Other TSVs
sample-block
Related files:
- đź“ť Excel template: For metadata entry.
- đź“ť TSV template: Alternative for metadata entry.
Metadata schema
Version 1 (use this one)
version
sample_id
type
source_storage_time_value
source_storage_time_unit
weight_value
weight_unit
volume_value
volume_unit
pathology_distance_value
pathology_distance_unit
preparation_media
preparation_condition
processing_time_value
processing_time_unit
storage_media
storage_method
quality_criteria
histological_report
notes
version
The version of the sample metadata specification used in the submission.
| constraint | value |
|---|---|
| enum | 1 |
| required | True |
sample_id
The unique Submission ID for the sample assigned by the ingest portal. An example value might be “VAN0010-LK-152-162”.
| constraint | value |
|---|---|
| required | True |
type
Denotes the type of sample, used to validate the field entries.
| constraint | value |
|---|---|
| enum | block |
| required | True |
source_storage_time_value
The amount of time that elapsed between when the source was generated and this sample was derived from the source. This would, for example, include how long the source was stored in a freezer.
| constraint | value |
|---|---|
| type | number |
| required | True |
source_storage_time_unit
Time unit. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | min, hours, days, or years |
| required | False |
| required if | source_storage_time_value present |
weight_value
Weight of a tissue block. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
weight_unit
Weight unit. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| enum | mg, g, or kg |
| required if | weight_value present |
volume_value
The volume of a tissue block. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
volume_unit
Volume unit. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| enum | mm^3 or um^3 |
| required if | volume_value present |
pathology_distance_value
If surgical sample, how far from the pathology was the sample obtained. Typically a number of centimeters. Leave blank if not applicable or unknown. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
pathology_distance_unit
Distance unit. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | mm or cm |
| required | False |
| required if | pathology_distance_value present |
preparation_media
The media used during preparation of the sample.
| constraint | value |
|---|---|
| enum | PFA (4%), Buffered Formalin (10% NBF), Non-Buffered Formalin (FOR), 1 x PBS, OCT, CMC, MACS Tissue Storage Solution, RNAlater, Methanol, Non-aldehyde based without acetic acid (NAA), Non-aldehyde with acetic acid (ACA), PAXgene tissue (PXT), Allprotect tissue reagent (ALL), or None |
| required | True |
preparation_condition
The condition under which the preparation occurred, such as whether the sample was placed in dry ice during the preparation.
| constraint | value |
|---|---|
| enum | frozen in liquid nitrogen, frozen in liquid nitrogen vapor, frozen in ice, frozen in dry ice, frozen at -20 C, ambient temperature, or unknown |
| required | True |
processing_time_value
The amount of time that elapsed from beginning of sampling to the first preservation (time from when received in lab to preservation). This would, for example, represent how long it took to cut the tissue and freeze it. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
processing_time_unit
Time unit. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| enum | min, hours, or days |
| required if | processing_time_value present |
storage_media
What was the sample preserved in.
| constraint | value |
|---|---|
| enum | PFA (4%), Buffered Formalin (10% NBF), Non-Buffered Formalin (FOR), 1 x PBS, OCT Embedded, CMC Embedded, OCT Embedded Cryoprotected (sucrose), Paraffin Embedded, MACS Tissue Storage Solution, RNAlater, Methanol, Tris-EDTA, 70% ethanol, Serum + DMSO, DMSO (no serum), PAXgene Tissue Kit (PXT), Allprotect Tissue Reagent (ALL), Sucrose Cryoprotection Solution, Carboxymethylcellulose (CMC), or None |
| required | True |
storage_method
The method by which the sample was stored, after preparation and before the assay was performed.
| constraint | value |
|---|---|
| enum | frozen in liquid nitrogen, frozen in liquid nitrogen vapor, frozen in ice, frozen in dry ice, frozen at -80 C, frozen at -20 C, refrigerator, ambient temperature, incubated at 37 C, none, or unknown |
| required | True |
quality_criteria
For example, RIN: 8.7. For suspensions, measured by visual inspection prior to cell lysis or defined by known parameters such as wells with several cells or no cells. This can be captured at a high level. “OK” or “not OK”, or with more specificity such as “debris”, “clump”, “low clump”. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
histological_report
histopathological reporting of key variables that are important for the tissue (absence of necrosis, comment on composition, significant pathology description, high level inflammation/fibrosis assessment etc. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
notes
Notes. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |