Table 1. Statistics of expression-positive Alu elements in selected cell lines.

Cell line	Total Alusa	Intergenic/antisense	Intergenic/antisense sharedb	Antisense to intronsc
Gm12878	149	48	21	13
H1-hESC	257	92	28	12
HeLa S3	276	44	32	7
HepG2	425	88	31	19
HUVEC	326	36	18	4
K562	154	71	33	20
NHEK	231	130	38	34
ALLd	1295	386	78	87

For each cell line, from left to right, the first column reports the number of Alus considered as expression-positive in both ENCODE RNA-seq replicates; the second column reports the number of intergenic/antisense Alus (including purely intergenic Alus and Alus overlapping to other transcription units in an antisense orientation); the third column reports the number of intergenic/antisense Alus that, in addition to the corresponding cell line, were also expression-positive in one or more different cell lines; the fourth column reports the numbers of Alus mapping with an antisense orientation to introns of either protein-coding or lncRNA genes. The numbers in the last (bottom) raw refer to the full set of individual Alus expressed in one or more cell lines.

^aFor each cell line, the column reports the number of Alus considered as autonomously expressed in both ENCODE RNA-seq replicates.

^bFor each cell line, the column reports the number of intergenic Alus that are also expressed in one or more different cell lines.

^cReported in this column are the numbers of intergenic Alus mapping with an antisense orientation to introns of both protein-coding and lncRNA genes.

^dThe numbers in this raw refer to individual Alus expressed in one or more cell lines.