Ghavi-Helm_2008_PMID_18628399.README
Last modified: 2016-04-20

Ghavi-Helm Y, Michaut M, Acker J, Aude JC, Thuriaux P, Werner M,
Soutourina J (2008) Genome-wide location analysis reveals a role of
TFIIS in RNA polymerase III transcription. Genes Dev 22(14):1934-47
PMID: 18628399

Ghavi-Helm et al. performed a genome-wide location analysis on the
transcription elongation factor TFIIS and RNA polymerase II and III,
finding an unexpected role in RNA polymerase III transcription.

A short summary of the contents of each data file compiled by SGD can
be found in the following secion. More in depth details can be found
within the file header of each file.

Data files last modified: March 19, 2012
SGD has compiled the following data files from this publication:

Ghavi-Helm_2008_WT_RNA_PolII_YPD_16C_ChIP_chip_V64.bedgraph
Ghavi-Helm_2008_WT_RNA_PolII_YPD_30C_ChIP_chip_V64.bedgraph

Ghavi-Helm_2008_WT_TFIIS_YPD_30C_ChIP_chip_V64.bedgraph
Ghavi-Helm_2008_WT_TFIIS_SD_30C_ChIP_chip_V64.bedgraph
Ghavi-Helm_2008_WT_TFIIS_SDMPA_30C_ChIP_chip_V64.bedgraph

Ghavi-Helm_2008_WT_RNA_PolIII_YPD_16C_ChIP_chip_V64.bedgraph
Ghavi-Helm_2008_WT_RNA_PolIII_YPD_30C_ChIP_chip_V64.bedgraph

Ghavi-Helm_2008_Dst1_RNA_PolIII_SC-L_16C_ChIP_chip_V64.bedgraph
Ghavi-Helm_2008_dst1_R200A_RNA_PolIII_SD-L_16C_ChIP_chip_V64.bedgraph
Ghavi-Helm_2008_dst1_E291A_RNA_PolIII_SC-L_16C_ChIP_chip_V64.bedgraph
Ghavi-Helm_2008_dst1D_RNA_PolIII_YPD_16C_ChIP_chip_V64.bedgraph

Ghavi-Helm_2008_Dst1_RNA_PolII_SC-L_16C_ChIP_chip_V64.bedgraph
Ghavi-Helm_2008_dst1_R200A_RNA_PolII_SC-L_16C_ChIP_chip_V64.bedgraph
Ghavi-Helm_2008_dst1_E291A_RNA_PolII_SC-L_16C_ChIP_chip_V64.bedgraph
Ghavi-Helm_2008_dst1D_RNA_PolII_YPD_16C_ChIP_chip_V64.bedgraph

These files were compiled from the processed data files "FGEM1.txt"
and "FGEM2.txt" provided to the authors to ArrayExpress under the
accession E-MTAB-10, representing normalized measured log2 ChIP-chip
ratios. Reported probe identifiers in "FGEM1.txt" and "FGEM2.txt" were
matched with the feature coordinates associated with the microarrays
used by the authors in their study, under accession numbers
A-MEXP-1053 and A-MEXP-1113 in ArrayExpress. According to the
microarray manufacturer documentation, the probes were designed based
on the October 2003 (sacCer1) genome sequence.

The feature coordinates were mapped to SGD V27 (October 2003, sacCer1)
version of the S. cerevisiae genome as reported by the authors
(Ghavi-Helm_2008_PMID_18628399_V27_track_files.zip) and lifted over to
the latest version (SGD V64, February 2011) by SGD in
Ghavi-Helm_2008_PMID_18628399_V64_track_files.zip.

The following contains features that could not be mapped from V27 to V64:
Ghavi-Helm_2008_dst1D_RNA_PolIII_SC-L_16C_ChIP_chip_V27toV64_unmapped.txt
Ghavi-Helm_2008_dst1D_RNA_PolIII_YPD_16C_ChIP_chip_V27toV64_unmapped.txt
Ghavi-Helm_2008_dst1D_RNA_PolII_SC-L_16C_ChIP_chip_V27toV64_unmapped.txt
Ghavi-Helm_2008_dst1D_RNA_PolII_YPD_16C_ChIP_chip_V27toV64_unmapped.txt
Ghavi-Helm_2008_dst1_E291A_RNA_PolIII_SC-L_16C_ChIP_chip_V27toV64_unmapped.txt
Ghavi-Helm_2008_dst1_E291A_RNA_PolII_SC-L_16C_ChIP_chip_V27toV64_unmapped.txt
Ghavi-Helm_2008_dst1_R200A_RNA_PolIII_SD-L_16C_ChIP_chip_V27toV64_unmapped.txt
Ghavi-Helm_2008_dst1_R200A_RNA_PolII_SC-L_16C_ChIP_chip_V27toV64_unmapped.txt
Ghavi-Helm_2008_WT_RNA_PolIII_YPD_16C_ChIP_chip_V27toV64_unmapped.txt
Ghavi-Helm_2008_WT_RNA_PolIII_YPD_30C_ChIP_chip_V27toV64_unmapped.txt
Ghavi-Helm_2008_WT_RNA_PolII_YPD_16C_ChIP_chip_V27toV64_unmapped.txt
Ghavi-Helm_2008_WT_RNA_PolII_YPD_30C_ChIP_chip_V27toV64_unmapped.txt
Ghavi-Helm_2008_WT_TFIIS_SD_30C_ChIP_chip_V27toV64_unmapped.txt
Ghavi-Helm_2008_WT_TFIIS_SDMPA_30C_ChIP_chip_V27toV64_unmapped.txt
Ghavi-Helm_2008_WT_TFIIS_YPD_30C_ChIP_chip_V27toV64_unmapped.txt


Additional supplementary information:
ArrayExpress accession: E-MTAB-10

http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-10