Thermo Fisher Scientific (4 mentions)
Mirvana mirna isolation kit, by Thermo Fisher Scientific (4 mentions)
Genechip scanner 3000 7g system, by Thermo Fisher Scientific (3 mentions)
Affymetrix expression console software, by Thermo Fisher Scientific (3 mentions)
Nanodrop nd 1000, by Thermo Fisher Scientific (3 mentions)
136 protocols using genechip mirna 4.0 array
1
miRNA Expression Profiling with Affymetrix Array
2
miRNA Profiling Using Affymetrix Arrays
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA was isolated and purified from cell lines using miRNeasy Mini kit (Qiagen, Tokyo, Japan) as recommended by the manufacturer. RNA yield and quality was determined using the Agilent RNA 6000 Nano kit and Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.). For all samples RNA integrity number (RIN) was >7.
Affymetrix GeneChip miRNA 4.0 array were used for miRNA profiling. Total RNA (1 μg per sample) was labeled using the FlashTag™ Biotin HSR RNA Labeling kit (Affymetrix, Inc., USA) as described by the manufacturer. The samples were hybridized on GeneChip miRNA 4.0 arrays (Affymetrix, Inc.) for 18 h at 48°C. Arrays were washed to remove non-specifically bound nucleic acids and stained on Fluidics Station 450 (Affymetrix, Inc.) and then scanned on GeneChip Scanner 3000 7G system (Affymetrix, Inc.). Finally, Microarray Data Analysis Tool version 3.2 (Filgen, Inc., Japan) was used as described in the manufacturer's instructions for all subsequent data analysis.
Affymetrix GeneChip miRNA 4.0 array were used for miRNA profiling. Total RNA (1 μg per sample) was labeled using the FlashTag™ Biotin HSR RNA Labeling kit (Affymetrix, Inc., USA) as described by the manufacturer. The samples were hybridized on GeneChip miRNA 4.0 arrays (Affymetrix, Inc.) for 18 h at 48°C. Arrays were washed to remove non-specifically bound nucleic acids and stained on Fluidics Station 450 (Affymetrix, Inc.) and then scanned on GeneChip Scanner 3000 7G system (Affymetrix, Inc.). Finally, Microarray Data Analysis Tool version 3.2 (Filgen, Inc., Japan) was used as described in the manufacturer's instructions for all subsequent data analysis.
3
Profiling cCFU-F-Exos miRNA Expression
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA was extracted from cCFU-F-Exos by using a Qiagen miRNeasy Mini Kit. Exosome replicas were derived from different cCFU-F isolates. Global miRNA expression patterns were then examined by using Affymetrix GeneChip miRNA 4.0 arrays. The Affymetrix GeneChip miRNA 4.0 array was designed based on miRBase version 20 (www.mirbase.org ). One microgram of total RNA was used as the input of the labeling reaction as recommended by the protocol of the Genisphere FlashTag Biotin RNA Labeling Kit. Labeled miRNA was then hybridized to the array at 60 rpm for 16 h at 48 °C. The gene chips were then scanned by using a Hewlett Packard Gene Array Scanner G3000 7G (Affymetrix). Expression data were generated by using Affymetrix Expression Console software and normalized according to the MAS5 method. The random variance model (RVM) t test was applied to filter the differentially expressed genes between the control and experimental groups. Differentially expressed miRNAs were defined based on a p value threshold and fold-change analysis. The criteria for significantly differentially expressed miRNAs were a p value < 0.05 and a fold change in expression of at least 2.0. Unsupervised hierarchical clustering was performed by using Cluster 3.0 and Java TreeView software.
4
Microarray Analysis of miRNA Expression
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The analysis of miRNAs was performed by Ebiogen Inc. (Seoul, Korea) using the Affymetrix GeneChip miRNA 4.0 array (Affymetrix, Santa Clara, CA, USA). A total of 24 animals were randomly separated into two treatment groups and two corresponding control groups. Treated rats were exposed to noise and assayed after 1 or 3 days. After hearing loss was confirmed, the CN and IC from two animals from the same group were combined and treated as a single sample, and three samples from each group were used for the analysis. Extracted total RNA was assessed for quality and quantity using a Bioanalyzer 2100 system (Agilent, Santa Clara, CA, USA). A total of 250 ng of RNA was analyzed. After ligating biotin-labeled 3DNA dendrimers, each RNA strand was labeled using poly-A polymerase. The biotinylated RNA strands were hybridized for 18 h at 48 °C on an Affymetrix GeneChip miRNA 4.0 array. The hybridized GeneChip was washed and stained using an Affymetrix 450 Fluidics station. Fluorescence signals from the 3DNA dendrimers were detected using an Affymetrix GeneChip 3000 7G scanner.
5
Microarray Profiling of Conjunctival miRNAs
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA was isolated and purified from conjunctival epithelium using the miRNeasy mini kit (Qiagen, Tokyo, Japan) for microarray profiling of miRNAs as recommended by the manufacturer. For all samples the RNA integrity number (RIN) was > 7. Affymetrix GeneChip miRNA 4.0 arrays were used for miRNA profiling. As described by the manufacturer, total RNA was labeled using the FlashTag Biotin HSR RNA labeling kit (Affymetrix Inc., USA). The samples were hybridized on GeneChip miRNA 4.0 arrays (Affymetrix) for 18 h at 48 °C. The arrays were then washed to remove non-specifically bound nucleic acids, stained on a Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G system (Affymetrix).
6
Profiling Blood miRNA via Affymetrix Microarray
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
During the screening phase, a volume corresponding to 500 ng of total RNA from each blood sample was processed using a FlashTag Biotin HSR RNA Labeling kit (Affymetrix, Santa Clara, CA, USA), following the manufacturer’s protocol. The RNA was subsequently hybridized onto Affymetrix GeneChip miRNA 4.0 Arrays that each contained 2,578 human miRNA sequences (Affymetrix, Santa Clara, CA, USA). The GeneChip miRNA 4.0 Arrays were washed and stained using aFluidics station 450 and a GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA, USA), respectively.
7
miRNA profiling of plasma samples
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
As previously reported and as recommended by the manufacturers, the total RNA was isolated and purified from plasma using the miRNeasy serum/plasma kit (Qiagen, Tokyo, Japan). Affymetrix GeneChip miRNA 4.0 arrays were used for miRNA profiling. Total RNA was labeled with the FlashTag™ Biotin HSR RNA labeling kit (Affymetrix, Inc., USA) (Ueta et al., 2020 (link); Ueta et al., 2021a (link)). The samples were hybridized on GeneChip miRNA 4.0 arrays (Affymetrix) for 18 h at 48°C. The arrays were washed to remove non-specifically bound nucleic acids and stained on Fluidics Station 450 (Affymetrix)) and then scanned on a GeneChip Scanner 3000 7G system (Affymetrix).
8
Profiling miRNA Changes in ALDH+ and ALDH- Cells
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
ALDH− and ALDH+ cells isolated from DOX-untreated SUM159-shXIST cells were treated with or without (CTL) DOX at 1 µg/ml for 3 days, miRNAs from each sample were extracted using miRNeasy Mini kit (Qiagen) and analyzed by GeneChip™ miRNA 4.0 Array (ThermoFisher Scientific) according to manufacturer’s instructions. miRNA-containing total RNA (300 ng) was biotin-labeled using the FlashTag Biotin RNA Labeling kit (Afymetrix, USA) and hybridized in the GeneChip Hybridization Oven 640 (Affymetrix, USA) at 48 °C for overnight. After washed and stained in the GeneChip Fluidics Station 450 (Afymetrix, USA), arrays of different samples were scanned with a GeneChip Scanner 3000 7 G (Afymetrix, USA) and signal strength was evaluated using the Expression Console Software (EC) v1.2 (ThermoFisher Scientific). To identify differentially expressed miRNAs in ALDH− and ALDH+ cells treated with or without DOX, acquired array data were analyzed using Multi Experiment Viewer (MeV v4.9.0; The Institute for Genomic Research) and miRNAs with an absolute value of fold change ≥ 0.6 were identified as potential miRNAs significantly changed upon DOX-induced XIST KD.
9
Biotin-Labeled miRNA Profiling in Biofluids
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA containing low molecular weight RNA was labelled using the FlashTag™ Biotin HSR RNA Labeling Kit (Thermo Fisher Scientific Inc, Waltham, MA, USA) according to the manufacturer’s instructions. Briefly, for each sample, 8 µL total RNA (isolated from a specific volume of urine and serum) was subjected to a tailing reaction for 15 min at 37 °C, followed by ligation of the biotinylated signal molecule to the target RNA sample for 30 min at room temperature and adding of stop solution. Each sample was hybridized to a GeneChip® miRNA 4.0 Array (Thermo Fisher Scientific Inc., Waltham, MA, USA) at 48 °C and 60 rpm for 18 h then washed and stained on Fluidics Station 450 (Fluidics script FS450_0002) and finally scanned on a GeneChip ® 3000 7G Scanner (Thermo Fisher Scientific Inc., Waltham, MA, USA). The expression values were RMA-normalized and summarized with robust multi-array average (RMA) using oligo package [19 (link)] under R 4.1.1. Differential expression analysis between the sample groups were conducted with limma package. miRNAs expressed with a fold change >1.5 and p-value < 0.05 between the groups were identified as significantly regulated.
10
Plasma ECmiRNA Profiling in Cystic Fibrosis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
An Affymetrix Genechip miRNA 4.0 array was used according to the manufacturer’s instruction (Thermofisher Scientific, USA) to identify plasma ECmiRNAs differentially expressed between CF (n = 5) and HC (n = 5) samples. For each sample, 8 µL of plasma RNA was labelled using the FlashTag Biotin RNA Labelling kit and spiked with synthetic control miRNAs for accessing labelling performance. Hybridization was performed by injecting the labelled samples, which were mixed with hybridization cocktail (130 μL total volume), into the 100 Format miRNA microarrays and subsequent incubation in a 48 °C hybridization oven with continuous agitation at 60 rpm for 16 hrs. The microarrays were then washed and stained with the Genechip Fluidics Station 450 using a locally installed miRNA 4.0 protocol. The washed and stained arrays were then scanned using the Affymetrix Genechip 3000 Scanner (Thermofisher Scientific, USA).
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!