RNA-Seq analysis

RNA-Seq analysis

Single-end 36bp tags (RNA-Seq tags) extracted from cytoplasm, nuclear and polysome in human DLD-1 cell were used. By detecting junctions from them by TopHat, we identified translationable and non-translationable AS junctions in RefSeq transcripts (release23) mapped on human genome (hg19).

Expression confirmation
Separation of sub-cellular fractions

Download

RNA-Seq tag sequence data: Cytoplasm, Nuclear, Polysome
RefSeq RASV sequence data: RASV_human_refseq.fa.gz
RefSeq RASV position data: refFlat_RASV_human_refseq.txt.gz

RNA-Seq statistics

	RNA-Seq tags	Mapped tags on genome*	Detected junctions**
Cytoplasm	46354137	28634895	548974
Nuclear	47120831	28808545	582576
Polysome	54901628	29485229	647181
Total	148376596	86928669	1778731

*by using Bowtie 0.12.5
**by using TopHat 1.0.14

RefSeq statistics

	Loci	Transcripts	Unique junctions	Junctions expressed at*			Junctions specifically-expressed at*
	Loci	Transcripts	Unique junctions	Cytoplasm	Nuclear	Polysome	Cytoplasm	Nuclear (Non-translationable)	Polysome (Translationable)
Total	20342	31616	197456	47256	43622	38518	10777	7869	7437
AS	5685	15951	21595	1197	957	722	487	267	196

*Two or more RNA-Seq tags were supported.