These tracks show the normalized read density for the 5′ and 3′ ends of short capped RNAs (scRNAs) in D. melanogaster S2 cells. Most of the scRNAs are produced by paused polymerases. The 5′ ends of the scRNAs demarcate the transcription start site while the 3′ ends of the scRNAs demarcate where RNA Polymerase II have paused.
Datasets from Nechaev S et al., 2010
This study analyzed the 5′ and 3′ scRNAs found in untreated S2 cells and in TFIIS-depleted S2 cells. The datasets were retrieved from the Gene Expression Omnibus database at NCBI under the accession number GSE18643.
Datasets from Henriques T et al., 2013
In addition to analyzing the 3′ scRNAs found in whole S2 cells, this study also analyzed the 3′ scRNAs that are associated with chromatin and 3′ scRNAs that are detergent-soluble. The datasets were retrieved from the Gene Expression Omnibus database at NCBI under the accession number GSE49078.
Each dataset was mapped to the D. melanogaster release 6 assembly using bwa with default parameters.
The alignment results were analyzed by CAGEr.
For the Nechaev S et al. study, the tag counts were normalized by the normalizeTagCount function in CAGEr with the following parameters: