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We have designed experiments and measured three different levels of variations, starting with the same membrane protein preparation, the same batch of cells and three batches of cells from the same cell line grown under the same conditions, respectively.
The same batch of cells was subjected to SA-β-Gal staining as described above.
The same batch of cells was used for extracting cell surface proteins and for analysis of conditioned media and whole cell lysate proteins.
The eGFP+ MHC class I- cells as well as untransduced hMSCs from the same batch of cells were then exposed to the vesicular stomatitis virus G protein-pseudotyped self-inactivating lentiviral vector LV.C-EF1a.cyt-bGal [70], encoding Escherichia coli β-gal.
We used the same batch of cells to prepare all the aliquots of the same time-course replicate experiment.
To confirm successful knockdown of APC in HCT116 cell lysates from the same batch of cells, lysates were immunoblotted against the APC antibody Ali12-28 or H-290.
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For the same batch of cell cultures, three time points were taken for analyses (see Figure 2A).
To isolate this complex, the same batch of cell-free extracts from H. jecorina transferred to glucose was subjected to affinity chromatography.
The same batch of cell lysates derived from RAW 264.7 cell line were processed following the protocol mentioned above as an external control to standardize the results of Western blot analyses from different membranes.
In order to obtain robust, valid comparative RNA expression values, total RNA was extracted from the same batch of cell lines, converted into Cy5-labeled cDNA, and hybridized in replicates together with a common Cy3-labeled reference, to both cDNA (30 k) and oligo (34 k) spotted microarrays.
Assay to assay (inter-assay) variability was assessed with normalized Ct values from three independent experiments, in which antibody binding, SH2 binding, ligation, protease treatment, and real-time PCR reactions were independently performed while using the same batch of cell lysate samples.
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CEO of Professional Science Editing for Scientists @ prosciediting.com