| author | ORC-ID | GitHub | version | created | last edit |
|---|---|---|---|---|---|
Leonardo Mendes-Silva |
1.02 |
20200718 |
20221121 |
The present files shows the strucutre of the .json files designed to log actions done in cell culture. To maintain things simple keep in mind that every entry should be considered as an action executed on a given culture. Also, to keep the format as a standard, below are shown the accepted fields and their respective possible values.
Each time there is a passage it is advised to create a new file for a given culture, instead of adding n-entries; this way the files are separated and the chances of losing all records are reduced in case of a mistake or bug happens -- and also, for the use of Obsidian/RoamResearch each entry being a new note makes it possible to backlink with [[foo]].
Hope that with this it would be easier to track problems, or good results.
When thawing a vial to start a new culture, the identification ("ID") is the ID in the freezing vial (the label should contain the information about the cell line, passage number, and data of storing). Example U2OS P13 ~1M 2022.10.31 leo that reads: U2OS cells on Passage number 13, aproximately 1 million, where frozen on 31th of october 2022 by leo.
- ☝ to avoid confusion the passage number is the number of the passage corresponding to the passage after cells were dissociated before freezing. This way when the cells are thawed the number is the same of that indicated in the vial.
When a field has no data to add, or it is unknown use null e.g passage:
[null], or confluency[null]
Never leave a data field without entry -- if the date of the original vial(s) is not known use either the last recorded date or the date of thawing or use an aproximated date, but take note of that in the comments.
Since each field can take different values, i.e some fields take numbers while other takes text (or strings) it is better to avoid leaving fields in black; either use the appropriate notation null or none: null for fields that are numbers or none for other fields. For example:
- A
passageisnull, because the input must be an integer - A
links_to_experimentisnone, because the name of the experiment is a string or an integer - A
treatmentinnone, because the number of posibilities are fixed but have multiple options
In lab_stage the entry culture means that either the medium was changed or that the cells are comming from a passage (which will be distinguishable from medium change because the dissociation agent will be filled, as well as the ID will have to change to consider the increased passage number).
When recording a passage the fields of confluency, cell_count and viability refer to the mother culture that is ID_mother.
If you want to consider culture splits, a new file for each culture/plate/flask needs to be created if they are going to have different ends. For eample, a passage from a T25 to three P60 would be: (1) "..._P60abc" if they will be pooled for the same experiment, but they should have their unnique ID if they are going to be use differently; thus, three new entries with their ID ending in "..._P60a" + "..._P60b" + "..._P60c", all the the same mother ID
patern text keys:
? -> means characters
## -> means digits, always use two digits e.g. '01' (not just '1')
... -> means that other values/labels can be added to the pool, or the pool can it self be modified
ID -> id_cell_line_passage#_user_vial.no. ????_P##_???## e.g. 20202020_cells_p01_t25
ID_mother -> as for ID
label -> should be the same or short starment of ID
date -> format YYYYMMDD e.g. 20200718
cell_type -> mESC iPSC ...
cell_line -> c2koa e14t la11 ad2 ...
passage -> a number ## e.g. 01; if unknown then use NA
culture_health -> great good ok bad unknown
confluency -> given as % -- a number in the format ##-### without % e.g. 60
lab_stage -> freeze thaw culture discarded experiment ...
culture_medium -> DMEM GMEM DMEM_sup GMEM_sup iPSC mTSER E8 freezing-mix ...
extra_supplements -> 2i LIF-esgro LIF-peptrotech LIF-peptrotech none ...
dissociation_agent -> trypsin accutase tryple dispase mechanic none ...
cell_count -> cells counted after dissociation or seed from frozen vial, expressed as .10^6 -- NA when unkown
viability -> given as % -- a number in the format ##-### without % e.g. 90
treatment -> puromycin none ...
links_to_experiment -> experiment_name/ID none
mycoplasma_free -> yes no unknown
tag_notes -> contamination spontaneous_differentiation other_issue_see_notebook faulty_incubator accident problems_with_freezing sent_to_collaborator sent_to_cell_bank handover none ...
user -> ??? initials of the name of the person that manipulated the cells
comments -> free writing , none
picture_filepicture_file_name_name -> if relevant add the name of a file file_name.jpeg none
Example of a culture that is only being maintained with few to none intermediate interventions (for example, medium changes)
{
"entry01":[
{
"ID" : ["20200103_e14t_p02"],
"ID_mother" : ["20200101_e14t_p01"],
"label" : ["e14t_p02_t25"],
"date" : ["20200103"],
"cell_type" : ["mESC"],
"cell_line": ["e14t"],
"passage" : ["02"],
"culture_health" : ["good"],
"lab_stage" : ["culture"],
"culture_medium" : ["DMEM_sup"],
"extra_supplements": ["2i"],
"dissociation_agent" : ["trypsin"],
"cell_count" : ["1"],
"viability" : ["90"],
"treatment" : ["puromycin"],
"links_to_experiment" : ["experiment_name"],
"mycoplasma_free" : ["unknown"],
"tag_notes" : ["none"],
"user" : ["glados"],
"comments" : ["the cake is a lie"],
"picture_file_name": ["file_name.jpeg"]
}]
}Example for cell culture structure for n-entries for the same flask/culture. When you want to prepare for an experiment (for example, after a passage the culture might need an antibiotic selection)
{
"entry01":[
{
"ID" : [""],
"ID_mother" : [""],
"label" : [""],
"date" : [""],
"cell_type" : [""],
"cell_line" : [""],
"passage" : [""],
"culture_health" : [""],
"confluency": [""],
"lab_stage" : [""],
"culture_medium" : [""],
"extra_supplements" : [""],
"dissociation_agent" : [""],
"cell_count" : [""],
"viability" : [""],
"treatment" : [""],
"links_to_experiment" : [""],
"mycoplasma_free" : [""],
"tag_notes" : [""],
"user" : [""],
"comments" : [""],
"picture_file_name": [""]
}],
"entry0n":[
{
"ID" : [""],
"ID_mother" : [""],
"label" : [""],
"date" : [""],
"cell_type" : [""],
"cell_line" : [""],
"passage" : [""],
"culture_health" : [""],
"confluency": [""],
"lab_stage" : [""],
"culture_medium" : [""],
"extra_supplements" : [""],
"dissociation_agent" : [""],
"cell_count" : [""],
"viability" : [""],
"treatment" : [""],
"links_to_experiment" : [""],
"mycoplasma_free" : [""],
"tag_notes" : [""],
"user" : [""],
"comments" : [""],
"picture_file_name" : [""]
}]
}version edit logs:
V1.0 -- the examples shown here come from routine tasks in the Stem Cell Biology Lab @ Universidade do Algarve -- Centre for Biomedical Research
V1.01 -- review text, replace NA for null
V1.02 -- typos