NFR Annotation and Cryptic RNA Analysis

Keyboard and notebook with data

Supplemental Data Files For:

Chromatin Remodeling around Nucleosome-Free Regions Leads to Repression of Noncoding RNA Transcription
Adam N. Yadon, Daniel Van de Mark, Ryan Basom, Jeffrey Delrow, Iestyn Whitehouse, and Toshio Tsukiyama. Mol. Cell. Biol. November 2010 30: 5110-5122; published ahead of print August 30, 2010, doi:10.1128/MCB.00602-10.

Processed data and locations of NFRs, cryptic transcripts, and transcriptional interference loci are located below in tab-delimited text files.  Raw microarray data files are available for download at Gene Expression Omnibus database under accession number GSE23108.

Table S1: Annotated core NFRs (ZIP file 53 kb)

Tab-delimited text file containing the chromosomal location (start and end), annotation (5-NFR, 3’-NFR, ORF-NFR, or Other-NFR), and Isw2 target NFR of each of the consensus NFRs identified.

Table S2:  Analyzed microarray hybridization signals and p-values (ZIP file 33.5 mb)

Tab-delimited text file containing the normalized, log2 microarray signal of each probe for all strains and replicates, the average microarray signal for all probes in each strain, and the calculated p-value for all probes between strains.

Table S3:  Annotated cryptic transcriptional units (ZIP file 18 kb)

 Tab-delimited text file displaying the locations of annotated cryptic transcripts between each strain.  “Pos” indicates an increase in transcription and “Neg” indicates a decrease in transcription across the indicated region for each strain comparison.

Table S4:  Identified transcriptional interference loci (ZIP file 1 kb)

Tab-delimited text file displaying genes identified having transcriptional interference in each strain.