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Successful microarray analysis on RNA isolated from minimal cell samples has been previously reported.
More recent members of the WT-Ovation RNA amplification system family may now provide further opportunity to exploit minimal cell samples.
In order to guarantee maximum RNA yield from these minimal cell samples, an optimised RNA isolation workflow was established specifically designed to minimise RNA loss throughout the procedure, whilst still being amenable to downstream array probe generation.
However, importantly, none of these address the issue of retrieving this level of RNA directly from minimal cell samples such that it is applicable to microarray workflows [17], [24].
cDNA probes generated using the WT-Ovation™ FFPE RNA amplification system V2 from RNA isolated from titrated minimal cell samples were purified prior to quantification using either the DNA clean and concentrator system (Zymo) or QIAquick PCR purification kit (Qiagen).
To ensure maximum exploitation of the minimal cell samples available to us, we also sought to establish an RNA amplification method capable of producing robust array hybridisation probes, resulting in data capable of capturing biological information of interest, from RNA within the picogram range.
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Protein expression measurements by quantitative immunofluorescence and immunoblotting have been carried out on these minimal endothelial cell samples [29], [33], along with restricted, targeted gene expression analyses [34].
Maximal CDM production was observed after 72 h of aerobic cultivation including the addition of 0.8 M NaCl to the sample after 60 h of aerobic cultivation in the presence of 0.3 M NaCl or in the control sample, whereas minimal cell growth was observed in the sample that included an additional 1.3 M NaCl.
Genomic DNA (gDNA) elimination was carried out on the total RNA samples from minimal cell numbers by gDNA Wipeout buffer treatment (Quantitect Reverse transcription kit, Qiagen).
Quantitect cDNA samples generated from minimal cell numbers and vascular endothelial biopsies or standard curve RNA dilutions were diluted 1∶25 or 1∶100, respectively for input in the real-time quantitative PCR.
We were mainly interested in TSSs recognized by the housekeeping sigma factor σA. Therefore the RNA samples for this data set originated from mixed C. glutamicum cell samples grown in minimal and in complex media.
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