Table 1.

LincRNA shortlist for functional testing.

Gene IDTranslation efficiencymESC (serum/LIF) expressionNPC (day 8) expressionReported namesThese lincRNAs were selected based on the following criteria
XLOC_004770NA1291linc1251/Platr7ESC specific; reported to be associated with pluripotency
XLOC_023375NA571linc1503ESC specific
XLOC_0466700.6785linc1400ESC specific
XLOC_0118410.21,95090linc1283/lncEnc1ESC specific; required for ESC colony formation
XLOC_0172400.235231linc1296ESC specific
XLOC_0213900.51172ESC specific
XLOC_0239340.4973ESC specific
XLOC_0299980.449357linc1333/Platr4ESC specific; reported to be required for pluripotency
XLOC_0493340.31324linc1405/Platr11ESC specific; reported to be required for pluripotency
XLOC_0182670.51414linc1611ESC specific
XLOC_0253670.160047linc1509ESC specific; reported to be required for pluripotency
XLOC_009546NA251TunaESC specific; reported to be required for pluripotency
XLOC_0513830.1608728linc1409/FirreWidely expressed; reported to regulate chromatin contacts
XLOC_0358050.297102linc1543Widely expressed; syntenic with human pluripotency lincRNA
XLOC_015936NA3423linc1476/Pvt1Widely expressed, with very high levels in some mESCs; oncogene
XLOC_036848NA1804,370MiatElevated 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).