The repository stores the codes and data files collected in an experiment in which protein restricted and non-restricted mice were placed in choice boxes to choose between diets varying in nutritional value to test their preference as a function of their diet history.
Age: 6 weeks at the time of arrival, ~8 weeks at the begining of the experiment depending on batch number
The figures show the overview of the 4 batches used in this experiment, plus the overall protocol for each cohort of animals and the choices in "food preference sessions"
- 2 main cohorts of protein-restricted and non-restriced mice, each containing 20 mice distributed in 4 batches
- FEDXD01-10 F and FEDXD01-10 M are protein-restricted(PR) mice
- FEDXD11-20 F and FEDXD11-20 M are non-restricted(NR) mice
- This Metafile shows the corresponding batches for each mouse
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All the mice started with 3 days of training with FEDs filled with a 50%-50% mix of Casein 5% and 20% pellets. On the first day the FEDs are set on free-feeding mode and for the next 2 days on FR1 mode.
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After training, depending on the batch number, the mice experienced 0-2 days of gap in standard cages with access to regular chow.
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Susbsequently PR mice were maintained on 5% Casein pellets(large pellets in standard cages, not FED cages) for 7 days.
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NR mice were maintained on 20% Casein pellets (large pellets in standard cages, not FED cages) for 7 days.
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After 7 days on diet, mice were placed in choice boxes(each mouse in a FED cage with access to two separate FED units at the same time)
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As shown in the figure at the top of this page, the routine of choice sessions for each diet group(PR and NR ) is as follows: 7 days standard cage with large pellets special diet → 1 day choice session 1 (FR1 20% vs 5% casein) → 3 days standard cage/large pellet/special diet → 1 day choice session 2 (FR1 20% casein vs Sucrose) → 3 days standard cage/large pellet/special diet → 1 day choice session 3 (FR 5% casein vs Suc) → 3 days standard cage/large pellet/special diet → choice session 4 (CE 5% casein vs Suc)
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Auxiliary procedure: After all choice sessions were over, mice spent 3-7 days in standard cages maintained on their original special diet and then finally were scanned in EchoMRI mahchine.
- From the first day of training, bodyweight was measured every 3 days, i.e. 9 times in total.
- The weight of the pellets in the standad dispenser was once measured after 7 days on special diet → then measured every 3 days , i.e. on each choice session day when the animals were transfered to choice boxes.
- /data stores FED files obtained during training and choice sessions
note1: FED015_041223_00.CSV and FED016_041623_00.CSV are corrupted, i.e FED15 and FED16 did not save the data on choice session 1 and 2 for mouse FEDXDM18, so must be excluded from analysis.
note2: Due to failure in some of the FED units, mice FEDXD12F because of FED JAMMING on the 3rd session and, FEDXD15M, FEDXD20F and FEDXD20M because of program error on FED units did not have their choice session on the designated dates. Therefore after the last session for the rest of the mice, these 4 mice experienced 3 more days on special diet in standard cages and afterwards were placed in choice boxes for their corresponding sessions.
IMPORTANT note3: FED005 did not store the the data of humidity and temprature due a failure in the sensor, therefore I added two empty columns to all the files generated by FED005 at 05 April 2024, these two extra columns after data-time column is needed to place the "pellet count" column at the correct order for my script
IMPORTANT note4: Mouse FEDXDM18 is excluded from metafile and I am not using the data of this mouse for choice session 1 and session 2, that is because one of the FEDs in that choice box failed to store the data for an unknown reason therefore we can not consider the data of a single FED as a "choice experiment" -- although the FED worked and delivered pellets but did not store the data!
- /notebooks will store python scripts to analyse or plot data
- /plots contains plots generated either via python script or plots obtained from FED3VIZ
- /results This file FEDXD_CHOICE_RESULTS_OVERALL.xlsx stores all the data of bodyweight, food intake, EchoMRI and data extracted from FED files via FED3VIZ
- /source containes figure files or any potential .py fi
Look at the Metafile for an overview of diets, batches, session numbers, etc.