Reference

This page contains links to supplementary online files for Exon-Intron Split analysis (EISA):

Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation.
Dimos Gaidatzis, Lukas Burger, Maria Florescu and Michael B. Stadler
Nature Biotechnology, 2015 Jul;33(7):722-9. doi: 10.1038/nbt.3269. Epub 2015 Jun 22.
Abstract | doi:10.1038/nbt.3269 | Full text (HTML) | Full text (PDF)

Supplementary Online Files

(to download archives of these files, see the bottom of this page)

List of non-overlapping genes for each genome assembly and strandedness

H. sapiens hg18 stranded
H. sapiens hg18 unstranded
M. musculus mm9 stranded
M. musculus mm9 unstranded

Figure 2a

• Bhatt et al. 2012
  Fig2a_GSE32916_rawcounts_exonic.txt.gz (0.4MB)
  Fig2a_GSE38892_rawcounts_exonic.txt.gz (0.2MB)
  Fig2a_GSE38892_rawcounts_intronic.txt.gz (0.2MB)

• Gene clusters from Bhatt et al. 2012 and expression changes as compared to the first time point
  Fig2a_genesInBhatt2012Clusters_normalized.txt.gz (0.1MB)

Figure 2bcd

• Menet et al. 2012
  Fig2bcd_GSE36916_rawcounts_exonic.txt.gz (0.6MB)
  Fig2bcd_GSE36916_rawcounts_intronic.txt.gz (0.6MB)
  Fig2bcd_GSE36916_normalized_forPhaseFitting.txt.gz (1.1MB)

• Koike et al. 2012
  Fig2bcd_GSE39978_rawcounts_exonic.txt.gz (0.3MB)
  Fig2bcd_GSE39978_rawcounts_intronic.txt.gz (0.3MB)
  Fig2bcd_GSE39978_normalized_forPhaseFitting.txt.gz (1.3MB)

• Vollmers et al. 2012
  Fig2bcd_SRA025656_rawcounts_exonic.txt.gz (0.3MB)
  Fig2bcd_SRA025656_rawcounts_intronic.txt.gz (0.3MB)
  Fig2bcd_SRA025656_normalized_forPhaseFitting.txt.gz (0.7MB)

• Fitted phases and amplitudes for detected genes (all three datasets)
  Fig2bcd_fittedPhasesAmplitudes_detectedGenes.txt.gz (0.6MB)

Figure 2ef

• Jin et al. 2013
  Fig2ef_GSE43070_rawcounts_exonic.txt.gz (0.2MB)
  Fig2ef_GSE43070_rawcounts_intronic.txt.gz (0.2MB)
  Fig2ef_GSE43070_rawcounts_groSeq.txt.gz (0.2MB)
  Fig2ef_GSE43070_normalized_exonic_intronic_groSeq.txt.gz (0.5MB)

Figure 3abc

• Tippmann et al. 2012
  Fig3abc_GSE33252_rawcounts_exonic.txt.gz (0.2MB)
  Fig3abc_GSE33252_rawcounts_intronic.txt.gz (0.2MB)
  Fig3abc_GSE33252_normalized_exonic_intronic.txt.gz (0.4MB)
  Fig3abc_GSE33252_normalized_exonic_intronic_halflives.txt.gz (0.2MB)

Figure 4ab

• Guo et al. 2010
  Fig4ab_GSE21992_rawcounts_exonic.txt.gz (0.2MB)
  Fig4ab_GSE21992_rawcounts_intronic.txt.gz (0.2MB)
  Fig4ab_GSE21992_normalized_exonic_intronic_mirSites.txt.gz (0.6MB)

Figure 4cd

• Nam et al. 2014
  Fig4cd_GSE52530_rawcounts_exonic.txt.gz (0.6MB)
  Fig4cd_GSE52530_rawcounts_intronic.txt.gz (0.6MB)
  Fig4cd_GSE52530_Huh7_normalized_exonic_intronic_mirSites.txt.gz (0.7MB)
  Fig4cd_GSE52530_IMR90_normalized_exonic_intronic_mirSites.txt.gz (0.4MB)
  Fig4cd_GSE52530_HEK293_normalized_exonic_intronic_mirSites.txt.gz (0.8MB)
  Fig4cd_GSE52530_HeLa_normalized_exonic_intronic_mirSites.txt.gz (0.7MB)

Figure 5ab

• ENCODE cell lines
  Fig5ab_GSE30567_PolyA_rawcounts_exonic.txt.gz (0.3MB)
  Fig5ab_GSE30567_PolyA_rawcounts_intronic.txt.gz (0.3MB)
  Fig5ab_GSE30567_nonPolyA_rawcounts_exonic.txt.gz (0.3MB)
  Fig5ab_GSE30567_nonPolyA_rawcounts_intronic.txt.gz (0.3MB)
  Fig5ab_GSE30567_normalized_exonic_intronic.txt.gz (1.4MB)

Figure 5cde

• Illumina Human Body Map 2.0
  Fig5cde_GSE30611_rawcounts_exonic.txt.gz (0.6MB)
  Fig5cde_GSE30611_rawcounts_intronic.txt.gz (0.5MB)
  Fig5cde_GSE30611_normalized_exonic_intronic_mirSites.txt.gz (3.2MB)

Code

• Supplementary Script 1: Example R code for fitting phases/amplitudes of oscillating genes (dataset from Figure 2)
  EISA_fitCircadianPhases_R-code.R
• Supplementary Script 2: Example R code using edgeR (dataset from Figure 3)
  EISA_edgeR_R-code.R

Archives with above files grouped by article figure

Supplementary_Data_1_nonOverlappingGenes.tar (lists of non-overlapping genes, 0.2MB)
Supplementary_Data_2_dataFigure2.tar (data for Figure 2, 7.7MB)
Supplementary_Data_3_dataFigure3.tar (data for Figure 3, 1.0MB)
Supplementary_Data_4_dataFigure4.tar (data for Figure 4, 4.8MB)
Supplementary_Data_5_dataFigure5.tar (data for Figure 5, 7.0MB)
Supplementary_Scripts.tar (Supplementary Scripts 1 and 2)