Supplementary Figure 2: RNA-sequencing after miRNA pulldown
From: MiCEE is a ncRNA-protein complex that mediates epigenetic silencing and nucleolar organization
a, Schematic representation of the experimental outline. MLE-12 cells were transfected with biotinylated Mirctrl or Mirlet7d. Nuclear extract from transfected cells was used for the pulldown with streptavidin magnetic beads. Total RNA was extracted from the precipitated material and sequenced. See Fig. 1c-g, S3b-d, 3f, and S6f. b, c, Description of the mir-Pd RNA-seq data sets supports the quality of the experiment. d, Distribution of Mirlet7d-bound ncRNA loci relative to either genome areas (top) or chromosomes (bottom). Base pairs, bp. e, Visualization of representative Mirlet7d targets loci using UCSC genome browser after Mirlet7d-pulldown and RNA-seq (blue). Images of Mirlet7d-pulldown were generated after subtracting the input. Visualization of the same loci after RNA-seq showed reduced levels of both, ncRNA and adjacent cRNA, after Mirlet7d-GOF (magenta) when compared to Mirctrl transfection (green). Images represent mapped sequence tag densities relative to the indicated loci. Black boxes, exons; lines, introns, arrow, transcription direction. See Fig. 1c-g
