LincRNA shortlist for functional testing.
| Gene ID | Translation efficiency | mESC (serum/LIF) expression | NPC (day 8) expression | Reported names | These lincRNAs were selected based on the following criteria |
|---|---|---|---|---|---|
| XLOC_004770 | NA | 129 | 1 | linc1251/Platr7 | ESC specific; reported to be associated with pluripotency |
| XLOC_023375 | NA | 57 | 1 | linc1503 | ESC specific |
| XLOC_046670 | 0.6 | 78 | 5 | linc1400 | ESC specific |
| XLOC_011841 | 0.2 | 1,950 | 90 | linc1283/lncEnc1 | ESC specific; required for ESC colony formation |
| XLOC_017240 | 0.2 | 352 | 31 | linc1296 | ESC specific |
| XLOC_021390 | 0.5 | 117 | 2 | — | ESC specific |
| XLOC_023934 | 0.4 | 97 | 3 | — | ESC specific |
| XLOC_029998 | 0.4 | 493 | 57 | linc1333/Platr4 | ESC specific; reported to be required for pluripotency |
| XLOC_049334 | 0.3 | 132 | 4 | linc1405/Platr11 | ESC specific; reported to be required for pluripotency |
| XLOC_018267 | 0.5 | 141 | 4 | linc1611 | ESC specific |
| XLOC_025367 | 0.1 | 600 | 47 | linc1509 | ESC specific; reported to be required for pluripotency |
| XLOC_009546 | NA | 25 | 1 | Tuna | ESC specific; reported to be required for pluripotency |
| XLOC_051383 | 0.1 | 608 | 728 | linc1409/Firre | Widely expressed; reported to regulate chromatin contacts |
| XLOC_035805 | 0.2 | 97 | 102 | linc1543 | Widely expressed; syntenic with human pluripotency lincRNA |
| XLOC_015936 | NA | 34 | 23 | linc1476/Pvt1 | Widely expressed, with very high levels in some mESCs; oncogene |
| XLOC_036848 | NA | 180 | 4,370 | Miat | Elevated in NPCs; expressed during specific cell cycle stages |
Gene IDs are defined as in Table S1 (from the combined set of published and ab initio lincRNA/mRNA annotations). For translation efficiency, NA = could not be calculated, and for comparison, the median value for mRNAs is 1.0. Expression values in mESCs and derived NPCs were calculated using bulk RNA-seq data, normalising with the DESeq2 size factor function, and averaging the results from the two cell lines we tested (BC8 and CB9). Previously reported names for the lincRNAs are indicated, as well as notable features that we considered when shortlisting these lincRNAs (ESC-specific expression is defined using our RNA-seq data) (Guttman et al, 2009; Hacisuleyman et al, 2014; Jain et al, 2016; Lin et al, 2014; Bergmann et al, 2015).