Microarray design files available for download

SureDesign offers many different microarray design files for download. See the table below for a description of each file.

Files for custom microarray designs (CGH, CGH+SNP, ChIP, and CH3)

CGH and CGH+SNP designs created in SureDesign with the standard CGH wizard have two design files that pertain to the design as a whole, as well as additional design files that pertain to the individual probegroups within the design.

Files for the whole design
[design name/ID]_Report.pdf	This PDF contains summary information on the submitted targets, probe selection parameters, coverage statistics, and overall success of the design in covering the targets. This same information, and additional information, is provided in spreadsheet format in the Report text file.
[design name/ID]_Report.txt	This text file contains summary information on the design, the probes, the targets, and the parameters used to create the design.
[design name/ID]_D_yyymmdd.gal	If you will be using an Axon microarray scanner, the GenePix software will need this file to process the images. The file provides details on the microarray's block information along with the probes information associated with each block. The probe information includes gene name, accession number, and description.
[design name/ID]_D_BED _yyymmdd.bed	This BED file lists the chromosome number, start position, end position, and external probe ID associated with each probe in the design.
[design name/ID]_D_DNABack_BCLeft _yyymmdd.tdt	If you will be using a 3rd party microarray scanner (other than the Axon GenePix), the scanner's software will need this file to process the images. The file lists the location of each probe in the design (from back, left orientation) along with its accession number, gene name, performance score, and other information.
[design name/ID]_D_DNAFront_Bottom _yyymmdd.tdt	If you will be using a 3rd party microarray scanner (other than the Axon GenePix), the scanner's software will need this file to process the images. This tab-delimited text file lists the location of each probe in the design (from front, bottom orientation)along with its accession number, gene name, performance score, and other information.
[design name/ID]_D_F_yyymmdd.xml	This XML file contains probe information including sequence and genomic coordinates.
[design name/ID]_D_Fasta_yyymmdd.txt	This text file contains the probe sequences in FASTA format.
[design name/ID]_D_GeneList_yyymmdd.txt	This text file lists the gene names, gene symbols, and accession numbers associated with each probe.
[design name/ID]_D_GEO_yyymmdd.txt	This text file lists the location of each probe on the microarray. The file is formatted to allow it to be uploaded into the NCBI GEO repository.
[design name/ID]_D_NormalizedProbes _yyymmdd.txt	This text file lists the probe IDs, genomic coordinates, and gene names for the normalizer probes. The file is used by Agilent's Feature Extraction software to process scanner images.
[design name/ID]_D_SequenceList _yyymmdd.txt	This text file lists the probes IDs and sequences of the probes in the design.
Files for the biological probegroup
[probegroup name]_Report.txt	This file contains summary information on the CGH probes, the targets, and the parameters used to create the design.
[probegroup name]_Regions.bed	This BED file contains a single track of the target regions of interest that SureDesign used to select the probes. You can use this track to see the exact regions that the program was attempting to cover when selecting the probes.
[probegroup name]_Covered.bed	This BED file contains a single track of the genomic regions that are covered by one or more CGH probes in the design, as based on median probe spacing. The fourth column of the file contains annotation information. You can use this file for assessing coverage metrics.
[probegroup name]_AllTracks.bed	This multitrack BED file includes the following tracks: The Target Regions track is identical to the track in the Regions BED file. The Covered track is identical to the track in the Covered BED file. The Missed Regions track contains any regions from the Target Regions track that are not included in the Covered track. The Probes track contains the regions of all CGH probes in the design.
[probegroup name]_Probes.txt	This file is a list of the CGH probes in the design, with specific information about each probe, including its probe ID, sequence, genomic coordinates, and the target it is intended to capture.
[probegroup name]_ReportDetails.txt	This file is only generated for advanced CGH and CGH+SNP designs and probegroups in which HD probes were selected using the Average Probe Spacing option and the target regions of interest were focused regions. For each target interval, this file displays the results of the probe search, including the total probes, the medium probe spacing, the extension size, and whether or not the search retrieved the desired minimum number of probes.
[probegroup name]_Targets.txt	This file contains a list of the target identifiers that you entered when creating the design.
Files for the backbone probegroup
[probegroup name]_Report.txt	This file contains summary information on the backbone probes included in the design.
[probegroup name]_Regions.bed	This BED file contains a single track of the target regions of interest that SureDesign used to select the probes. You can use this track to see the exact regions that the program was attempting to cover when selecting the probes.
[probegroup name]_Covered.bed	This BED file contains a single track of the genomic regions that are covered by one or more backbone probes in the design, as based on median probe spacing.
[probegroup name]_AllTracks.bed	This multitrack BED file includes the following tracks: The Target Regions track is identical to the track in the Regions BED file. The Covered track is identical to the track in the Covered BED file. The Missed Regions track contains any regions from the Target Regions track that are not included in the Covered track. The Probes track contains the regions of all backbone probes in the design.
[probegroup name]_Probes.txt	This file is a list of the backbone probes in the design, with specific information about each probe, including its probe ID, sequence, genomic coordinates, and other annotations.
Files for the normalization probegroup
[probegroup name]_Covered.bed	This BED file contains a single track of the genomic regions that are covered by one or more normalization probes in the design, as based on median probe spacing.
[probegroup]_Report.txt	This file lists the total number of normalization probes in the design.
[probegroup name]_AllTracks.bed	This BED file contains a single track of the regions of all normalization probes in the design.
Files for the replicate probegroup
[probegroup name]_Covered.bed	This BED file contains a single track of the genomic regions that are covered by one or more replicate probes in the design, as based on median probe spacing.
[probegroup]_Report.txt	This file lists the total number of replicate probes in the design.
[probegroup name]_AllTracks.bed	This BED file contains a single track of the regions of all replicate probes in the design.
Files for the SNP probegroup (for CGH+SNP designs only)
[probegroup name]_Probes.txt	This file is a list of the SNP probes in the design, with specific information about each probe.
[probegroup name]_Covered.bed	This BED file contains a single track of the genomic regions that are covered by one or more SNP probes in the design, as based on median probe spacing.
[probegroup]_Report.txt	This file contains summary information on the SNP probes included in the design.