Numbers indicate programs or filtering steps as follows: (1) filtering to retain only those libraries with a minimum of 50,000 raw tag counts, (2) identifying unique SAGE tags and constructing SAGE tag expression matrix, (3) mapping SAGE tags to Unigene IDs using SAGE Genie mapping files, (4) filtering lists to retain only tags with ≥2 raw counts in a ≥3 of 272 libraries, (5) determining gene identity using SAGE Genie, (6) separating Unigene tags mapping to lncRNAs and ambiguous transcripts, (7) pooling ambiguous tags and unmapped tags, (8) mapping sequence tags to the reference list of 9,891 lncRNAs using SeqMap, a tag-to-gene mapping program, (remaining tags may map to unannotated lncRNAs or antisense transcripts not included in our reference list) (9) filtering tag matches for strand sense, (10) pooling forward mapping tags and tags determined from Unigene, and (11) confirming tag-to-lncRNA matches and summing tag counts for lncRNAs with multiple tag matches. A complete list of lncRNAs is provided as Table S5 and tag-to-lncRNA matches are provided as Table S6.