Wells
The Wells section includes the WellLocation, WellLabel, CellType, and CellDiameter columns. When the Wells section is populated, the WellLabel and WellLocation columns are required. When the Wells section is unpopulated or the user does not include a run manifest in run planning, then the default well label of every well is the well's location (example, A1).
Columns
| Column | Constraints | Definition | Allowed Values |
|---|---|---|---|
WellLocation | Required | The location of the well on the flow cell. | Valid values for this column are a letter and number combination, where the letter is between A–F and the number is between 1–2. Use + to link multiple locations. |
WellLabel | Required | The label for the well(s) that are specified in the well location column. | 1–64 case-sensitive alphanumeric characters, hyphens (-), and underscores (_) |
CellType | Optional | The cell type in the well(s). This determines the segmentation model that is used onboard the instrument. | HeLa, HUVEC, PC-3, Hep-G2, MCF-7, HCT-116, Jurkat, SH-SY5Y, or Other. All values are agnostic to spaces, capitalization, or hyphens. |
CellDiameter | Optional | The predicted diameter, in pixels, of the cell line in the well(s). The conversion from pixels to diameter is size (µm) = size (pixels) * 0.48 (µm/pixel). This field is used to improve onboard cell segmentation performance when the well contains a cell type of "Other". Otherwise, the segmentation model for the specified cell type is used. | Numeric values above 15 |
TargetSites | Optional | (For Teton Atlas™ and only for use with a Target Cell Assignment manifest) If left blank and the run has target to cell assignment, then it is assumed that all targets are present in all wells. To add multiple targets to one well, use + to separate targets. | Valid values are None, blank (empty), or target site names that are composed of 1–64 case-sensitive alphanumeric characters, hyphens (-), and underscores (_) |
Custom Sample-Level Metadata
Custom columns are an optional addition to the Samples section and specify additional key-value metadata for samples. Custom columns must meet the following requirements:
- Each custom column name is unique and includes case-sensitive variations.
- A custom column cannot have the same name as a required column.
- When a sample name is repeated, each corresponding value in the custom column must match exactly.
- The key character limit is 1–64. Valid characters include lower- and upper-case letters, numbers, hyphens, and underscores.
- The value character limit is 0–255 ASCII characters.
Well Specification Examples
The following examples show how to construct a manifest for specific use cases:
Defining Cell Type for a 1-Well Flow Cell
Define HeLa as the cell type for a culture in a 1-well flow cell:
[Wells],,,,
WellLocation,WellLabel,CellType
A1,Well_One_Label,HeLa
Adding Custom Metadata for a 12-Well Flow Cell
Add a custom column, Custom_Metadata, with metadata Well_1_metadata, Well_2_metadata, and Well_3_metadata, and so on:
[Wells],,,,
WellLocation,WellLabel,CellType,CellDiameter,Custom_Metadata
A1,Well_1_Label,HeLa,,Well_1_metadata
A2,Well_2_Label,HeLa,,Well_2_metadata
B1,Well_3_Label,HeLa,,Well_3_metadata
B2,Well_4_Label,HeLa,,Well_4_metadata
C1,Well_5_Label,HeLa,,Well_5_metadata
C2,Well_6_Label,HeLa,,Well_6_metadata
D1,Well_7_Label,HeLa,,Well_7_metadata
D2,Well_8_Label,HeLa,,Well_8_metadata
E1,Well_9_Label,HeLa,,Well_9_metadata
E2,Well_10_Label,HeLa,,Well_10_metadata
F1,Well_11_Label,HeLa,,Well_11_metadata
F2,Well_12_Label,HeLa,,Well_12_metadata
Adding Custom Metadata for a 48-Well Flow Cell
Add a custom column, Custom_Metadata, with metadata Well_1_metadata, Well_2_metadata, and Well_3_metadata, and so on:
[Wells],,,,
WellLocation,WellLabel,CellType,CellDiameter,Custom_Metadata
A1,Well_1_Label,HeLa,,Well_1_metadata
B1,Well_2_Label,HeLa,,Well_2_metadata
C1,Well_3_Label,HeLa,,Well_3_metadata
D1,Well_4_Label,HeLa,,Well_4_metadata
E1,Well_5_Label,HeLa,,Well_5_metadata
F1,Well_6_Label,HeLa,,Well_6_metadata
G1,Well_7_Label,HeLa,,Well_7_metadata
H1,Well_8_Label,HeLa,,Well_8_metadata
I1,Well_9_Label,HeLa,,Well_9_metadata
J1,Well_10_Label,HeLa,,Well_10_metadata
K1,Well_11_Label,HeLa,,Well_11_metadata
L1,Well_12_Label,HeLa,,Well_12_metadata
A2,Well_13_Label,HeLa,,Well_13_metadata
B2,Well_14_Label,HeLa,,Well_14_metadata
C2,Well_15_Label,HeLa,,Well_15_metadata
D2,Well_16_Label,HeLa,,Well_16_metadata
E2,Well_17_Label,HeLa,,Well_17_metadata
F2,Well_18_Label,HeLa,,Well_18_metadata
G2,Well_19_Label,HeLa,,Well_19_metadata
H2,Well_20_Label,HeLa,,Well_20_metadata
I2,Well_21_Label,HeLa,,Well_21_metadata
J2,Well_22_Label,HeLa,,Well_22_metadata
K2,Well_23_Label,HeLa,,Well_23_metadata
L2,Well_24_Label,HeLa,,Well_24_metadata
A3,Well_25_Label,HeLa,,Well_25_metadata
B3,Well_26_Label,HeLa,,Well_26_metadata
C3,Well_27_Label,HeLa,,Well_27_metadata
D3,Well_28_Label,HeLa,,Well_28_metadata
E3,Well_29_Label,HeLa,,Well_29_metadata
F3,Well_30_Label,HeLa,,Well_30_metadata
G3,Well_31_Label,HeLa,,Well_31_metadata
H3,Well_32_Label,HeLa,,Well_32_metadata
I3,Well_33_Label,HeLa,,Well_33_metadata
J3,Well_34_Label,HeLa,,Well_34_metadata
K3,Well_35_Label,HeLa,,Well_35_metadata
L3,Well_36_Label,HeLa,,Well_36_metadata
A4,Well_37_Label,HeLa,,Well_37_metadata
B4,Well_38_Label,HeLa,,Well_38_metadata
C4,Well_39_Label,HeLa,,Well_39_metadata
D4,Well_40_Label,HeLa,,Well_40_metadata
E4,Well_41_Label,HeLa,,Well_41_metadata
F4,Well_42_Label,HeLa,,Well_42_metadata
G4,Well_43_Label,HeLa,,Well_43_metadata
H4,Well_44_Label,HeLa,,Well_44_metadata
I4,Well_45_Label,HeLa,,Well_45_metadata
J4,Well_46_Label,HeLa,,Well_46_metadata
K4,Well_47_Label,HeLa,,Well_47_metadata
L4,Well_48_Label,HeLa,,Well_48_metadata
Assigning Information to Multiple Well Locations
For multiple well locations, associate a set of well information and include the well label, cell type, and cell diameter:
[Wells],,,,
WellLocation,WellLabel,CellType,CellDiameter
A1+A2,Well_A_Label,HeLa,
B1+B2,Well_B_Label,Other,30
C1+C2,Well_C_Label,Other,45
D1+D2,Well_D_Label,Jurkat,
E1+E2,Well_E_Label,Huvec,
F1+F2,Well_F_Label,HeLa+Jurkat,
Adding TargetSites to a 12-Well Target Cell Assignment Manifest
For Teton Atlas runs with a Target Cell Assignment manifest, add a TargetSiteNames column with targets 1_FirstTarget for a well with a single target, or 1_FirstTarget+2_SecondTarget for a well with multiple targets:
[Wells],,,,
WellLocation,WellLabel,CellType,TargetSiteNames,Custom_Metadata
A1,thisiswell_1,Hela,1_FirstTarget,
A2,thisiswell_2,Hela,1_FirstTarget,
B1,thisiswell_3,Hela,1_FirstTarget,
B2,thisiswell_4,Hela,1_FirstTarget,
C1,thisiswell_5,Hela,1_FirstTarget,
C2,thisiswell_6,Hela,1_FirstTarget+2_SecondTarget,
D1,thisiswell_7,Hela,2_SecondTarget,
D2,thisiswell_8,Hela,2_SecondTarget,
E1,thisiswell_9,Hela,2_SecondTarget,
E2,thisiswell_10,Hela,2_SecondTarget,
F1,thisiswell_11,Hela,2_SecondTarget,
F2,thisiswell_12,Hela,2_SecondTarget,