RNA-Seq analysis

Single-end 36bp tags (RNA-Seq tags), which were generated by RNA-Seq, extracted from cytoplasm, nuclear and polysome in human DLD-1 cell were used. By using junctions detected by TopHat, we identified translationable and non-translationable AS junctions in RefSeq transcripts (release23) mapped on human genome (hg18).

Experimental confirmation for the separation of DLD-1 sub-cellular fractions

RNA-Seq statistics

RNA-Seq tags Mapped on genome* Detected junctions**
Cytoplasm 46354139 28906833 (62%) 1312273
Nuclear 47120831 28939028 (61%) 1952803
Polysome 54901628 29720537 (54%) 4131266
Total 148376598 87566398 (59%) 7396342
*Bowtie 0.10.0.2
**TopHat 1.0.9

RefSeq statistics

Loci Transcripts Junctions *Junctions expressed in *Junctions specifically-expressed in
Cytoplasm Nuclear Polysome Cytoplasm Nuclear
(Non-translationable)		 Polysome
(Translationable)
Total 19181 26814 186137 47615 47260 51041 6649 6980 9799
AS 4090 10923 14491 1067 1021 1114 260 254 299
*Two or more RNA-Seq tags were supported.

H-DBAS: human-transcriptome database for alternative splicing: update 2010 (NAR Database Issue)