Other TSVs

sample-section

Related files:

Metadata schema

Version 1 (use this one)

version
sample_id
type
source_storage_time_value
source_storage_time_unit
preparation_media
preparation_condition
processing_time_value
processing_time_unit
storage_media
storage_method
quality_criteria
histological_report
section_thickness_value
section_thickness_unit
section_index_number
area_value
area_unit
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 section
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

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

section_thickness_value

Thickness of the section.

constraint value
type number
required True

section_thickness_unit

Thickness unit. Leave blank if not applicable.

constraint value
enum um, mm, or cm
required False
required if section_thickness_value present

section_index_number

The index number for the section if the sample is a single section.

constraint value
type integer
required True

area_value

The area of a tissue section. Leave blank if not applicable.

constraint value
type number
required False

area_unit

Area unit. Leave blank if not applicable.

constraint value
required False
enum mm^2 or um^2
required if area_value present

notes

Notes. Leave blank if not applicable.

constraint value
required False