Total RNA was isolated using the protocol described above. RNA integrity was verified using a Bioanalyser 2100 with RNA 6000 Nano chips (Agilent Technologies, Palo Alto, CA, USA). Transcriptional profiling was performed on mouse colon samples using the SurePrint G3 Mouse GE 8 × 60 K Microarray kit (design ID: 028005, Agilent Technologies). Cyanine-3 (Cy3)-labeled cRNAs were prepared with 100 ng of total RNA using a One-Color Low Input Quick Amp Labeling kit (Agilent Technologies), following the recommended protocol. The specific activities and cRNA yields were determined by using a NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA). For each sample, 600 ng of Cy3-labeled cRNA (specific activity > 11.0 pmol Cy3/μg of cRNA) were fragmented at 60 °C for 30 min and hybridized to the microarrays for 17 h at 65 °C in a rotating hybridization oven (Agilent Technologies). After hybridization, the microarrays were washed and then immediately dried. After washing, the slides were scanned using a G2565CA Scanner System (Agilent Technologies) at a resolution of 3 μm and a dynamic range of 20 bits. The resulting TIFF images were analyzed using the Feature Extraction Software v10.7.3.1 (Agilent Technologies) according to the GE1_107_Sep09 protocol. The microarray data were submitted to GEO under accession number GSE67577.
Rotating hybridization oven
Manufactured by Agilent Technologies
The Rotating Hybridization Oven is a laboratory equipment designed for performing hybridization processes. It features a rotating mechanism that ensures even distribution of samples during the hybridization procedure.
Automatically generated - may contain errors
Lab products found in correlation
G2565ca scanner system, by Agilent Technologies (2 mentions)
Feature extraction software v10, by Agilent Technologies (2 mentions)
Rna 6000 nano chip, by Agilent Technologies (2 mentions)
Nanodrop nd 1000, by Thermo Fisher Scientific (2 mentions)
One color low input quick amp labeling kit, by Agilent Technologies (2 mentions)
Sureprint g3 mouse ge 8 60k microarray kit, by Agilent Technologies (2 mentions)
2100 bioanalyser, by Agilent Technologies (2 mentions)
Agilent genomic dna labeling kit plus, by Agilent Technologies (1 mentions)
Gene expression hybridization kit, by Agilent Technologies (1 mentions)
4 protocols using rotating hybridization oven
1
Microarray Transcriptional Profiling of Mouse Colon
2
Genomic Imbalances in iPSC Clones
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The genomic imbalances in lymphocytes from the patient and in derived iPS clones 12 and 32 at passages p11 and p12, respectively, were investigated by array-CGH with 1M oligonucleotide arrays (Agilent Technologies). Array hybridization was performed according to the manufacturer’s instructions. In brief, 0.5 μg of genomic DNA was fluorescently labeled with the Agilent Genomic DNA labeling kit PLUS (Agilent Technologies). Male human genomic DNA was used as a reference. Cy5-dUTP patient DNA and sex-matched reference DNA labeled with Cy3-dUTP were denatured and preannealed with Cot-1 DNA and Agilent blocking reagent before hybridization for 40 h, with rotation at 20 rpm, at 65 °C in a rotating hybridization oven (Agilent Technologies). The slides were then washed and scanned on an Agilent Microarray Scanner. The captured images were processed with Feature Extraction 10.7.3.1 software and data analysis was performed with Cytogenomics 3.0.1.1 software. Copy number variations (CNVs) were considered significant if they were defined by three or more contiguous oligonucleotides spanning at least 2 kb and were not identified in the Database of Genomic Variants. The Genome Browser used to analyze gene content was hg19, Build37 (http://genome.ucsc.edu/ ).
3
Breast Cancer RNA Profiling by Microarray
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Example 4
RNA samples derived from breast cancer tissue were analyzed with 44 k human whole genome oligo microarrays (Agilent Technologies).
RNA expression levels from different samples were analyzed on a single microarray using the Single-Color Low RNA Input Linear Amplification Kit PLUS (Agilent Technologies, Waldbronn, Germany). For each amplification, 200 ng of total RNA were employed and amplified samples were prepared for hybridization using the Gene Expression Hybridization Kit (Agilent Technologies). Hybridization was performed over night at 65° C. in a rotating hybridization oven (Agilent Technologies). Stringency washes, image acquisition and feature extraction was performed according to the manufacturer's protocol (Agilent Technologies, Waldbronn, Germany).
4
Transcriptional Profiling of Mouse Colon
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA was isolated using the protocol described above. RNA integrity was verified using a Bioanalyser2100 with RNA6000 Nano chips (Agilent Technologies). Transcriptional profiling was performed on mouse colon samples using the SurePrint G3 Mouse GE8 × 60 K Microarray kit (design ID: 028005, Agilent Technologies). Cyanine-3 (Cy3)-labeled cRNAs were prepared with 100 ng of total RNA using a One-Color Low Input Quick Amp Labeling kit (Agilent Technologies). The specific activities and cRNA yields were determined by using a NanoDrop ND-1000 (Thermo Fisher Scientific). For each sample, 600 ng of Cy3-labeled cRNA (specific activity > 11.0 pmol Cy3/μg of cRNA) was fragmented at 60 °C for 30 min and hybridized to the microarrays for 17 h at 65 °C in a rotating hybridization oven (Agilent Technologies). After hybridization, the microarrays were washed and then immediately dried. After washing, the slides were scanned using a G2565CA Scanner System (Agilent Technologies) at a resolution of 3 μm and a dynamic range of 20 bits. The resulting TIFF images were analyzed using the Feature Extraction Software v10.7.3.1 (Agilent Technologies) according to the GE1_107_Sep09 protocol. The microarray data were submitted to GEO under accession number.
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!