Sample attributes
Custom and predefined sample attributes can be viewed in the Samples table in Ion Reporter™ Software. Each column in the Samples table represents a single sample attribute.
A set of default columns is always visible in the table. You can also add additional attributes to the table. To add more attribute columns to the table, or create a reusable table preference, see Customize the Samples table. After you add more attributes to the table, you can further customize the table with filters that you can use to find the attributes. For more information, see Find samples.
Several sample attributes can be edited in Ion Reporter™ Software. For more information, see Edit a sample, Edit a sample used in an analysis, and Define samples with a CSV file.
Each description indicates which attributes cannot be changed.
Attribute |
Description |
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Default columns—These columns are selected by default when you open the Samples table if no table preferences are applied. |
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Selection checkbox—Use to select samples to include in analyses. |
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Analyzed sample—Indicates that the sample has already been analyzed. |
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Locked sample—Indicates that the sample attributes cannot be edited. After a sample is locked, the sample attributes and the files that make up the sample cannot be edited. |
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Transferred sample—Indicates that the sample was transferred to a user in another organization. |
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The name of the sample. |
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Information about the gender of the sample. |
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Information about the type of sample. |
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A list of one or more project names that have been associated with a sample. |
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The role in a pair or a group of samples, such as mother, father, proband, or unknown. |
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The user name of the person who imported the sample. |
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The date that the sample was imported. |
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Available columns—These attributes can be added to the Samples table. |
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Only one bacterial marker type can be associated with each barcode in a sample. |
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The name of the specific barcode in the selected barcode kit. This attribute cannot be changed. |
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The time point post-fertilization at which the biopsy was taken from an embryo. |
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The type of cancer of the sample. |
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The cell count of the biopsy material. |
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The number assigned to the chip. This attribute cannot be changed. |
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The chip type, such as Ion 550™ Chip. This attribute cannot be changed. |
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The control kit used when preparing the sample. This attribute cannot be changed. |
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An identifier for use with the Reproductive research application. |
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The number of the sequencing instrument. This attribute cannot be changed. |
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The number or name assigned to the embryo. |
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The name of the sequencer. This attribute cannot be changed. |
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The type of sequencer, such as Ion GeneStudio™ S5 Sequencer. This attribute cannot be changed. |
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The software version number for the IonReporterUploader plugin. This attribute cannot be changed. |
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The name of the library kit used to prepare the sample. This attribute cannot be changed. |
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If a mouse sample was used, the strain of the mouse sample. For use with the T-cell and B-cell receptor sequencing analyses. Samples that use the mouse strain attribute can be added to a custom analysis workflow. Available options are based on the most common mouse strains in the IRGT database. |
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The percent of tumor cells in the sample. IMPORTANT! Do not change this setting for workflows that are used with the Oncomine™ TagSeq Breast DNA Regions, Oncomine™ TagSeq Lung DNA Regions, and Ion AmpliSeq™ HD assays. These assays are targeted to cell free DNA (cfDNA) and do not estimate tumor cellularity because calls are based on P values and cannot be quantified as a ploidy value. |
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The name of the Planned Run used in Torrent Suite™ Software. This attribute cannot be changed. |
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The ethnicity indicator for the sample. If European is selected, the haplotype of a T-Cell receptor is included in the analyses results for an Ion AmpliSeq™ Immune Repertoire Assay Plus—TCRβ assay. You can download a corresponding Haplotype Group Assignment plot. For more information about a TCRB-LR assay, see Immune repertoire analysis results Note: The haplotype assignment compares a query sample against a reference database that is derived from European ethnicity samples. You must therefore select the European population value to assign a haplotype. The haplotype assignment will be blank if other population values are selected. The super populations from the 1000 Genomes Project are available as values. For information about super populations, see www.1000genomes.org. |
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The date of the sequencing run. This attribute cannot be changed. |
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The number of the sequencing run. This attribute cannot be changed. |
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The name of the Planned Run used in Torrent Suite™ Software. This attribute cannot be changed. |
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The date that the sample was collected from the biological subject. The Sample Collection Date must precede the Sample Receipt Date. |
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The date that the sample was received by the processing laboratory. The Sample Receipt Date must be later than or the same as the Sample Collection Date. |
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A unique identification code (SampleID) for each barcode in a sample. This helps to track samples or possibly identify misassignment between samples and barcodes in a sequencing run. If you manage samples in an external system (for example, a LIMS), you can use the identifier from that system. This attribute cannot be changed. |
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The name of the sample preparation kit used in Torrent Suite™ Software. This attribute cannot be changed. |
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The name of the sequencing kit used in Torrent Suite™ Software. This attribute cannot be changed. |
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This value defines the type of sequencing run, for example, Single End or Paired End. In single-end reading, the sequencer reads a fragment from only one end to the other, generating the sequence of base pairs. In paired-end reading, it starts at one read, finishes this direction at the specified read length, and then starts another round of reading from the opposite end of the fragment. In the software, "FRAGMENT" appears for Single End and "PE" appears for Paired End. This attribute cannot be changed. |
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The name of the templating kit used in Torrent Suite™ Software. This attribute cannot be changed. |
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The name of the hotspots file used in Torrent Suite™ Software. This attribute cannot be changed. |
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The name of the target regions file used in Torrent Suite™ Software. This attribute cannot be changed. |
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The name of the Torrent Suite™ Software run report. This attribute cannot be changed. |
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The Torrent Suite™ Software version number. This attribute cannot be changed. |
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Custom attributes are denoted with an asterisk (*) in the available columns list. Each custom attribute is listed in the Samples table and included in a CSV file of sample attributes. |