The HybMap microarray was custom designed to represent genes with a range of RSC and ISW1 occupancies, and included 448 coding genes, 93 tRNA genes, and 52 non-coding genes. Gene regions were extended by either 300 bp (coding and non-coding) or 150 bp (tRNA). Probes were selected from a pool of tiled 60mers and adjusted for length to match melting temperatures as necessary. Both strands for each probe were included in the design. Probes have a mean spacing of ~ 50 bp. As a control, 502 probes with sequences from zebra fish were included as non-hybridizing control probes; sequences were confirmed not to have significant homology to yeast sequences.
Description
The column 'Chr_coordinate' represents the original coordinates based on the SGD (Saccharomyces Genome Database) genome release version 55 to which the array was originally designed. These coordinates are also listed in the raw Agilent text data files. The RANGE_START, RANGE_End columns represent the coordinates based on the recent and stable genome version 64 (equivalent to UCSC SacCer3) and the coordinates used in GSE65591 study.
The Chromatin Remodelers RSC and ISW1 Display Functional and Chromatin-based Promoter Antagonism
Data table header descriptions
ID
Agilent feature number
SPOT_ID
The probe name
Column
The column position on the microarray
Row
The row position on the microarray
ControlType
Boolean value for the Agilent control type
Source
The source of the probe sequence: cerevisiae or zebra fish. The zebra fish probes were used for non-hybrdizing signal to determine absolute expression levels.
GB_ACC
GenBank Accession number
Sequence
The sequence of the cerevisiae and zebra fish probes.
GeneName
The name of the gene associated with the region from which the cerevisiae probe was derived.
Chr_coordinate
the original coordinates based on the SGD genome release version 55 to which the array was originally designed
Chromosome
The chromosome name of the unique mapping position of the probe sequence on SGD version 64, UCSC sacCer3
RANGE_START
The start position of the unique mapping position of the probe sequence on SGD version 64, UCSC sacCer3
RANGE_END
The stop position of the unique mapping position of the probe sequence on SGD version 64, UCSC sacCer3
RANGE_STRAND
The strand of the unique mapping position of the probe sequence on SGD version 64, UCSC sacCer3
