Fig. 8.

Probe set quality control. The RNA-seq button performs alignment of a probe set sequence against the appropriate reference genome using UCSC Genome Browser ‘s BLAST-like alignment tool (BLAT). The results are shown for probe set 1450486_a_at in the top panel. The SCORE is a function of the size and match. For large sequences a perfect score is 255. START, END, and QSIZE provide information about the size in base pairs of the query sequence. IDENTITY provides information about the match with 100 % indicating a perfect match to the reference C57BL/6J genome. The location and span of the match are given by CHRO (chromosome) STRAND, START, END, and SPAN. Note that both the probe set and the 11 perfect match probes that comprise the probe set are shown and that the best match for the individual probes and entire probe set is on the positive strand on Chr 2 around 181.45 Mb. Clicking the browser link for the best match directs to a graphical display of the probe set alignment, shown in the bottom panel. The genome browser display can be cluttered for the uninitiated. The basic layout is a display of several different Tracks of information. These tracks can be modifi ed by scrolling down to the track tables at the bottom of the page. The display in the above panel was generated by selecting the hide option for all tracks EXCEPT the Mapping and Sequencing, Genes and Gene Prediction, and the DBA/2J Sequence and Structural Variation tracks. The position of all 11 probes and the composite probe set are shown in the bottom panel in black with the corresponding IDs shown to the left. The arrowheads designate the alignment of the probe set on the positive (or sense) strand. The targeted gene (Oprl1) is shown below and indicates that the probe set is designed to target the 3′ UTR according to the UCSC gene model. The location of sequence variants in the DBA/2J strain relative to the C57BL/6J reference genome are shown in the last two tracks (D2 InDels and D2 SNPs). Note probes 299709 and 452573 overlap a DBA/2J SNP