Table 1.

Pairwise comparison of upregulated and downregulated transcripts in CRISPR/Cas9 KO clones

Comparison Set	Up/Downregulated Transcripts Relative to the Comparison Set
	Cubn KO	Lrp2 KO	Dab2 KO
Control (1.0)	101/18	230/212	110/66
Cubn KO (0.9–1.1)		38/80	3/16
Lrp2 KO (0.9–1.1)	4/2		4/2
Dab2 KO (0.9–1.1)	19/0	44/63

Transcripts with an average count of <350 (∼0.1% of the highest expressed gene) were excluded from the analysis. To compare knockout (KO) clones against one another, we first generated comparison sets by collecting “unaffected” transcripts that were expressed at 0.9- to 1.1-fold of control values in each KO clone. Next, we identified transcripts in KO clones that were expressed at ≥1.7-fold greater/less than these values. The number of upregulated/downregulated transcripts is shown for each pairwise comparison. The gene that was knocked out in each CRISPR/Cas9 clone was not included in the counts of downregulated transcripts [e.g., the only transcript downregulated in cubilin (Cubn) KO cells relative to Dab2 (Dab2) KO cells was cubilin itself]. Lrp2, megalin.