Table 1. Summary of sequencing data lactating mouse, bovine and AGO2 mammary gland miRNA libraries.

	Mouse		Bovine		AGO2
	Sample 1	Sample 2	Sample 1	Sample 2	Sample 1	Sample 2
Raw reads	10,782,945	10,738,221	10,847,425	12,034,673	12,940,967	13,643,425
Clean readsa	9,909,832	8,760,102	9,951,849	11,245,052	5,485,346	7,610,033
Sized readsb	9,817,286	8,708,817	9,877,580	11,149,432	5,307,791	7,368,804
All unique sequences corresponding to sized reads	128,806	90,569	97,136	111,437	55,616	305,201*
Mapped readsc	9,369,334	8,402,247	9,549,490	10,802,108	4,674,418	6,508,282
Unique sequences corresponding to mapped reads	72,653	51,438	40,750	51,587	26,843	230,688*

^apoly-A stretches removed.

^b17–28 nt size filtering,reads used by miRDeep2 quantification process.

^creads with at least one and at most five reported alignments, used by the miRDeep2 prediction process.

* In AGO sample 2, many reads below 10 counts were present, subsequently discarded by miRDeep2 processes.