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Significant deviation of the mean value of each sample group from a fold difference of 1 (no change compared to the comparator sample) was tested using a t-test on Log10 transformed data.
Results were analysed with the delta-delta method normalised to two housekeeping genes (Ppia and Rpl13a or UBC and TBP for mouse and human samples, respectively) and compared with a comparator sample (nonclonogenic luminal (NCL) cells).
Quantitative real time PCR (qPCR) reactions were carried out as described previously [ 14] to determine fold changes in expression of Esr1 (estrogen receptor-α) and Prlr (prolactin receptor) [ 14] in mammary epithelial cell subpopulations compared with a leucocyte-depleted, bulk mammary cell (CD45-) comparator sample.
Qualitative analyses were also performed to detect proteins found in at least 3 replicates of a sample, but undetectable in the comparator sample.
For endometrium from across the menstrual cycle, mRNA results were expressed as the quantity relative to a comparator sample of RNA from the liver.
Note that in cases where expression of the gene being analysed could not be detected in the comparator sample, an artificial Ct value of 40 was assigned purely to make the comparisons.
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The BLMO films are good comparator samples because they exhibit good magnetic properties and FE at RT with reasonable sample thickness, (i.e., not too thin; they are ∼30 nm), and with lattice parameter information reported.
The labeled peptides from the comparator samples are then combined in equal amounts and analyzed by MS. Thus, the basic premise of our analysis was that most proteins would be unchanged between T0 and T12 and would have reporter ion ratios of approximately 1 for their component peptides.
For endometrial biopsy specimens from across the menstrual cycle, results are given as quantity relative to a comparator, a sample of RNA from the liver.
For endometrial biopsies from across the menstrual cycle, results were expressed as quantity relative to a comparator, a sample of RNA from the liver.
Input signals from the comparators are sampled at 200 MHz (period 5 ns).
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