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An RNA-Seq Strategy to Detect the Complete Coding and Non-Coding Transcriptome Including Full-Length Imprinted Macro ncRNAs

Figure 4

Ribo-depleted RNA-Seq detects tissue specific expression of known protein-coding and non-coding genes.

(A) UCSC genome browser (, mm9) screen shots of RNA-Seq data for CCE (black, top) and FH (grey, bottom). The genome position is given on top, black or grey bars indicate the number of sequence tags (tag numbers >10 are cut off) at this position. The position of RefSeq genes (black line) with exons (black boxes), are shown below with the gene name. Left: the alpha-crystallin A chain gene is specific for the mouse eye and therefore sequence tags over exons (indicating gene expression) are only found in FH and are absent from CCE. Right: the well-known stem cell marker Pou5f1 (Oct4) shows sequence tags over exons only in CCE but not in FH. (B) Putative pri-miRNAs indicating either the specific expression of all miRNAs of the cluster in CCE and the >10 fold reduced expression in FH (left) or the similar expression of the two miRNAs in the region in CCE and FH (right). Red boxes indicate the position of annotated miRNAs (, mm9) with the name given below. Asterisks mark miRNAs overlapped by a low number of sequence tags. The position of the putative pri-miRNA, not annotated in the RefSeq database, is shown at the bottom by a double-headed arrow. Details as in (A). (C) Putative pri-miRNAs indicating the >10 fold increased expression of the single miRNAs of the respective cluster in FH compared to CCE. Details as in (A). Note that in A, B, and C RiboMinus data is shown and that the Ribo-Zero data produced similar results (data not shown).

Figure 4