Extracted RNA was then used in microarray experiments using Illumina Sentrix HT-12_v3_BeadChip arrays (Illumina, San Diego, California).
Microarray experiments using mRNA from air-dried leaves and roots of rice were performed in an attempt to study genes involved in acute dehydration response.
Microarray experiments using mRNA from air-dried leaves and roots of rice were performed in an attempt to study genes involved in dehydration response.
All reactions were performed on the cDNA synthesized from the same RNA extraction as the microarray experiments using SuperScript™ III First-Strand Synthesis SuperMix (Invitrogen, Carlsbad, CA, USA).
All qRT-PCR reactions were performed on complementary DNA (cDNA), synthesized from the same RNA extracted for use in the microarray experiments, using SuperScript™ III First-Strand Synthesis SuperMix (Invitrogen, CA, USA).
A number of papers have described methods for assessing selected dataset requirements in microarray experiments using statistical criteria [12].
We have validated our approach by interpreting several publicly available expression microarray experiments using the Atlas of Signaling pathway.
Reverse transcription was performed with 500 ng total RNA (same as used in microarray experiments) using the iScript cDNA synthesis kit (Bio-Rad).
These experiments indicate that for a wide range of experimental conditions, microarray experiments using the Fundulus array are both accurate and precise.
However, some attempts at microarray experiments using these clinical samples of reduced cell content have either pooled individual samples to gain sufficient RNA [21] or focussed on optimising the crucial RNA isolation step to obtain the nanograms of RNA required for microarray analysis [22].
Since RA is known by its ability to induce major changes in the cell transcriptome, we performed microarray experiments using the Affymetrix GeneChip Human Gene 1.0 ST oligonucleotide arrays of cDNA produced from hMSC cultured for 5 days in 0.5 µM RA in DMEM or in DMEM with or without 10%FBS.
