Upload data for probe searches |
When you do certain probe searches, you can upload files that contain entries for specific probe search criteria. For example, in a Standard HD-CGH Genomic Intervals Search, you can upload a file of the desired genomic intervals. This feature is especially useful if you have many items to enter, or need to do several related searches that use the same list of items. The information in this topic also applies when you want to upload a file of search parameters for bait searches in the SureSelect Target Enrichment and SureSelect RNA Enrichment application types.
This help topic contains the following sections:
Information for specific search parameters appears below.
Accessions – For Search Your Probes, Search Your Baits, Exon Probe Search, Interval Finder, and Exon Interval Finder
Put one accession on each line. Enter accession values without sources, as the sources are already provided by eArray. So sgd|Q0055 will be only Q0055.
Advanced Search Interval – For Advanced Genomic Interval HD Search
Put one interval on each line. You can include column headings as the first line of the file, but eArray does not interpret them. Each line must contain the following entries, separated by tabs, in this order:
Genomic Interval – A cytoband (for example, 1p36.33) or a chromosomal location, for example:
chr1:1-500001
chr1 (all of chromosome 1)
chrX:2000500 (X chromosome from 2000500 to the end)
For a given search, all the intervals must be of the same type (for example, all chromosomal locations or all cytobands).
Average Spacing – Average number of base pairs between each of the retrieved probes within the interval.
Guidance from Agilent on probe density for CGH microarrays
TM Filtered – Yes or No. For this interval, removes probes with TMs that lead to poor performance on the Agilent platform.
HM Filtered – Yes or No. Removes probes that bind to more than one location on the genome. (Homology filtering)
Example:
chr1:1-1000000 500 Yes Yes
chr2:500-5000000 1000 Yes No
chr2:5000000-8000000 1000 Yes Yes
Bait ID – For Search Your Baits
Put one bait ID on each line
Bait Sequence – For Search Your Baits
Put one sequence on each line. Use only the capital characters A, C, G, and T. The length of the bait sequences must match the value you select in Length.
Chromosomal Location – For Search Your Probes, Search Your Baits, and Exon Probe Search
Put one chromosomal location on each line. Use the format illustrated in the following examples.
chr1:1-500001 (Chromosome 1, base pairs 1 to 500001)
chr1 (all of chromosome 1)
chrX:2000500 (X chromosome from 2000500 to the end)
Cytoband — For Search Your Probes, Search Your Baits, Exon Probe Search, Interval Finder, and Exon Interval Finder
Put one cytoband on each line.
Exclusion Intervals – For SNP searches by genomic interval, and HD searches
Put one interval on each line.
Gene Annotations – For HD-CGH Gene Annotations Search
Put one annotation on each line. Annotations can be either accession numbers (for example, NM_016660 or AY884282) or gene symbols (for example, H3N2 or CTSB), but for a given search the annotations must all be of the same type.
GeneSymbol – For Search Your Probes, Search Your Baits, Interval Finder, and Exon Interval Finder
Put one gene symbol on each line. Use capital (upper case) letters in gene symbols
Example:
H3N1
CTSB
BRCA1
microRNA name – For microRNA Search Your Probes
Put one microRNA name on each line.
miMAT# – For microRNA Search Your Probes
Put one miMAT# on each line. For example:
MIMAT0000068
MIMAT0000069
Probe ID – For Search Your Probes, HD Probe ID Search, Exon Probe Search, and SNP probe searches by probe ID
Put one probe ID on each line. For example:
A_14_P100053
A_14_P100055
A_14_P100056
A_14_P100057
A_14_P100059
A_14_P100227
Probe Sequence – For Search Your Probes and Exon Probe Search
Put one sequence on each line. For example:
ACGTAGCTAGAGCTAGCTGAGCTGAGCTGAGATCGATGCTAGTGATCGAT
ATTATGGATGATTGATGAGTAGTAGAGAGGCGCGCTAGCATCGCTAGCTA
ACGTACGATAGCGCGCAGCTAATGATGACGCAGATCAGAGACGATCGCGA
CCTACCGATGTCTGCTACAGACGGCGGGGATGACGATACGATACGGCGTG
SNP ID – For SNP probe searches by SNP ID
Put one SNP ID on each line. For example:
rs7172939
rs6549950
rs4490399
If other instructions do not appear in the specific help topic, follow these steps to upload the file.
Next to the desired search criterion, click Upload (or the similarly-named button that appears there).
A file name window appears.
Click Browse.
A Choose File dialog box appears.
Select the desired file, then click Open.
The name of the file appears in File Name.
Click Upload File.
eArray uploads the file, and the entries from the file appear in pipe-separated format in the appropriate box on the search page.
Example 1 – Probe Sequences
To create a text file that contains multiple probe sequences for the Probe Sequence search criterion in Search Your Probes, do the following:
Open a text editor such as Notepad.
Type the first probe sequence, for example:
CCTACTTGACCGGAATGAATCCAATGCTCGGAGCAATGAATGCGGCTCATCAGCACGCGT
Press ENTER.
The insertion point moves to the beginning of a new line.
Type the second probe sequence, for example:
AAATCCAAATGTTATTTATGGACAAACACCAAGGATAACGCCCTATGAGA
Press ENTER. Continue to add more probe sequences, as desired.
Save the text file.
Give the file an extension of .txt
When you upload this file to eArray from the Search Your Probes page, all of the probe sequences appear in pipe-separated format in the search term box in Search Type.
Example 2 – Accessions
To create a text file that contains multiple accession values for the Accessions search criterion for Search Your Probes, follow these steps:
Open a text editor such as Notepad.
Type the first accession value, for example Q0055
Press Enter.
The insertion point moves to the beginning of a new line.
Type the second accession value, for example Q0061
Press Enter, then add more accession values, as desired.
Save the text file.
Give the file an extension of .txt
When you upload this file to eArray from the Search Your Probes page, all of the Accession values appear in pipe-separated format in the search term box in Search Type.
See also