Exact(7)
A two color protocol (NimbleGen Roche) was used, labeling the input DNA with Cy3 and the MeDIP DNA with Cy5.
Amplified RNA was used for further processing and hybridization to the Agilent arrays using the manufacturer's established one color protocol.
All hybridizations were carried out in the two color protocol by combining one Cy3-CTP-labeled experimental target and Cy5-CTP-labeled reference target.
Total RNAs were amplified and labeled by using an Agilent Quick Amp labeling kit (part number 5190 0444, Santa Clara, CA) and following the two color protocol (v.5.7).
Microarrays were done using the "Low RNA Input linear Amplification Kit Plus, One Color" protocol (Cat. No.: 5188-5339, 2007; Agilent Technologies, Inc., Santa Clara, CA) and the Agilent RNA Spike-In Kit for One color (Agilent Technologies, Inc. 2007; Cat. No.: 5188-5282) following the manufacturer's standard protocol.
Microarrays were done using the 'Low RNA Input linear Amplification Kit Plus, One Color' protocol (Agilent Technologies, Cat. No.: 5188 5339) and the Agilent RNA Spike-In Kit for One color (Agilent Technologies, Cat. No.: 5188 5282) following the manufacturer's standard protocol.
Similar(53)
For other microarrays, a one-color protocol was used.
In the two-color protocol, two RNA samples differently labeled by Alexa 532 and Alexa 645 were simultaneously hybridized on the same microarray chip.
On the other hand, in a one-color protocol, each RNA sample was labeled using a single dye, and two RNA samples were hybridized separately on two microarray chips.
Slides were scanned on the Agilent DNA Microarray Scanner and data extracted using the feature extraction software package (v9.1.3.1) using a standard two-color protocol.
In each experiment, RNA from directly-, bystander- or mock-irradiated cells was hybridized to human whole genome microarrays using the Agilent one-color protocol.
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