Fig. 4: The performance of INSCRIBE at various sequencing depths and ultra-low RNA input. | Nature Communications

Fig. 4: The performance of INSCRIBE at various sequencing depths and ultra-low RNA input.

From: High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues

Fig. 4

a The enrichment of UGCAUG motif at confident edit clusters center with different sequencing depths of RBFOX2-INSCRIBE and enzyme-only control. Increasing sequencing depth from 20 to 40, 60, 80, 100 million (M) reads enhanced the enrichment of UGCAUG, while the improvement from 80 M to 100 M was marginal. b Integrative genome viewer (IGV) tracks of representative RBFOX2 target gene (APP) examining the effect of sequencing depth on SAILOR-quantified C-to-U conversion pattern and FLARE confident edit clusters. The tracks include eCLIP peaks (orange), 3-replicate overlay of SAILOR-quantified edit fraction (blue, upper tracks) and FLARE confident edit clusters (blue, lower tracks) of RBFOX2-INSCRIBE. c The enrichment of UGCAUG motif at confident edit clusters center with libraries of different input total RNA of RBFOX2-INSCRIBE and enzyme-only controls. Both 1 ng (dark blue) and 100 pg (light blue) input RNA showed evident enrichment of UGCAUG motif as compared to standard input (>1000 ng RNA) (purple) in RBFOX2-INSCRIBE, while lower amount of input material decreased the enrichment. d IGV tracks of representative RBFOX2 target gene (APP) examining the effect of input starting total RNA on SAILOR-quantified C-to-U conversion pattern and FLARE confident edit clusters. The tracks include eCLIP peaks (orange), 3-replicate overlay of SAILOR-quantified edit fraction (blue, upper tracks) and FLARE confident edit clusters (blue, lower tracks) of RBFOX2-INSCRIBE. E Continued IGV tracks showing the FLARE-identified edit clusters in individual replicates for the 100 pg input RNA libraries.

Back to article page