supp_figure7: lnc34a splice junction analysis.

In GranderLab/miR34a_asRNA_project: The miR34AasRNAproject package facilitates the transparency and reproducibility of the miR34a asRNA project and associated publication.

Description

All available whole cell RNAseq splice junction data from the ENCODE project originating from the Cold Spring Harbor Lab from 38 cell lines was downloaded from the UCSC genome browser with the script entitled "lnc34a splice junctions" in the data-raw/saveRDS.R file. Of these cell lines, 36 had spliced reads mapping to the plus strand of chromosome 1 and in the region between the lnc34a start (9241796) and transcription termination (9257102) site (note that miR34a asRNA resides totally within this region). Splice junctions from the following cell lines were included in the final figure: A549, Ag04450, Bj, Cd20, Cd34mobilized, Gm12878, H1hesc, Haoaf, Haoec, Hch, Helas3, Hepg2, Hfdpc, Hmec, Hmepc, Hmscat, Hmscbm, Hmscuc, Hob, Hpcpl, Hpiepc, Hsavec, Hsmm, Huvec, Hvmf, Hwp, Imr90, Mcf7, Monocd14, Nhdf, Nhek, Nhemfm2, Nhemm2, Nhlf, Skmc, Sknsh. All splice junctions were plotted and colored according to the number of reads corresponding to each.

Format

A tibble with 373 rows and 10 variables:

Source

https://www.encodeproject.org

Examples

getData('Supplementary Figure 7')

GranderLab/miR34a_asRNA_project documentation built on May 26, 2019, 7:26 a.m.