M-A scatterplots of values from the differential RNA-seq analysis. (A) and (B) show data for cells sub-cultured without and with a potassium downshift, respectively. (C) and (D), as (A) and (B), except data is for a duplicate starter culture. The M values correspond to Log2 (plus/minus) and A values to (Log2 plus + Log2 minus)/2, where minus and plus refer to the number of reads before and after treatment with TAP. For further details, see Methods. The red and blue points represent the upper and lower boundaries, respectively, of an envelope that contains sites of processing and degradation. The upper and lower boundaries were defined by the equation μ ± 3σ, where μ and σ are the average and standard deviation, respectively, of M in a moving window of 5,000 data-points sorted in ascending order of A [22, 23].