Gating: The process of classifying cell events into biologically descriptive cell populations and cell states based on marker expression. This involves drawing boundaries or “gates” over specific cell populations to classify those cell populations’ respective lineages.
Clustering: The process of using unsupervised machine learning to identify cell types defined by their expression of markers without prior knowledge of cell populations.
FCS: Flow Cytometry Standard, a .fcs file format for cytometry data containing mass cytometry acquisition events and their associated channel values. The files provided will be version 3.1. Specifications for this format can be found here.
GatingML2.0: a .gatingml file format used to store a representation of cytometry gates. The file format version to be provided will be version 2.0. Specifications for this format can be found here.
Data Description and Usage
Teiko Bio’s analysis produces one FCS file per sample and one GatingML2.0 file per sample. We will also generate five results files per analysis summarizing different outputs of our analysis pipeline:
FCS file per sample. Will provide a directory containing all files per sample.
UMN002_fcs_YYYY_MM_DD_HH_MM_SS
<sample_name>.fcs
Gating ml per sample. Will provide a directory containing all files per sample.
UMN002_gatingml_YYYY_MM_DD_HH_MM_SS
<sample_name>.gatingml
Each file contains metadata to identify results associated with a particular sample and subject.
For example, if a client sends Teiko Bio four cohorts, with nine samples in each cohort (36 samples total), the client will receive 36 FCS files, 36 GatingML files, and the three results files described above.
File Structure
Metadata
Column
Definition
Data Type
Example value(s)
sample_name
Teiko code associated with the patient sample from a single time point
Alphanumeric
UMN002-037
accession_id
Accession number from external CRO, if applicable
Alphanumeric
160816P001
subject_name
Code associated with the patient
Alphanumeric
14020-UMN-6876
metadata_id_1
Any metadata to associate with the sample. For example dosage.
tbd
tbd
…
Any metadata to associate with the sample.
tbd
tbd
metadata_id_n
Any metadata to associate with the sample.
tbd
tbd
File 0: Customer metadata associated with the project. This file is used for reconciliation across files 1 to 5.
Gated population frequencies by sample
Column
Definition
Data Type
Example value(s)
teiko_sample_name
Teiko code associated with the patient sample from a single time point
Alphanumeric
UMN002-037
sample_name
Accession number from external CRO, if applicable
Alphanumeric
160816P001
subject_name
Code associated with the patient
Alphanumeric
14020-UMN-6876
top_level_cell_population
Code defining top-level population of the population being reported
Alphanumeric
nonGRAN
top_level_cell_population_display_name
Top-level population name in plain language
Alphanumeric
non-Granulocyte
cell_population
Code defining population being quantified
Alphanumeric
B_CELL
cell_population_display_name
Population name in plain language
Alphanumeric
B Cell
cell_population_event_count
Number of events associated with population
Numeric
2157
top_level_cell_population_event_count
Number of events associated with top-level population
Numeric
199448
percentage_of_top_level_gate
Percentage of top-level population associated with population
Numeric
1.081485
low_cell_count
Indicates whether a parent population is below (TRUE) or above (FALSE) the threshold for analysis. The standard threshold is 100 cells.
Boolean(TRUE or FALSE)
FALSE
File 1: Gated population frequencies by sample, column descriptions
Gated population cell state frequencies by sample
Column
Definition
Data Type
Example value(s)
teiko_sample_name
Teiko code associated with the patient sample from a single time point
Alphanumeric
UMN002-037
sample_name
Accession number from external CRO, if applicable
Alphanumeric
160816P001
subject_name
Code associated with the patient
Alphanumeric
14020-UMN-6876
parent_cell_population
Code defining the parent population of the population being reported
Alphanumeric
B_CELL
parent_cell_population_display_name
Parent population name in plain language
Alphanumeric
B Cell
cell_state
Code defining population being quantified
Alphanumeric
PDL1
cell_state_display_name
Cell state name in plain language
Alphanumeric
PD-L1
cell_state_event_count
Number of events associated with population
Numeric
1917
parent_cell_population_event_count
Number of events associated with the parent population
Numeric
2157
percentage_of_parent
Percentage of parent population associated with population
Numeric
88.873435
low_cell_count
Indicates whether a parent population is below (TRUE) or above (FALSE) the threshold for analysis. The standard threshold is 100 cells.
Boolean(TRUE or FALSE)
FALSE
File 2: Gated population cell state frequencies by sample, column descriptions.
Gated population marker expression by sample
Column
Definition
Date Type
Example value(s)
teiko_sample_name
Teiko code associated with the patient sample from a single time point
Alphanumeric
UMN002-037
sample_name
Accession number from external CRO, if applicable
Alphanumeric
160816P001
subject_name
Code associated with the patient
Alphanumeric
14020-UMN-6876
parent_cell_population
Code defining parent population of the population being reported
Alphanumeric
B_CELL
parent_cell_population_display_name
Parent population name in plain language
Alphanumeric
B Cell
cell_state
Code defining population being quantified
Alphanumeric
PDL1
cell_state_display_name
Cell state name in plain language
Alphanumeric
PD-L1
is_state_filter_applied
Indicates whether the population contains all cells (FALSE) or only contains cells positive for a specific state marker (TRUE)
Boolean(TRUE or FALSE)
FALSE
<Marker 1 of n> (ex. AREG)
Arcsinh-transformed median channel value of <Marker 1 of n> within the population; if a median channel value was not computed for this marker in this population, the value is reported as <blank>
Numeric
0.093265
<Marker 2 of n> (ex. CCR7)
Arcsinh-transformed median channel value of <Marker 2 of n> within the population; if a median channel value was not computed for this marker in this population, the value is reported as <blank>
Numeric
2.995684
[additional markers]
…
…
<Marker n of n> (ex. VISTA)
Arcsinh-transformed median channel value of <Marker n of n> within the population; if a median channel value was not computed for this marker in this population, the value is reported as <blank>
Numeric
1.484823
File 3: Gated marker expression by sample column descriptions
Clustered population frequencies by sample
Column
Definition
Data Type
Example value(s)
teiko_sample_name
Teiko code associated with the patient sample from a single time point
Alphanumeric
UMN002-037
sample_name
Accession number from External CRO, if applicable
Alphanumeric
160816P001
subject_name
Code associated with the patient
Alphanumeric
14020-UMN-6876
top_level_cell_population
Code defining top-level population of the population being reported
Alphanumeric
nonGRAN
top_level_cell_population_display_name
Top-level population name in plain language
Alphanumeric
non-Granulocyte
cell_population
Code defining population being quantified
Alphanumeric
MONO.0
percentage_of_top_level_gate
Percentage of top-level population associated with population
Numeric
1.8132
cell_population_event_count
Number of events associated with population
Numeric
3611
File 4: Clustered population frequencies by sample column descriptions
Clustered population marker expression by sample
Column
Definition
Date Type
Example value(s)
teiko_sample_name
Teiko code associated with the patient sample from a single time point
Alphanumeric
UMN002-037
sample_name
Accession number from external CRO, if applicable
Alphanumeric
160816P001
subject_name
Code associated with the patient
Alphanumeric
14020-UMN-6876
cell_population
Code defining clustered cell population
Alphanumeric
B_MEM.38
<Marker 1 of n> (ex. AREG)
Arcsinh-transformed median channel value of <Marker 1 of n> within the population; if a median channel value was not computed for this marker in this population, the value is reported as <blank>
Numeric
0.00000
<Marker 2 of n> (ex. CCR7)
Arcsinh-transformed median channel value of <Marker 2 of n> within the population; if a median channel value was not computed for this marker in this population, the value is reported as <blank>
Numeric
2.665345
[additional markers]
…
…
<Marker n of n> (ex. VISTA)
Arcsinh-transformed median channel value of <Marker n of n> within the population; if a median channel value was not computed for this marker in this population, the value is reported as <blank>
Numeric
1.446879
File 5: Clustered populations marker expression by sample
Glossary of Gated Populations (to change depending on project)
