Use Study and Cohort Tags
 | Abbreviations Key |
| BR | Benaroya Research Institute |
| CRA | contractor risk agreement |
| CU | University of Colorado–Anschutz Medical Campus |
| EMR | electronic medical record |
| FH | Fred Hutchinson |
| HISE | Human Immune System Explorer |
| IDE | integrated development environment |
| IRB | institutional review board |
| JAK | Janus kinase |
| MTA | material transfer agreement |
| PBMCs | peripheral blood mononuclear cells |
| PID | program ID (not affiliated with HISE) |
| PLAN | pathway-level analysis of networks |
| SLIMS | Simple Laboratory Information Management System |
| SOP | standard operating procedure |
| STAT | signal transducer and activator of transcription |
| TEA-seq | transcripts, epitopes, and chromatin accessibility sequencing |
At a Glance
To associate your files with specific samples during data ingestion into the Project Store, the subjects, samples, and specimens must be ingested from SLIMS with cohort tags or study tags assigned at the project level in HISE.
Description
Proper tagging is a fundamental best practice that enables us to enable track HISE data as it's stored, transformed, or moved through the analysis pipeline. Descriptive tags help us track data provenance and produce accurate certificates of reproducibility. Study and cohort labels remain independent of one another, since samples from a single cohort can be used in multiple studies.
Study Tags
SLIMS administrators generate study tags that you can assign to individual sample content in the SLIMS system. If the tags you need aren't available, work with your SLIMS administrator to create them.
In the context of SLIMS, a study tag indicates what the sample was used for (for example, the biological hypothesis or scientific methodology). Study tags are generated when a study is initiated. These tags show what scientific question is being asked. The following are examples of study tags:
- PLAN-00054 10x Multiome / TEA-seq
- PLAN-00072 JAK/STAT
Cohort Tags
A cohort is a group of subjects from a common origin (for example, Seattle Children's Allenspach Lab) who share certain characteristics, such as age and health status (for example, young, healthy adults). For convenience, the term cohort is sometimes used interchangeably to refer to the subjects themselves or to the set of samples provided by those subjects. However, only subjects (people) can be enrolled into cohorts.
When AIFI receives a set of samples, the Laboratory Operations team generates cohort tags to indicate the origin of the material. Cohort tags are linked to legal agreements that specify proper handling and show who has assumed responsibility for the samples. To comply with IRB requirements, users can define and restrict sample types by cohort (for example, a user could specify that only PBMCs can be collected for a given cohort). The following are examples of cohort tags:
FH1; FH3
UP2
CU1
BR1; BR2
Cohort Assignment and Study Enrollment
As a reminder, use the "Enroll Sample in Study" macro on the SLIMS Protocol tab. Sample content is imported into HISE by one of two mechanisms:
| Mechanism | Description |
| Cohort assignment | When AIFI receives a set of samples, they're automatically assigned to a subject cohort. |
| Study enrollment | Sample content can then be enrolled in a study when it's used in a lab procedure, assay, experiment, or similar process. Study enrollment isn't required, but we strongly encourage it as a means of tracking sample material and managing its use. To enroll sample content in a study, follow the instructions below: 1. Click on the sample content to be enrolled. 2. From the Selection menu, choose Enroll content. 3. In the Study field, choose a study from the drop-down list. Your sample is then updated with a study tag that identifies the data and its corresponding samples in HISE. If legal/regulatory data is available, those values populate here as well. |
Related Resources