14 Results
for author "Thomas Drake"
Figure 1RDD in mouse liver and adipose identified by RNA-Seq. (A) RDD numbers resulting from different filters. The results found for the same filters by Kleinman and Majewski (2012) are in italics. (B) Percentages of RDD reads found in comparison with reads from the EST database.
Figure 2Contribution of sequencing strand bias to RDD. Histogram with the distribution of RDD (y-axis) according to the proportion of reads belonging to the forward sequencing strand (x-axis) in liver (sample M.CH.BxD) and adipose (sample F.BxD). Open bars and the dashed line correspond to the RDD sites. Shaded bars and the solid line correspond to the dbSNP sites that are polymorphic in the sample and used as a control data set. The false positives are calculated using the tails of the distributions where the RDD and SNP distributions intersect. The same shape of distribution was observed for all samples of the same tissue.
Figure 3Contribution of end of read sequencing to RDD. Histogram with the distribution of RDD (y-axis) according to the proportion of reads where the alternative base is found in the first or last base or in the 5 first or 5 last bases of the sequencing read (x-axis). (A) Liver (sample M.CH.BxD) and (B) adipose (sample F.BxD). Open bars and the dashed line correspond to the RDD sites. Shaded bars and the solid line correspond to the dbSNP sites that are polymorphic in the sample and used as a control data set. The false positives are calculated using the tails of the distributions where the RDD and SNP distributions intersect. The same shape of distribution was observed for all samples of the same tissue.
Figure 4RDD categories in liver and adipose tissue. (A) RDD categories observed with liver RNA-Seq data after the multiple and unique mapping procedures and filtering for sequencing bias. (B) RDD categories observed with adipose RNA-Seq data after the unique mapping procedure and filtering for sequencing bias.- Table 1RDD tested by Sequenom mass spectrometry
Figure 5Validation by Sequenom technology of four RDD observed by RNA-Seq in liver. (A) Results obtained by Sequenom technology and expressed as percentage of total mRNA sequences containing the DNA base (open) vs. the edited base (solid) (total, 100%). (B) Results obtained by RNA-Seq technology and expressed as number of reads mapping to the RDD position.- TABLE 1Comparison of experimental design between the crosses
Figure 1.—Replication of local (a) and distal (b) eQTL between crosses. The percentage of eQTL that replicated between crosses at various LOD thresholds is depicted in adipose, brain, liver, and muscle tissue. The eQTL at LOD > 2.7, 4.3, and 6 of the mouse crosses were screened for detection at LOD > 2.7 in their respective comparison crosses. The percentage indicates the degree of replication of eQTL at LOD > 4.3 in cross I that overlap in cross II at LOD > 2.7 over the total number of eQTL at LOD > 4.3 detected in cross I and vice versa. For example, at LOD > 6, >80% of the local eQTL in cross I were preserved in cross II of the adipose tissue.