Using the RNA-Seq and Microarray Experiment Search
Using the RNA-Seq and Microarray Experiment Search
This help document answers the following questions:
The RNA-Seq and Microarray Experiment Search uses GXD’s standardized metadata annotations to allow users to quickly and reliably find studies of interest that examine expression in adult and embryonic mice. These experiments are stored in EBI's ArrayExpress and NCBI's GEO. Both repositories rely on their submitters to provide the annotations, resulting in samples and experiments being described in a non-standardized fashion with only a limited use of controlled vocabularies. Thus, searching for experiments at either repository is heavily reliant on free text with its attendant pitfalls. Therefore, to facilitate reliable searching for experiments, GXD curators have annotated experiment samples using controlled vocabularies for age, anatomical structure, mutant alleles, and sex. In addition, they have annotated the study type and key variables for each experiment. The integration of these standardized annotations with free text searching of experiment title and description allows for searches that accurately return experiments of interest.
GXD's annotation efforts focus on experiments examining endogenous gene expression in wild-type and mutant mice. Studies from all developmental stages, including adult, are included. In addition, studies examining expression differences within and between species are available (although non-mouse samples are not annotated). As is consistent with GXD policy, studies using transgenic mice (i.e., animals containing randomly inserted transgenes); animals that have been manipulated, either by substances, surgical procedures, or diet regimens; cultured tissues; or cell lines are not included. When we began this project (late 2016) we focused on experiments stored in ArrayExpress and evaluated their relevance to GXD. This included ~3,000 experiments that were directly submitted to ArrayExpress as well as ~13,000 experiments that were originally submitted to GEO (and then imported into ArrayExpress); ~3,200 of these experiments were deemed relevant and curated. In 2022 we shifted our focus to evaluating (and curating) experiments stored in GEO.
Curators rely on the information provided in the repository submission when annotating sample metadata. However, they will consult the publication when clarification/additional information is required.
To browse all annotated experiments in the database, click Search.
To limit your return, enter or select values in one or more of the search form fields described in the following table. After entering values in the search form fields, click Search or use the carriage return to submit the search. Click Reset to clear the fields and return any default values.
| Anatomical structure | Developmental stage | Mutant | Strain | Sex | Method | Text | ID |
| Anatomical structure | Enter an anatomy term to search for experiments with samples derived from that tissue. An autocomplete list activates on the second character. This list shows all the possible anatomy terms and their synonyms that match your search characters. Terms are greyed out if there are no samples annotated to the term.
The anatomical structures are taken from the Mouse Developmental Anatomy Ontology. Any anatomical structure term search will include substructures. This means if you search by "brain," for example, your search will also return annotations for all substructures of brain, such as hypothalamus, telencephalon, and others. |
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| Developmental stage | The Use Ages tab (default) enables searching for experiments with samples of a particular age. You can limit your search to the general terms, Embryonic or Postnatal, or choose specific days post conception (dpc).
Alternatively, you can use the Use Theiler Stages tab to select one or more Theiler stages (TS) to limit your search to samples at a particular stage of embryonic development. The Theiler system organizes development into stages defined by the appearance of specific developmental features. Since embryos of the same gestational age can vary considerably with respect to development, a Theiler stage does not precisely correspond to a particular age. For example, TS 21 applies to embryos between 12.5 and 14.0 days post conception (dpc), while TS 22 applies to embryos between 13.5 and 15.0 dpc. You can browse Stage descriptions for a list of the defining features for each Theiler stage. To select multiple stages or ages:
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| Mutant | To limit your search to experiments that contain mutant samples, enter the symbol, synonym, or MGI marker ID of the mutated genetic marker of interest into the field. |
| Strain | Enter a text string to search the name of the strain annotated to each sample.
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| Sex | Use the radio button to limit the search to experiments that contain samples of a specified sex: Female, Male or Pooled samples. All is selected by default. |
| Method | Use the radio button to limit the search to experiments of the specified type. |
| Text | Enter a text string to search for experiments with titles and/or descriptions that contain the terms of interest.
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| ArrayExpress or GEO ID | Enter one experiment accession number (e.g. E-MTAB-7794, GSE85727). The wild card (*) can be used in this field. |
Yes. If you want to edit a search or change output options:
Yes. You can further refine the list of returned experiments by using the Experimental Variable and Study Type filters found above the Experiment table.
Your search may have been too specific. Try searching for a less specific anatomical structure or more ages. Alternatively, the experiment of interest may not exist or may not have been entered into GXD yet. You may try free-text searching at either ArrayExpress or GEO.
A summary of the search can be found in the You searched for: section at the top of the summary return. The return is sorted by experiment ID; first by GEO ID and then by ArrayExpress ID for experiments lacking GEO IDs.
The search summary presents information about each returned experiment in a table. The following fields are part each experiment’s table:
| Title | Details | Description | Note |
Fifty samples are displayed on each page of the summary return. Use the toggles to navigate the return to see more.
| Name | Organism | Age | Structure | Cell Type | Genetic background | Mutant allele(s) | Sex | Note |
| Name | Of sample. | ||||||||||||||
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| Organism | Species sampled. Only displayed when multiple species are examined. | ||||||||||||||
| Age | Age of the sample used in the experiment. The abbreviations for age annotations are as follows:
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| Structure | Tissue the sample was derived from, given as a Theiler stage (TS) and anatomical structure name. | ||||||||||||||
| Cell Type | Only displayed when annotations are present | ||||||||||||||
| Genetic background | Strain information for the sample, if specified. Use of involves: in the annotation indicates that the strains listed (separated by asterisks) contributed to the genetic background of the sample; additional unspecified strains may also be part of the sample's genetic background. | ||||||||||||||
| Mutant allele(s) | If the sample is a mutant, the allele pairs describing the mutant genotype appear in this field. | ||||||||||||||
| Sex | Sex of the sample, if specified. | ||||||||||||||
| Note | Provides additional information about the sample, if needed. |
Samples that match your search criteria will be displayed in colored-shaded rows.
Note: We do not include detailed metadata about non-mouse samples or mouse samples obtained from transgenic mice (i.e., animals containing randomly inserted transgenes); animals that have been manipulated, either by substances, surgical procedures, or diet regimens; cultured tissues; or cell lines.