Science Glossary
| Term | Abbreviation | Definition |
| Numbers | ||
| 10x genomics | Single-cell RNA-seq (scRNA-seq) technology (file output: .fastq). | |
| A, B, C | ||
| agent | Individual or group that collects, analyzes, or monitors datasets or projects. | |
| aliquot | A subsample of a larger sample that's extracted for analysis. | |
| assay | An investigative (analytic) procedure in laboratory medicine, pharmacology, environmental biology, and molecular biology for qualitatively assessing or quantitatively measuring the presence, amount, or functional activity of a target entity (the analyte). | |
| batch | A set of biological samples processed in tandem, such as a sequencing batch, in which multiple libraries or pools are prepared and submitted together for sequencing. | |
| binary base call format | BCL format | Contains the base calls and quality values for each cycle. These files are generated by the sequencing process. |
| cell barcode | A unique identifier for an individual cell from a well, given a by Cell Ranger in the dry lab (see cell hashing). A sequence that uniquely identifies one or more cells that shared a droplet. Each droplet in a well should have a unique cell barcode, but multiple wells can share a cell barcode. Cell barcodes are attached to 10x GEM beads, and become physically attached to gene sequences during reverse transcription. | |
| cell gating | Placement of gates and regions around populations of cells with common characteristics (see BiteSize Bio). | |
| cell hashing | A combination of methods used to tag individual cells from a number of populations (in our case, usually patient samples) by attaching a population-specific label or barcode. This allows multiple populations to be mixed for experimental steps to reduce handling variation between samples. Later, the original populations can be identified based on their population labels/hashes. | |
| cytometry by time of flight | CYTOF or CyTOF | Use of mass spectroscopy on single cells to measure metal isotope labels on antibodies. |
| cytometer | instrument that counts the blood cells in the common blood test. | |
| cytometry | Measurement of cell characteristics. | |
| D, E, F | ||
| data hydration | Filling in an object or structured entity with data from various sources. | |
| dataset | A collection of files generated in a single acquisition or analysis session. | |
| decorator service | Microservice designed and built by the AIFI software development team to tag files/data with metadata. | |
| FASTQ format | Text-based sequencing data file format that stores both raw sequence data and quality scores and is refined via BCL. | |
| flow cell | A component of Illumina sequencing. A glass slide containing small fluidic channels (lanes) onto which one or more sequencing libraries or sequencing pools are applied. Each flow cell has one or more lane(s) (depending on the sequencer). Our pipeline work is performed on sequencers with multiple lanes. Lab pilots are performed on a MiSeq, which has a single lane. | |
| flow cytometry | Technique in which a laser is used to detect and measure physical and chemical characteristics of a population of cells or particles. | |
| flow cytometry standard | FCS | A data file standard developed in 1984 for reading and writing data from flow cytometry experiments (see the Wikipedia entry on this topic). |
| G, H, I | ||
| gating, supervised | The traditional, typically manual process of distinguishing types of cell, such as T cells and B cells. Experts decide on a particular method and series of steps to do the gating. When the process is automated, software runs through that series of steps, mimicking the behavior of a subject matter expert. | |
| gating, unsupervised | Analysis of data distribution to arrive at the statistically most promising way to cluster groups of cells. | |
| Globus | A commercial research data management service (see the company's website). | |
| h5 | A scientific data file that's saved in the hierarchical data format (HDF) and contains multidimensional arrays. | |
| hashtag oligo | HTO | Application of a piece of single-stranded DNA to a cell-surface-targeted antibody in order to tag all cells in an individual sample for the purpose of identification (see cell hashing). These antibodies should be able to bind to all cell types. HTOs contain a barcode sequence (an HTO barcode) that can be used to identify a population of cells labeled with this antibody after capture and sequencing. |
| hierarchical stochastic neighbor embedding | HSNE | Technique used for analysis of mass cytometry data sets. HSNE constructs a hierarchy of non-linear similarities that can be interactively explored with a stepwise increase in detail up to the single-cell level. |
| high-performance computing | HPC | |
| Human Immune System Explorer | HISE | Open science platform used to share, analyze, and interpret studies of the human immune system in health and disease. |
| i7 index | Identifier for a 10x chromium well channel. | |
| J, K, L | ||
| lab, dry | Refers to any lab work that does not involve a physical lab. | |
| lab, wet | Refers to any lab work involving a physical lab. | |
| laboratory information management system | LIMS | A software system for efficient, compliant laborabory operations, such as management of samples and resulting data sets. |
| ledger data service | LDS | The store for ingested data of all types, including samples, subjects, subject lab results, and survey data. |
| ligand | A molecule that binds to another (usually larger) molecule. | |
| M, N, O | ||
| metadata | User-defined data enabling interpretation of primary data. | |
| P, Q, R | ||
| PCR primer | A (usually short) single strand of DNA used to initiate PCR. Primers set the boundaries of the DNA to be copied/amplified. They can be used to add Indexes to the ends of pieces of DNA. | |
| policy group | A group of agents with a shared access policy. | |
| polymerase chain reaction | PCR | A method for copying (often called "amplifying") specific DNA sequences. |
| pool | A mixture of biological samples that are then processed together as a single entity. | |
| pool/batch | In the context of cell hashing, a pool or batch consists of one group of samples uniquely labeled by HTO. | |
| pool, sample | A sample pool is a mixture of patient samples, usually after each sample has been separately labeled by cell hashing. | |
| pool, sequencing | A sequencing pool is a mixture of sequencing libraries that is applied together to one or more flow cells. | |
| project | Work with a common purpose associated with one or more datasets. | |
| pub/sub | A publisher–subscriber relationship in the cloud (see What is Cloud Pub/Sub?). | |
| S, T, U | ||
| sample | Genetic data attributed to an individual. | |
| Scientific Advisory Board | SAB | The advisory board for the Allen Institute. |
| TEA-seq | Trimodal assay for integrated single-cell measurement of transcription, epitopes, and chromatin accessibility. | |
| toolchain | Set of programming tools used to perform a complex software development task or to create a software product, which is typically another computer program or a set of related programs. | |
| V, W | ||
| well | A physical vessel used by the 10x chromium device to handle and process genetic data. | |
| X, Y, Z |