Experimental Mapping Data Records
Experimental Mapping Data Records
This document provides a brief description of the fields and values in the query results for:
See also:
MGD contains genetic mapping and linkage data, including haplotype data for linkage crosses, recombinant inbred (RI) strain distribution patterns, in-situ hybridization data, deletion mapping information, translocation breakpoint mapping, somatic cell hybrids, concordance tables, congenic strain information, and physical mapping information. Genetic Mapping Data records have the following fields:
| FIELD | DESCRIPTION |
|---|---|
| Experiment Type | Experiment types include Cross, RI, Hybrid, In Situ (including FISH), Contig, TEXT: Physical Mapping, TEXT: QTL, and TEXT: Radiation Hybrid. |
| Reference | J number (MGI accession ID format for references), Primary author, Journal, Date, Issue, Pages) |
| Ref Comment | Comments by data editors |
| Experiment | Name of experiment |
| Chromosome | Chromosome |
| Markers | Markers reported on in the experiment include: symbol, assay-type, description. |
In addition, fields related to experiment type appear in query results. The fields for each experiment type appear in subsections that follow.
TopMIT created a physical map of the mouse by screening MIT primers against a large YAC library (WI/MIT-820) and building a contig map of the mouse genome. The goal was to include 10,000 markers (roughly 7000 MIT primers and 3000 STSs). This mapping information has been downloaded into MGD. To accommodate this information and make it accessible, the experiment type CONTIG has been added to the MGD mapping data set. There is one experiment per chromosome. An "experiment," in this case, consists of a set of ordered contigs assigned to a chromosome. For each contig, the following information is available:
| FIELD | DESCRIPTION |
|---|---|
| Name | Name of the contig. For example, WC11.21. Each contig name is linked to "hit" data, i.e., a record showing a correlation between STS primers and target YAC. |
| Chromosome | Chromosome mapped by contig |
| Reference Accession ID | Unique ID for the reference. |
| cM Range | Estimate of cM range covered by the contig. |
| STSs | Ordered set of STSs. An STS may be designated by an MIT primer symbol, or GenBank ID. The STS symbol is linked to the probe record for the STS |
| FIELD | DESCRIPTION | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| MGD Accession ID | Unique MGD ID assigned to an experiment record (format: MGD-CREX-####....) These numbers not assigned to new records after May 1997. | ||||||||||
| MGI Accession ID | Unique ID assigned to an experiment record in MGD. Format: MGI:####, Range: 1-up. These IDs are assigned to all experiment records as of June 1997. | ||||||||||
| Type | Type of cross (backcross, intercross, etc.) AND gender of F1 parent. | ||||||||||
| Female Parent | Genotype of female parent. | ||||||||||
| Strain | Strain of female parent. | ||||||||||
| Male Parent | Genotype of male parent. | ||||||||||
| Strain | Strain of male parent. | ||||||||||
| Whose Cross | Last name of person or laboratory responsible for the mapping panel. | ||||||||||
| Symbols | Symbols used to designate progenitor alleles. | ||||||||||
| Matrix Data | Tabular representation of the typing of progeny resulting from the specified cross. (Note that for some experiments, matrix data are not available; in such cases, only 2 X 2 data are displayed reporting # of RIs and parentals.) The fields are described below:
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The RI/RC Data Line represents the strain distribution pattern with respect to a particular marker in the given experiment.
| FIELD | DESCRIPTION |
|---|---|
| Origin | Progenitor strain of the RI strain set. |
| Designation | RI strain set name. |
| Abbrev1,2 | Abbreviations for progenitor alleles. |
| RI Data | The RI Data Line represents the strain distribution pattern with respect to a particular marker in the given experiment. Tabular display includes - Marker - RI Data Line. |
| Notes | Text entered by MGD editors. |
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| FIELD | DESCRIPTION |
|---|---|
| Band assignment | Cytogenetic band of marker |
| Cell type | Type of cell analysed in metaphase spread |
| Strain | Mouse strain of origin for cell type |
| Karyotype method | Method of staining chromosomes in the metaphase spread |
| Robertsonian translocation | Chromosome aberration used to identify marker assignment |
| # metaphases analyzed | # of metaphase spreads analyzed in expt. |
| Total # Single signals | # of single fluorescent signals indicating presence of marker as reported by authors |
| Total # Double signals | # of double fluorescent signals indicating presence of marker as reported by authors |
| Region/Single-/Double signals | Tabular representation of signals |
| Label | Type of fluorescent label on probe |
For this type of experiment, the somatic cell hybrid data are presented in a table indicating the presence or absence of a particular marker or chromosome vs. the presence or absence of the marker being tested for linkage.
Concordance Values are given as a table with the following columns:
Experimental results may be discussed in a paper but the actual data are not included in the report. In the case of Physical Mapping reports, the experimental results are given a text description. The record may include distances between markers in a tabular representation which includes the following columns:
This record contains the following fields:
Experimental results may be discussed in a paper but the actual data are not included in the report. In the case of QTL experiments, the experimental results are described in the Notes field.
This record contains the following fields:
Experimental results may be discussed in a paper but the actual data are not included in the report. In the case of radiation hybrid experiments, the experimental results are described in the Notes field.
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