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 |
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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)