Perform a High Density (HD) search

A High Density (HD) search, also known as a zoom-in search, retrieves CGH or ChIP probes that span specific regions of the genome of a given species. For a general discussion of HD Search, see What is a High Density (HD) search?.

eArray provides several different search methods to retrieve HD probes from the eArray HD probe database, based on the way that you specify the regions of the genome to be searched. Click one of the links below for instructions on how to do a specific type of search.

Standard Genomic Intervals HD Search – Available for both HD-CGH and HD-ChIP searches. In this kind of search, you provide the coordinates of genomic regions to search. It lets you apply filters and set the desired probe spacing across all intervals. The result is a balanced probe density across all selected intervals.
Advanced Genomic Intervals HD Search – Available for both HD-CGH and HD-ChIP searches. In this kind of search, as in the Standard Genomic Intervals Search, you provide the coordinates of the genomic regions to search. However, you specify the desired probe density and Hm and Tm filtering for each interval individually. eArray selects probes independently for each interval, even when intervals overlap. An Advanced HD Probe Search takes more time, and the probe density for each of the selected intervals can differ.
Standard Probe ID HD Search – Available for both HD-CGH and HD-ChIP searches. In this kind of search, you provide the names of the desired probes. This is the only kind of HD search that can return probes for multiple species.
Standard Gene Annotations HD Search – Available only for HD-CGH searches. In this kind of search, you provide annotations such as GenBank accession numbers or gene symbols. It lets you apply filters and set the desired probe spacing across all intervals. The search returns HD probes that cover the regions that correspond with the annotations, with a balanced probe density across all selected regions.

Note: Consider using Interval Finder to generate the necessary genomic intervals for certain HD searches. This tool produces a list of genomic intervals that are associated with annotations that you specify.

To do a Standard Genomic Intervals HD Search

Click the Workspace tab (or enter a collaboration).
Set the application type to CGH or ChIP.
In the Probe tab, select HD Probe Search.

The HD Probe Search pane appears. Standard HD Probe Search is selected by default.
In Select HD Search by, select Genomic Intervals.
Set the following search parameters. Parameters that appear on the search page with a red asterisk "*" are required. All other parameters are optional. To restore all parameters to their original states at any time, click Reset.

Parameter	Instructions/Details
Job Information
Search Name	Type a name that will help you later identify the results from this search.
Species	Select the desired species from the list. Information about the applicable current genome build appears in Build Number.
Probe Options
Filters	Select one of the options below. If relevant, a field appears in which you can type a filter value. Click here for a description of how HD search applies filters. None – The program does not apply any of the filters in the list. Average Spacing – Type a number of base pairs in the field that appears. This defines the average number of base pairs between the centers of the retrieved probes in each genomic interval. See Example. Probes Per Interval – Type a number of probes in the field that appears. This defines the maximum number of probes that HD Search retrieves for each genomic interval. See Example. Total Probes – Type a number of probes in the field that appears. This defines the total number of probes HD Search collectively returns for all specified genomic intervals. See Example. Guidance from Agilent on probe density for CGH microarrays
Prefer Catalog Probes	(Available for HD-CGH probe searches) To give preference to Agilent catalog probes in the probe selection process, mark this check box. If two probes are close to each other for a given probe interval, HD search selects the Agilent Catalog probe.
Use TM Filter	For HD-ChIP searches, select YES or NO. For HD-CGH Searches, the program always applies this filter for genomic intervals searches. Most probes in the Agilent HD database have been Tm-matched. However, probes that do not pass the Agilent Tm filters are also available. These probes lie in regions in which no optimal-Tm probes exist. To access these probes, select NO in Use TM Filter. Select YES (the default) if you only want Tm-matched probes.
Similarity Filter	Optimally, Agilent HD probes will hybridize to one, and only one genomic location. However, sequence redundancy is observed within most target genomes. To enable you to investigate non-unique regions, eArray provides probes that hybridize to more than one genomic location. Three options with varying levels of similarity stringencies are provided to select the appropriate subset of probes. The availability of these options varies by species and by application type. No Filter – The program does not apply a similarity filter, and no probes in the queried region are filtered out based on sequence similarity. With this option, the Use Non-Unique Probe Filter option becomes available, which you can use to select an upper limit of probe perfect matches to the genome. Perfect Match Filter – Filters out all probes that have 100% similarity to more than one genomic location. Similarity Score Filter – The most stringent filter. Filters out all probes with secondary genomic alignments that could potentially impact probe performance. Guidance from Agilent on similarity filters for HD-CGH searches In the CGH HD Probe Search, which ‘Similarity Filter’ will work for my design? What are the consequences of using or not using the filters? When ‘No Filter’ is selected any probe may be selected, regardless of similarity to other genomic sites. Keep in mind that data from “non-unique” probes will be harder to interpret, and it can be beneficial to limit the maximum number of perfect genomic hits by using the Non-Unique Probe Filter option. When the Perfect Match Filter (or when the maximum number of perfect genomic hits is set to 1 in the Non-Unique Probe Filter) is selected, probes with more than one perfect match to the genome are excluded and as a result it will not be possible to find probes in Segmental Duplication or Pseudo-Autosomal Regions (PAR). The Similarity Score Filter is the most stringent filter. This filter excludes probes with significant similarity to other sites in the genome and there will be genomic regions where no probes can be found.
Use Non-Unique Probe Filter	(Available if you select No Filter in Similarity Filter) Non-unique probes map to more than one location in the target genome. Mark this check box to remove these probes. When you select this option, Max Perfect Genomic Hits becomes available. By default, this value is set to 1, which removes probes if they map to more than one genomic location. However, you can set this to a higher number. For example, if you type 3 in Max Perfect Genomic Hits, the filter only removes a probe if it maps to four or more locations in the target genome.
Interval Options
Select HD Search by	Keep this parameter set to Genomic Intervals.
Extended Interval Boundary	Type the number of 5' base pairs and 3' base pairs by which you want to move out the start and end points of all of your genomic intervals. This can help retrieve additional probes that lie outside your initially defined regions. For example, if you type 500 in 5' base pairs and 300 in 3' base pairs, eArray extends an original interval of 9000–10000 to 8500–10300.
Genomic Intervals	(Required) Type either a chromosomal location or a cytoband in the box. You can specify multiple intervals separated by pipe "\|" characters, but all of the intervals must be of the same type. See Genomic interval formats. To upload a file of chromosomal locations or cytobands, click Upload. See Upload data for probe searches.
Include Regions	(Available for HD-CGH searches) Select one of the options below. You can use this parameter to restrict your HD-CGH probe search to only exonic, or only intragenic regions of the genome. All – Retrieves probes in all of the specified genomic region, both within and outside of gene boundaries. Exonic – Retrieves probes in exonic sequences within genes in the specified genomic region. When you select this option, the Gene Confidence list appears. Select the appropriate Gene Confidence. Intragenic – Retrieves probes found within gene boundaries, whether or not they are found in exonic sequences. When you select this option, the Gene Confidence list appears. Select the appropriate Gene Confidence. Additional guidance from Agilent on how to target exons In the CGH HD Probe Search, how do I target exons only, not just genes? Using the Include Regions and selecting Exonic will limit the probes returned to those marked as overlapping exons only. This will work when searching by genomic intervals or gene annotations (transcript and gene identifiers). The designer should be aware that exons typically are more GC-rich than the rest of the genome, these probes, in general, will have a lower probe scores. See the FAQ ”What is a CGH probe score?” for more information. Using this “Exonic” approach there is no possibility to select the nearest probes in introns instead. Identify the coordinates for the exons outside of eArray and use them as Genomic Intervals to select probes in. Then with the “Extended Interval Boundary” option in eArray the Genomic Intervals can be extended beyond the exon boundaries with a selected number of base pairs. Here are the instructions on how to identify coordinates for exons in UCSC. Using the Table Browser utility from the UCSC genome browser, make sure the proper species and genome build are selected from the drop-down lists. It is important that the build matches eArray. For “track”, select desired gene definition track, Agilent recommends “CCDS”, “RefSeq Genes”, or “UCSC genes”. Follow the UCSC instructions on how to restrict the search. Options include filtering on genomic regions or track identifiers (names/accessions). Make sure the output contains chrom, exonStarts and exonEnds. This will give you all of the exon coordinates for the regions you defined. To input these locations into an eArray HD Probe Search, split the line into pieces (one for each exon) and adjust the start coordinate (the output is 0-based, eArray expects 1-based). The orientation (i.e., strand information) does not matter in an eArray probe search. For example, the following line defining three exons (chrom; exon count; exon starts; exon ends): chr1; 3; 2450045, 2451144, 2451409; 2451048, 2451310, 2451544 Can be converted to the format needed in eArray.: chr1:2450046-2451048 chr1:2451145-2451310 chr1:2451410-2451544
Standard Exclusion Interval	Agilent provides many sets of standard exclusion intervals, based on annotation tracks. To ignore the genomic regions that are defined in one or more of these sets, mark this option, then select the desired set(s) from the list that appears. Control-click the names of additional sets to select them. During an HD search, exclusion intervals are ignored, and no probes are returned for these regions.
Custom Exclusion Interval	To ignore the genomic intervals defined in a file of genomic intervals, mark this option, then click Upload Interval File. See Upload data for Probe Searches. During an HD search, exclusion intervals are ignored, and no probes are returned for these regions.

Click Search.

eArray begins your requested HD search, and a message informs you that your search has been submitted.
Click OK.

The HD Probe Search page displays your HD search in the Search Results pane at the bottom of the page with a status of Not Started. As eArray performs your HD search, the status of the search changes to Searching, and then to Complete. A status of Failure indicates that an error occurred, and that you must resubmit the search. Click Refresh to view the current status. In the Job Position column, you can track the position of each HD probe search job in the queue. eArray sends you an e-mail when it finishes your search.

From the search results pane, you can take several actions:
- View the results of any HD search with a status of Complete — In the Actions column, click View next to the desired search. See View the High Density (HD) search results. When you view the results, you can also download them and create a probe group with them.
- Delete a search with any status other than Searching — In the Actions column, click Delete next to the desired search. When you delete a search, eArray removes the search and all of its detailed results from the system, but does not remove any probe groups that you created with the search.
- View the search criteria for any search — In the Actions column, click Search Criteria next to the desired search. See View the search criteria for HD searches.
- Sort the order of the HD Search jobs in the list — Click an underlined column heading to sort the list based on the contents of the column. Click the column heading again to reverse the order of the sort.

To do an Advanced Genomic Intervals HD Search

Before you begin, you must have a *.txt file that contains search interval settings. See Upload data for probe searches.

Click the Workspace tab (or enter a collaboration).
Set the application type to CGH or ChIP.
In the Probe tab, select HD Probe Search, then select Advanced HD Probe Search.

The Advanced HD Probe Search pane appears. In Select HD Search by, eArray selects Genomic Intervals automatically. This is the only advanced HD search method currently available.
Set the following search parameters. Parameters that appear on the search page with a red asterisk "*" are required. All other parameters are optional. To restore all parameters to their original states at any time, click Reset.

Parameter	Instructions/Details
Job Information
Search Name	(Required) Type a name that will help you later identify the results from this search.
Species	(Required) Select the desired species from the list. Information about the applicable current genome build appears in Build Number.
Prefer Catalog Probes	(Available for HD-CGH probe searches) To give preference to Agilent catalog probes in the probe selection process, mark this check box. If two probes are close to each other for a given probe interval, HD search selects the Agilent Catalog probe.
Advanced Search Interval	(Required) Follow these steps to upload your file of search interval settings: Prepare a file of intervals and settings. For details, see Upload data for probe searches. Click Browse. A Choose file dialog box appears. Select the desired search intervals file, then click Open. This file must contain the required information for each desired interval Click Upload. The Preview of Search Intervals pane appears. The pane lists the first few rows from the file. To see a list of all of the imported rows, click Show All. If the first row of your uploaded file contains column headings, mark My uploaded file contains column headings. This prevents eArray from interpreting your column headings as actual search interval information. eArray depends on the order of columns, not column headings, to interpret the information in your uploaded file.
Interval Options
Select HD Search by	This parameter is set to Genomic Intervals, and it cannot be changed.
Extend Interval Boundary	Type the number of 5' base pairs and 3' base pairs by which you want to move out the start and end points of all of your genomic intervals. This can help retrieve additional probes that lie outside the initially defined regions of your genomic intervals. For example, if you type 500 in 5' base pairs and 300 for 3' base pairs, eArray extends an original interval of 9000–10000 to 8500–10300.
Include Regions	(Available for HD-CGH searches) Select one of the options below. You can use this parameter to restrict your HD-CGH probe search to only exonic, or only intragenic regions of the genome. All – Retrieves probes in all of the specified genomic region, both within and outside of gene boundaries. Exonic – Retrieves probes in exonic sequences within genes in the specified genomic region. When you select this option, the Gene Confidence list appears. Select the appropriate Gene Confidence. Intragenic – Retrieves probes found within gene boundaries, whether or not they are found in exonic sequences. When you select this option, the Gene Confidence list appears. Select the appropriate Gene Confidence. Additional guidance from Agilent on how to target exons In the CGH HD Probe Search, how do I target exons only, not just genes? Using the Include Regions and selecting Exonic will limit the probes returned to those marked as overlapping exons only. This will work when searching by genomic intervals or gene annotations (transcript and gene identifiers). The designer should be aware that exons typically are more GC-rich than the rest of the genome, these probes, in general, will have a lower probe scores. See the FAQ ”What is a CGH probe score?” for more information. Using this “Exonic” approach there is no possibility to select the nearest probes in introns instead. Identify the coordinates for the exons outside of eArray and use them as Genomic Intervals to select probes in. Then with the “Extended Interval Boundary” option in eArray the Genomic Intervals can be extended beyond the exon boundaries with a selected number of base pairs. Here are the instructions on how to identify coordinates for exons in UCSC. Using the Table Browser utility from the UCSC genome browser, make sure the proper species and genome build are selected from the drop-down lists. It is important that the build matches eArray. For “track”, select desired gene definition track, Agilent recommends “CCDS”, “RefSeq Genes”, or “UCSC genes”. Follow the UCSC instructions on how to restrict the search. Options include filtering on genomic regions or track identifiers (names/accessions). Make sure the output contains chrom, exonStarts and exonEnds. This will give you all of the exon coordinates for the regions you defined. To input these locations into an eArray HD Probe Search, split the line into pieces (one for each exon) and adjust the start coordinate (the output is 0-based, eArray expects 1-based). The orientation (i.e., strand information) does not matter in an eArray probe search. For example, the following line defining three exons (chrom; exon count; exon starts; exon ends): chr1; 3; 2450045, 2451144, 2451409; 2451048, 2451310, 2451544 Can be converted to the format needed in eArray.: chr1:2450046-2451048 chr1:2451145-2451310 chr1:2451410-2451544
Standard Exclusion Interval	Agilent provides many sets of standard exclusion intervals, based on annotation tracks. To ignore the genomic regions that are defined in one or more of these sets, mark this option, then select the desired set(s) from the list that appears. Control-click the names of additional sets to select them. During an HD search, exclusion intervals are ignored, and no probes are returned for these regions.
Custom Exclusion Interval	To ignore the genomic intervals defined in a file of genomic intervals, mark this option, then click Upload Interval File. See Upload data for Probe Searches. During an HD search, exclusion intervals are ignored, and no probes are returned for these regions.

Click Search.

eArray begins your requested HD search, and a message informs you that your search has been submitted.
Click OK.

The HD Probe Search page displays your HD search in the Search Results pane at the bottom of the page with a status of Not Started. As eArray performs your HD search, the status of the search changes to Searching, and then to Complete. A status of Failure indicates that an error occurred, and that you must resubmit the search. Click Refresh to view the current status. In the Job Position column, you can track the position of each HD probe search job in the queue. eArray sends you an e-mail when it finishes your search.

From the search results pane, you can take several actions:
- View the results of any HD search with a status of Complete – In the Actions column, click View next to the desired search. See View the High Density (HD) search results. When you view the results, you can also download them and create a probe group with them.
- Delete a search with any status other than Searching – In the Actions column, click Delete next to the desired search. When you delete a search, eArray removes the search and all of its detailed results from the system, but does not remove any probe groups that you created with the search.
- View the search criteria for any search – In the Actions column, click Search Criteria next to the desired search. See View the search criteria for HD searches.
- Sort the order of the HD Search jobs in the list – Click an underlined column heading to sort the list based on the contents of the column. Click the column heading again to reverse the order of the sort.

To do a Standard Probe ID HD Search

Before you begin, if you have many probes that you want to retrieve, prepare a *.txt file that contains the desired probe IDs. See Upload data for probe searches.

Click the Workspace tab (or enter a collaboration).
Set the application type to CGH or ChIP.
In the Probe tab, select HD Probe Search.

The HD Probe Search pane appears.
In Select HD Search by, select Probe ID.
Set the following search parameters. Parameters that appear on the search page with a red asterisk "*" are required. All other parameters are optional. To restore all parameters to their original states at any time, click Reset.

Parameter	Instructions/Details
Search Name	Type a name that will help you later identify the results from this search.
Probe ID	Type at least one probe ID. Separate multiple probe IDs with pipe "\|" characters. Example: A_14_P100053\|A_14_P100055\|A_14_P100056 You can also upload a .txt file that contains the desired probe IDs. Follow these steps: Click Upload.* A new window appears. Click Browse. A choose file dialog box appears. Select the desired file of probe IDs, then click Open. For information about the required file format, see Upload data for probe searches. Click Upload File. The names of the probes from the file appear in Probe ID.
Select HD Search by	Keep this parameter set to Probe ID.
Species	Select the desired species from the list.

Click Search.

eArray begins your requested HD search, and displays a message that your search has been submitted.

Click OK.

The HD Probe Search page displays your HD search in the Search Results pane at the bottom of the page with a status of Not Started. As eArray performs your HD search, the status of the search changes to Searching, and then to Complete. A status of Failure indicates that an error occurred, and that you must resubmit the search. Click Refresh to view the current status. In the Job Position column, you can track the position of each HD probe search job in the queue. eArray sends you an e-mail when it finishes your search.

From the search results pane, you can take several actions:
- View the results of any HD search with a status of Complete — In the Actions column, click View next to the desired search. See View the High Density (HD) search results. When you view the results, you can also download them and create a probe group with them.
- Delete a search with any status other than Searching — In the Actions column, click Delete next to the desired search. When you delete a search, eArray removes the search and all of its detailed results from the system, but does not remove any probe groups that you created with the search.
- View the search criteria for any search — In the Actions column, click Search Criteria next to the desired search. See View the search criteria for HD searches.
- Sort the order of the HD Search jobs in the list — Click an underlined column heading to sort the list based on the contents of the column. Click the column heading again to reverse the order of the sort.

To do a Standard Gene Annotations HD Search

This search method is only available for HD-CGH probe searches.

Click the Workspace tab (or enter a collaboration).
Set the application type to CGH.
In the Probe tab, select HD Probe Search.

The HD Probe Search pane appears.
In Select HD Search by, select Gene Annotations.
Set the following search parameters. Parameters that appear on the search page with a red asterisk "*" are required. All other parameters are optional. To restore all parameters to their original states at any time, click Reset.

Parameter	Instructions/Details
Job Information
Search Name	Type a name that will help you later identify the results from this search.
Species	Select the desired species from the list. Information about the applicable current genome build appears in Build Number.
Probe Options
Filters	Select one of the options below. If relevant, a field appears in which you can type a filter value. Click here for a description of how HD search applies filters. None – The program does not apply any of the filters in the list. Average Spacing – Type a number of base pairs in the field that appears. This defines the average number of base pairs between the centers of the retrieved probes in each genomic interval. See Example. Probes Per Interval – Type a number of probes in the field that appears. This defines the maximum number of probes that HD Search retrieves for each genomic interval. See Example. Total Probes – Type a number of probes in the field that appears. This defines the total number of probes HD Search collectively returns for all specified genomic intervals. See Example. Guidance from Agilent on probe density for CGH microarrays
Prefer Catalog Probes	(Available for HD-CGH probe searches) To give preference to Agilent catalog probes in the probe selection process, mark this check box. If two probes are close to each other for a given probe interval, HD search selects the Agilent Catalog probe.
Use TM Filter	For HD-ChIP searches, select YES or NO. For HD-CGH Searches, the program always applies this filter for genomic intervals searches. Most probes in the Agilent HD database have been Tm-matched. However, probes that do not pass the Agilent Tm filters are also available. These probes lie in regions in which no optimal-Tm probes exist. To access these probes, select NO in Use TM Filter. Select YES (the default) if you only want Tm-matched probes.
Similarity Filter	Optimally, Agilent HD probes will hybridize to one, and only one genomic location. However, sequence redundancy is observed within most target genomes. To enable you to investigate non-unique regions, eArray provides probes that hybridize to more than one genomic location. Three options with varying levels of similarity stringencies are provided to select the appropriate subset of probes. The availability of these options varies by species and by application type. No Filter – The program does not apply a similarity filter, and no probes in the queried region are filtered out based on sequence similarity. With this option, the Use Non-Unique Probe Filter option becomes available, which you can use to select an upper limit of probe perfect matches to the genome. Perfect Match Filter – Filters out all probes that have 100% similarity to more than one genomic location. Similarity Score Filter – The most stringent filter. Filters out all probes with secondary genomic alignments that could potentially impact probe performance. Guidance from Agilent on similarity filters for HD-CGH searches In the CGH HD Probe Search, which ‘Similarity Filter’ will work for my design? What are the consequences of using or not using the filters? When ‘No Filter’ is selected any probe may be selected, regardless of similarity to other genomic sites. Keep in mind that data from “non-unique” probes will be harder to interpret, and it can be beneficial to limit the maximum number of perfect genomic hits by using the Non-Unique Probe Filter option. When the Perfect Match Filter (or when the maximum number of perfect genomic hits is set to 1 in the Non-Unique Probe Filter) is selected, probes with more than one perfect match to the genome are excluded and as a result it will not be possible to find probes in Segmental Duplication or Pseudo-Autosomal Regions (PAR). The Similarity Score Filter is the most stringent filter. This filter excludes probes with significant similarity to other sites in the genome and there will be genomic regions where no probes can be found.
Use Non-Unique Probe Filter	(Available if you select No Filter in Similarity Filter) Non-unique probes map to more than one location in the target genome. Mark this check box to remove these probes. When you select this option, Max Perfect Genomic Hits becomes available. By default, this value is set to 1, which removes probes if they map to more than one genomic location. However, you can set this to a higher number. For example, if you type 3 in Max Perfect Genomic Hits, the filter only removes a probe if it maps to four or more locations in the target genome.
Interval Options
Select HD Search by	Keep this parameter set to Gene Annotations.
Extended Interval Boundary	Type the number of 5' base pairs and 3' base pairs by which you want to move out the start and end points of all of your genomic intervals. This can help retrieve additional probes that lie outside the initially defined regions of your genomic intervals. For example, if you type 500 in 5' base pairs and 300 for 3' base pairs, eArray extends an original interval of 9000–10000 to 8500–10300.
Gene Annotations	(Required) Type a gene annotation such as a GenBank accession number (for example, NM_016660 or AY884282) or a gene symbol (for example, H3N2 or CTSB) in the box. Use pipe "\|" characters to separate multiple annotations. You can also upload a .txt file of gene annotations. For information on the required file format, see Upload data for probe searches. Follow these steps: Click Upload.* A file name window appears. Click Browse. A file browser appears. Select the desired file, then click Open. The location of the file appears in File Name. Click Upload File. eArray uploads the gene annotations, and displays them in pipe-separated format in the HD search pane. eArray resolves annotations to genomic intervals before it starts your search.
Include Regions	(Available for HD-CGH searches) Select one of the options below. You can use this parameter to restrict your HD-CGH probe search to only exonic, or only intragenic regions of the genome. All – Retrieves probes in all of the specified genomic region, both within and outside of gene boundaries. Exonic – Retrieves probes in exonic sequences within genes in the specified genomic region. When you select this option, the Gene Confidence list appears. Select the appropriate Gene Confidence. Intragenic – Retrieves probes found within gene boundaries, whether or not they are found in exonic sequences. When you select this option, the Gene Confidence list appears. Select the appropriate Gene Confidence. Additional guidance from Agilent on how to target exons In the CGH HD Probe Search, how do I target exons only, not just genes? Using the Include Regions and selecting Exonic will limit the probes returned to those marked as overlapping exons only. This will work when searching by genomic intervals or gene annotations (transcript and gene identifiers). The designer should be aware that exons typically are more GC-rich than the rest of the genome, these probes, in general, will have a lower probe scores. See the FAQ ”What is a CGH probe score?” for more information. Using this “Exonic” approach there is no possibility to select the nearest probes in introns instead. Identify the coordinates for the exons outside of eArray and use them as Genomic Intervals to select probes in. Then with the “Extended Interval Boundary” option in eArray the Genomic Intervals can be extended beyond the exon boundaries with a selected number of base pairs. Here are the instructions on how to identify coordinates for exons in UCSC. Using the Table Browser utility from the UCSC genome browser, make sure the proper species and genome build are selected from the drop-down lists. It is important that the build matches eArray. For “track”, select desired gene definition track, Agilent recommends “CCDS”, “RefSeq Genes”, or “UCSC genes”. Follow the UCSC instructions on how to restrict the search. Options include filtering on genomic regions or track identifiers (names/accessions). Make sure the output contains chrom, exonStarts and exonEnds. This will give you all of the exon coordinates for the regions you defined. To input these locations into an eArray HD Probe Search, split the line into pieces (one for each exon) and adjust the start coordinate (the output is 0-based, eArray expects 1-based). The orientation (i.e., strand information) does not matter in an eArray probe search. For example, the following line defining three exons (chrom; exon count; exon starts; exon ends): chr1; 3; 2450045, 2451144, 2451409; 2451048, 2451310, 2451544 Can be converted to the format needed in eArray.: chr1:2450046-2451048 chr1:2451145-2451310 chr1:2451410-2451544
Standard Exclusion Interval	Agilent provides many sets of standard exclusion intervals, based on annotation tracks. To ignore the genomic regions that are defined in one or more of these sets, mark this option, then select the desired set(s) from the list that appears. Control-click the names of additional sets to select them. During an HD search, exclusion intervals are ignored, and no probes are returned for these regions.
Custom Exclusion Interval	To ignore the genomic intervals defined in a file of genomic intervals, mark this option, then click Upload Interval File. See Upload data for Probe Searches. During an HD search, exclusion intervals are ignored, and no probes are returned for these regions.

Click Search.

eArray begins your requested HD search, and a message appears telling you that your search has been submitted.
Click OK.

The HD Probe Search page displays your HD search in the Search Results pane at the bottom of the page with a status of Not Started. As eArray performs your HD search, the status of the search changes to Searching, and then to Complete. A status of Failure indicates that an error occurred, and that you must resubmit the search. Click Refresh to view the current status. In the Job Position column, you can track the position of each HD probe search job in the queue. eArray sends you an e-mail when it finishes your search.

From the search results pane, you can take several actions:
- View the results of any HD search with a status of Complete — In the Actions column, click View next to the desired search. See View the High Density (HD) search results. When you view the results, you can also download them and create a probe group with them.
- Delete a search with any status other than Searching — In the Actions column, click Delete next to the desired search. When you delete a search, eArray removes the search and all of its detailed results from the system, but does not remove any probe groups that you created with the search.
- View the search criteria for any search — In the Actions column, click Search Criteria next to the desired search. See View the search criteria for HD searches.
- Sort the order of the HD Search jobs in the list — Click an underlined column heading to sort the list based on the contents of the column. Click the column heading again to reverse the order of the sort.