Effects of short photoperiod and carbohydrate consumption on sleep, liver steatosis, and the gut microbiome in diurnal grass rats
Data files
Dec 18, 2023 version files 1.86 MB
Abstract
Seasonal affective disorder (SAD) is a recurrent depression triggered by exposure to short photoperiods, with a subset of patients reporting hypersomnia, increased appetite, and carbohydrate craving. Dysfunction of the microbiota–gut–brain axis is frequently associated with depressive disorders, but its role in SAD is unknown. Nile grass rats (Arvicanthis niloticus) are potentially useful for exploring the pathophysiology of SAD, as they are diurnal and have been found to exhibit anhedonia and affective-like behavior in response to short photoperiods. Further, given grass rats have been found to spontaneously develop metabolic syndrome, they may be particularly susceptible to environmental triggers of metabolic dysbiosis. We conducted a 2x2 factorial design experiment to test the effects of short photoperiod (4h:20h Light:Dark (LD) vs. neutral 12:12 LD), access to a high concentration (8%) sucrose solution, and the interaction between the two, on activity, sleep, liver steatosis, and the gut microbiome of grass rats. We found that animals on short photoperiods showed disrupted activity and sleep patterns but maintained robust diel rhythms and similar subjective day lengths as controls in neutral photoperiods. We found no evidence that photoperiod influenced sucrose consumption. By the end of the experiment, some grass rats were overweight and exhibited signs of non-alcoholic fatty liver disease (NAFLD) with micro- and macro-steatosis. However, neither photoperiod nor access to sucrose solution significantly affected the degree of liver steatosis. The gut microbiome of grass rats varied substantially among individuals, but most variation was attributable to parental effects and the microbiome was unaffected by photoperiod or access to sucrose. Our study indicates short photoperiod leads to disrupted activity and sleep in grass rats but does not impact sucrose consumption or exacerbate metabolic dysbiosis and NAFLD.
README: SAD rats: Effects of short photoperiod and carbohydrate consumption on sleep, liver steatosis, and the gut microbiome in diurnal grass rats
General Info
Dataset contains 4 zipped files, corresponding to data used for analysis. AnimalData.zip contains data files (in .csv format) to analyze data corresponding to animal weights, fat pad data, liver steatosis data, and phase 1 and phase 2 animal metadata. ConsumptionData.zip contains all data (in .csv format) necessary for analyze sucrose/water consumption stats. microBiome.zip contains data files (in .csv, .qza, and .txt format) necessary to analyze fecal/intestine microBiome data. sleepData.zip contains all data to analyze sleep data obtained from the piezo system.
We used a 2x2 experimental design, with animals subjected to either a short (4h Light: 20h Dark [4:20 LD]) or neutral (12:12 LD) photoperiod and provided with either access to 8% sucrose or only water. Room temperatures were always maintained at 22°C. Grass rats were given ad libitum food (Prolab RMH 2000 5P06 rodent chow from PMINutrition International, St. Louis, Missouri, USA) and ad libitum water access from a water bottle. Every three days, slip cages and bottles were changed, and animals were weighed. Prior to the experiment, animals were co-housed with littermates on a neutral photoperiod (lights on: 05:00-17:00). Animals were then moved into individual cages and provided two weeks to acclimate to their experimental rooms prior to altering photoperiod. After acclimation, we kept 23 rats (11 males, 12 females) on this neutral photoperiod, and shifted 22 rats (10 males, 12 females) to the short photoperiod treatment (lights on: 09:00-13:00). Four weeks later, half of the animals were given a second bottle with sucrose solution whereas the other half were given a second bottle of water. At the end of the experiment, animals were euthanized (using CO2), weighed, fat pads were extracted and weighed, liver samples were taken, and fecal pellets were extracted from the large intestine. Liver samples were fixed in 10% buffered formalin, trimmed, and then stained with a hematoxylin & eosin (H&E) stain. Fecal samples from the large intestine were immediately frozen on dry ice and then stored at -80°C for further analyses. Fecal samples were also collected directly from animal tubs (Trial 2 only) for microbiome analyses immediately prior to photoperiod treatment (0 weeks), after 4 weeks of photoperiod treatment, and at the end of the experiment after 7 weeks of photoperiod treatment and 3 weeks of sucrose treatment.
Description of the data and file structure
All data filenames are referenced in the appropriate code (upload on github: https://github.com/ckdeal/Grass_Rats)
Data files:
AnimalData:
Data in this folder are used to calculate animals weight data, fat pad data, liver steatosis data. Folder has metadata files to correlate animals to other experimental information.
Animal_weights_forMassChange.csv
Chamber_Animal_IDs_Sex_bothPhases.csv
Fat_pads.csv
Merged_Liver.csv
Meta_litter_parents.csv
metadata.csv
--Information relevant for Chamber_Animal_IDs_Sex_bothPhases.csv:
Number of variables: 23
Number of rows: 47
Variable list:
GrassRat_ID - Unique animal identifier
Phase - specifies if animals were in phase 1 or phase 2 of the experiment
Chamber - Chamber room animals were located
Sex - male (M) or female (F)
Photoperiod - Photoperiod treatment animals were subjected too, Short or Long
Sugar_conc - Sugar concentration animals were given in bottle; 0 - no sugar, 0.02 - 2% sugar concentration, 0.04 - 4% sugar concentration, 0.06 - 6% sugar concentration, 0.08 - 8% sugar concentration
Sugar - Animals were under No sugar (0 sugar_conc) or High sugar (0.08 sugar_conc) treatment
Parent_Sire - Unique ID of animals biological father
Parent_Dame - Unique ID of animals biological mother\
ParentPair - Animals were obtained from 4 parental pairs (1- pair 1, 2- pair 2, 3 - pair 3, 4 - pair 4)
Litter - Litter that animal belonged to.
AgeAtDeath_days - Age in days (from birth (0), to death) animals died
Percent_liver_fat - Percent area of liver occupied by fat (NA values indicate no measurement taken)
Weight g - Weight of animals (in grams) and time of death
Fat_pad_wt_g - Weight of fat pad (in grams) and time of death
DOB_Day - Day of birth
DOB_Month - Month of birth\
DOB_Year - Year of birth
DOB_MMDDYYYY - combined date of birth (mm/dd/yyyy)
DOD_Day - Day of death
DOD_Month - Month of death
DOD_Year - Year of death
DOD_MMDDYYYY - combined date of death (mm/dd/yyyy)
--Information relevant for Animal_weights_forMassChange.csv:
Number of variables: 20
Number of rows: 45
Variable list:
Individual - Unique animal identifier
Litter - Litter that animal belonged to.
Room - Room identifier animals were kept in
Sugar - Animals were under No sugar (0 sugar_conc) or High sugar (0.08 sugar_conc) treatment
Photoperiod - Photoperiod treatment animals were subjected too, Short or Long
Group - Specify if animals were under short photoperiod and high or low sugar (ShortHigh or ShortNone) or long photoperiod and high or low sugar (NeutralHigh or NeutralNone)
DOB_Day - Day of birth
DOB_Month - Month of birth\
DOB_Year - Year of birth\
DOB - Date of birth (mm/dd/yyyy)
Euthanized_date - Date (mm/dd/yyyy) animals were euthanized
Age_death - Age (in days) at death
Chamber - Chamber room animals were located
Weight_start - Weight (in grams) at start of experiment under Short or Neutral/Long photoperiods
Weight_2wk - Weight (in grams) after 2 weeks under Short or Neutral/Long photoperiods
Weight_presugar - Weight (in grams) under Short or Neutral/Long photoperiods prior to recieving high or no sugar.
Weight_euthanasia - Weight (in grams) at time of euthanasia under ShortNone, ShortHigh, NeutralHigh, or NeutralNone treatments
pct_2wk - Percent change in body weight after 2 weeks under Short or Neutral/Long photoperiods
pct_presugar - Percent change in body weight prior to switching to recieveing suagr treatments
pct_euthanasia - Percent change in body weight at time of euthanasia
--Information relevant for Fat_pads.csv:
Number of variables: 6
Number of rows: 46
Variable list:
Individual - Unique animal identifier
Treatment - Animals under different photoperiod treatments (Short or Neutral/Long)
Sex - male (M) or female (F)
Weight g - Animal body weight (in grams) at time of euthanasia\
Fat_pad_wt_g - Fat pad weight (in grams) at time of euthanasia
Sugar - Animals were under high sugar yreatment (Y) or no sugar treatment (N)
--Information relevant for Merged_liver.csv:
Number of variables: 33
Number of rows: 70
Variable list:
ID - Unique animal ID
Phase_Slide_Casette_Region - Animals phase (1 or 2), slide number, cassette number tissue is mounted in, region of liver imaged\
Slice - .tif formats of prior Phase_Slide_Cassette_Region
Count - Count (number) of steatosis idetified in liver
TotalArea - Area that the count occupied
AverageSize - Average size (mm) of liver steatosis
PercentArea - Percent area that the liver steatosis occupied in the image
Mean -
Slide - slide number
Casette - cassette number tissue is mounted in
Region - region of liver imaged
Slide_Casette_Region - slide number_cassette number tissue is mounted in_region of liver imaged
Size - size range in an image
Size_units - units of the image size range, inches square (in2) or micrometer (um2)
Cropped - Image cropped (Y) or not cropped (N)
Distance_calibrated - Was image dstance calibrated (Y) or not (N)
Circularity - Range of image particle circularity between polygon shape (0.5)to a perfect circle (1.0)
ColorThreshold - ImageJ color threshold value
X - Specifies manual thresholding
AutoThresholdWas - Auto color threshold value specified by ImageJ
Use - Was authotheshold value used (Y) or not used (N)
Microsteatosis_0min_4max - Range of microsteatosis from not present (0) to very present (4)
Checked_With_Original Image verification check (Y)
Phase - Animals in epxeriment Phase 1 (1) or phase 2 (2)
Comments - Imager comments
CropArea - Crop area used (value) or not used (NA)
NecropsyID - Necropsy identifier
Chamber - Chamber animals was housed in (1-24)
Photoperiod - Animals under Neutral/Long or Short experimental photoperiod
Sugar - Animals were under No sugar (0 sugar_conc) or High sugar (0.08 sugar_conc) treatment
AgeAtDeath_days - Age (in days) at death
Sugar_conc - No sugar (0 sugar_conc) or High sugar (0.08 sugar_conc) treatment
PhotoSugar - Specify if animals were under short photoperiod and high or low sugar (ShortHigh or ShortNone) or long photoperiod and high or low sugar (NeutralHigh or NeutralNone)
--Information relevant for Meta_litter_parents.csv:
Number of variables: 13
Number of rows: 47
Variable list:
GrassRat_ID - Unique animal ID
Parent_Sire - Unique ID of animals biological father
Parent_Dame - Unique ID of animals biological mother\
ParentPair - Animals were obtained from 4 parental pairs (1- pair 1, 2- pair 2, 3 - pair 3, 4 - pair 4)
Litter - Litter that animal belonged to.
AgeAtDeath_days - Age in days (from birth (0), to death) animals died
Percent_liver_fat - Percent area of liver occupied by fat (NA values indicate no measurement taken)
Phase - specifies if animals were in phase 1 or phase 2 of the experiment
Chamber - Chamber room animals were located
Sex - male (M) or female (F)
Photoperiod - Photoperiod treatment animals were subjected too, Short or Long
Sugar_conc - Sugar concentration animals were given in bottle; 0 - no sugar, 0.02 - 2% sugar concentration, 0.04 - 4% sugar concentration, 0.06 - 6% sugar concentration, 0.08 - 8% sugar concentration
Sugar - Animals were under No sugar (0 sugar_conc) or High sugar (0.08 sugar_conc) treatment
--Information relevant for metadata.csv:
Number of variables: 25
Number of rows: 161
Variable list:
SampleID - Unique animal identifier for microbiome analysis
Type - Tissue type taken, Int: Intestine sample; Fecal: Fecal sample
Daylength - Photoperiod treatment, Normal/Long or Short
Sample - Sample identifier A, B, C or D
Experimental.Trial - Treatment animals were under. 2wk acclim: 2 weeks of acclimation to Neutral/Long photoperiod; 4wk photoperiod: 4 weeks under Neutral/Long or Short photoperiods; 0% HCS: animals recieving no sugar solution; 8% HCS: animals recieving 8% sugar solution. NA specify animals not under any specific experimental trial and are disregarded in downstream analysis.
GrassRat_ID - Unique animal identifier
Trial - Which phase animals were in, 1 or 2
Sex - male (M) or female (F)
Sucrose - Animals given sugar (yes) or not (no)
Sugar_conc - Sugar concentration animals were given in bottle; 0 - no sugar, 0.08 - 8% sugar concentration
Photoperiod - Animals under Neutral/Long or Short photoperiod
Chamber - What experimental chamber animals were in
Plate - PCR plate identifier (A or B)
PCRRow - What row of the PCR plate sample was in
PCRCol - What column of the PCR plate sample was in
TrialA - Which phase animals were in, 1 or 2
LightDay - Numeric for if animals were under Neutral/Long photoperiod (12) or Short photoperiod (4)
TubeID - Microcentrifuge tube ID samples were in
Parent_Sire - Unique ID of animals biological father
Parent_Dame - Unique ID of animals biological mother\
ParentPair - Animals were obtained from 4 parental pairs (1- pair 1, 2- pair 2, 3 - pair 3, 4 - pair 4)
Litter - Litter that animal belonged to.
AgeAtDeath_days - Age in days (from birth (0), to death) animals died
Percent_liver_fat - Percent area of liver occupied by fat (NA values indicate no measurement taken)
ConsumptionData:
Data files in this folder are used to calculate sugar consumption data across the various experimental treatments and phases. The sleep data is included in this folder to calculate the time spent asleep while animals were on high (8%) sucrose during the second phase of the experiment.
Phase2_8%sucrose_12Aug2019_long.csv
Phase2_8%sucrose_12Aug2019_short.csv
Phase2_8%sucrose_21Aug2019_short.csv
Phase2_8%sucrose_30Aug2019_short.csv
SucroseTest.csv
SugarConcTest_weights_05Feb2020.csv
--Information relevant for Phase2_8%sucrose_12Aug2019_long.csv, Phase2_8%sucrose_12Aug2019_short.csv, Phase2_8%sucrose_21Aug2019_short.csv, and Phase2_8%sucrose_30Aug2019_short.csv:
Number of variables: 18, 50 or 60
Number of rows: 23
Variable list; these are common variable names shared across the files, and only differ by the numeric at the end, which corresponds to the day/night, i.e., PERCENTSLEEPTOT1 and PERCENTSLEEPTOT2 correspond to percentage sleep for day/night or day/night 2:
MOUSE_ID - Unique animals identifier
TESTDATE - Date of when sleep data is recored (mm/dd/yyyy)
PERCENTSLEEPTOT - Total percentage of time spent asleep
PERCENTSLEEPNIGHT - Percentage of time spent asleep during the night\
PERCENTSLEEPDAY - Percentage of time spent asleep during the day\
BOUTLENGTHTOT - Total percentage of sleep bouts across day and night
BOUTLENGTHNITE - Total percentage of sleep bouts across the night
BOUTLENGTHDAY - Total percentage of sleep bouts across the day
DIURNAL WAKE RATIO - Ratio of time awake versus asleep during the active period
PEAKACT - Maximum peak amplitude value across the day and night
--Information relevant for SucroseTest.csv, SugarConcTest_weights_05Feb2020.csv, SugarConcTest_weights.xlsx; All share the same variables. Primary difference between the five is SucroseTest.csv and is cleaned to contain sugar consumption information for animals under high (8%) or no (0%) sugar solution; SugarConcTest_weights_05Feb2020.csv and SugarConcTest_weights.xlsx are identifical, except SugarConcTest_weights.xlsx contain formulas in cells for calculations of sugar/water solutions consumed during the experiment:
Number of variables: 30
Number of rows: 1182
Variable list:
IndivSugarDay - Unique animals ID, sugar treatment: 0 - no sugar, 0.02 - 2% sugar concentration, 0.04 - 4% sugar concentration, 0.06 - 6% sugar concentration, 0.08 - 8% sugar concentration, and days since treatment start.
Day - Day of the month
Month - Numerical month
Year - Year
Date - day, month, year (ddmmyyyy)
DaySinceStart - Day since start of expoeriment\
Time - Time of day bottle measurement was taken (hhmm)
Indiv - Unique animal identifier
Chamber - Chamber ID animals were in
Pre_test - specify if animals were in a Pre-Test period (Pre), prior to receiving a sugar solution (Test)
Treatment - Photoperiod animals were under Neutral/Long or Short
DopamineStage - Animals under no treatment (NA), a pre treatment period (Pre), high sugar solution (HCS), low dopamine concentraion (DopLO2) or high dopamine concentration (DopHI2)
Animal_wt_g - Animals weight (in grams) at time of sugar measurement on the 3rd day of treatment
Sex - male (M) or female (F)
Sugar_conc - Sugar concentration animals were given in bottle; 0 - no sugar, 0.02 - 2% sugar concentration, 0.04 - 4% sugar concentration, 0.06 - 6% sugar concentration, 0.08 - 8%
Sugar_ConcDay - Days under a given sugar concentration treatment
Sugar_Total1_g - Weight (in grams) of bottle number 1\
Sugar_Total2_g - Weight (in grams) of bottle number 2
Fed_sugarsoln_g - Weight (in grams) of difference bottle 2 versus bottle 1 consumption
Fed_sugarsoln_g_perday - Weight (in grams) of solution consumed accounting for how many days animals have been under the treatment (Fed_sugarsoln_g/Sugar_ConcDay)\
Sugar_mmt_good - Did bottle 1 or 2 spill (Y) or not spill (N)
Water_ConcDay - Days under a given sugar concentration treatment
Water_Total1_g - Weight (in grams) of bottle number 1\
Water_Total2_g - Weight (in grams) of bottle number 2
Fed_water_g - Weight (in grams) of difference bottle 2 versus bottle 1 consumption
Fed_water_g_perday - Weight (in grams) of solution consumed accounting for how many days animals have been under the treatment (Fed_water_g/Water_ConcDay)
Consumed - Consumption of bottle 1 versus bottle 2 (Fed_sugarsoln_g/(Fed_sugarsoln_g + Fed_water_g))
Water_mmt_good - Did bottle 1 or 2 spill (Y) or not spill (N)
Initials - Initial of researcher who checked animals and weighed bottle
Comments - Researcher comments
SleepData
Files in folder are used to calculate percent hourly sleep for animals under a 2 week acclimation period, 4 weeks under a photoperiod treatment, or 3 weeks under a no sgar or high sugar solution.
2WeekAcclimation_26Mar2019_longTime.csv
4WeekPhotoperiod_08Apr2019_long.csv
4WeekPhotoperiod_08Apr2019_short.csv
4WeekPhotoperiod_15Apr2019_dailySS_combinedTime.csv
4WeekPhotoperiod_24Apr2019_combined_with_sub_day.csv
4WeekPhotoperiod_24Apr2019_long.csv
4WeekPhotoperiod_24Apr2019_short.csv
4WeekPhotoperiod_24Apr2019SleepBout_MeanSB.csv
Chamber_Animal_IDs_Sex_bothPhases.csv
Chamber_Animal_IDs.csv
DailySleepBothPhases_FINAL.csv
HighSucrose_29May2019_combined_with_sub_day.csv
HighSucrose_29May2019_PercentHourlySleep_processed.csv
HighSucrose_29May2019SleepBout_MeanSB_processed.csv
HourlySleepBouts_PrePostSugar.csv
LowSucrose_andTest_07May2019_combined_with_sub_day.csv
Phase2_2WeekAcclimation_19Jun2019_long.csv
Phase2_4WeekPhotoperiod_03Jul2019_combined.csv
Phase2_4WeekPhotoperiod_22Jul2019_combined_with_sub_day.csv
Phase2_4WeekPhotoperiod_22Jul2019_combined.csv
Phase2_4WeekPhotoperiod_22Jul2019SleepBout_MeanSB.csv
Phase2_8%sucrose_12Aug2019_long.csv
Phase2_8%sucrose_12Aug2019_short.csv
Phase2_8%sucrose_21Aug2019_combined_with_sub_day.csv
Phase2_8%sucrose_21Aug2019_long.csv
Phase2_8%sucrose_21Aug2019_PercentHourlySleep_processed.csv
Phase2_8%sucrose_21Aug2019_short.csv
Phase2_8%sucrose_21Aug2019SleepBout_MeanSB.csv
Phase2_8%sucrose_30Aug2019_long.csv
Phase2_8%sucrose_30Aug2019_short.csv
Phase2_LowSucroseTest_03Aug2019_combined_with_sub_day.csv
--Information relevant for 2WeekAcclimation_26Mar2019_longTime.csv, 4WeekPhotoperiod_08Apr2019_long.csv, 4WeekPhotoperiod_08Apr2019_short.csv, 4WeekPhotoperiod_15Apr2019_dailySS_combinedTime.csv, 4WeekPhotoperiod_24Apr2019_combined_with_sub_day.csv, 4WeekPhotoperiod_24Apr2019_long.csv, 4WeekPhotoperiod_24Apr2019_short.csv, 4WeekPhotoperiod_24Apr2019SleepBout_MeanSB.csv, HighSucrose_29May2019_combined_with_sub_day.csv, LowSucrose_andTest_07May2019_combined_with_sub_day.csv, Phase2_2WeekAcclimation_19Jun2019_long.csv, Phase2_4WeekPhotoperiod_03Jul2019_combined.csv, Phase2_4WeekPhotoperiod_22Jul2019_combined_with_sub_day.csv, Phase2_4WeekPhotoperiod_22Jul2019_combined.csv, Phase2_8%sucrose_12Aug2019_long.csv, Phase2_8%sucrose_12Aug2019_short.csv, Phase2_8%sucrose_21Aug2019_combined_with_sub_day.csv, Phase2_8%sucrose_21Aug2019_long.csv, Phase2_8%sucrose_21Aug2019_short.csv,Phase2_8%sucrose_30Aug2019_long.csv, Phase2_8%sucrose_30Aug2019_short.csv, Phase2_LowSucroseTest_03Aug2019_combined_with_sub_day.csv
Variable list; these are common variable names shared across the files, and only differ by the numeric at the end, which corresponds to the day/night, i.e., PERCENTSLEEPTOT1 and PERCENTSLEEPTOT2 correspond to percentage sleep for day/night or day/night 2:
MOUSE_ID - Unique animals identifier
TESTDATE - Date of when sleep data is recored (mm/dd/yyyy)
PERCENTSLEEPTOT - Total percentage of time spent asleep
PERCENTSLEEPNIGHT - Percentage of time spent asleep during the night\
PERCENTSLEEPDAY - Percentage of time spent asleep during the day\
BOUTLENGTHTOT - Total percentage of sleep bouts across day and night
BOUTLENGTHNITE - Total percentage of sleep bouts across the night
BOUTLENGTHDAY - Total percentage of sleep bouts across the day
DIURNAL WAKE RATIO - Ratio of time awake versus asleep during the active period
PEAKACT - Maximum peak amplitude value across the day and night
--Information relevant fo Chamber_Animal_IDs_Sex_bothPhases.csv
Number of variables: 18
Number of rows: 47
Variable list:
GrassRat_ID - Unique animal identifier
Phase - specifies if animals were in phase 1 or phase 2 of the experiment
Chamber - Chamber room animals were located
Sex - male (M) or female (F)
Photoperiod - Photoperiod treatment animals were subjected too, Short or Long
Sugar_conc - Sugar concentration animals were given in bottle; 0 - no sugar, 0.02 - 2% sugar concentration, 0.04 - 4% sugar concentration, 0.06 - 6% sugar concentration, 0.08 - 8% sugar concentration
Sugar - Animals were under No sugar (0 sugar_conc) or High sugar (0.08 sugar_conc) treatment
Parent_Sire - Unique ID of animals biological father
Parent_Dame - Unique ID of animals biological mother\
ParentPair - Animals were obtained from 4 parental pairs (1- pair 1, 2- pair 2, 3 - pair 3, 4 - pair 4)
Litter - Litter that animal belonged to.
AgeAtDeath_days - Age in days (from birth (0), to death) animals died
Percent_liver_fat - Percent area of liver occupied by fat (NA values indicate no measurement taken)
Weight g - Weight of animals (in grams) and time of death
Fat_pad_wt_g - Weight of fat pad (in grams) and time of death
DOB_Day - Day of birth
DOB_Month - Month of birth\
DOB_Year - Year of birth
DOB_MMDDYYYY - combined date of birth (mm/dd/yyyy)
DOD_Day - Day of death
DOD_Month - Month of death
DOD_Year - Year of death
DOD_MMDDYYYY - combined date of death (mm/dd/yyyy)
--Information relevant to Chamber_Animal_IDs.csv
Number of variables: 6
Number of rows: 25
Variable list:
GrassRat_ID - Unique animal identifier
Phase - specifies if animals were in phase 1 or phase 2 of the experiment
Chamber - Chamber room animals were located
Sex - male (M) or female (F)
Photoperiod - Photoperiod treatment animals were subjected too, Short or Long
Sugar_conc - Sugar concentration animals were given in bottle; 0 - no sugar, 0.02 - 2% sugar concentration, 0.04 - 4% sugar concentration, 0.06 - 6% sugar concentration, 0.08 - 8% sugar concentration
Sugar - Animals were under No sugar (0 sugar_conc) or High sugar (0.08 sugar_conc) treatment
--Information relevant to 4WeekPhotoperiod_24Apr2019SleepBout_MeanSB.csv, HighSucrose_29May2019_PercentHourlySleep_processed.csv, HighSucrose_29May2019SleepBout_MeanSB_processed.csv, Phase2_4WeekPhotoperiod_22Jul2019SleepBout_MeanSB.csv, Phase2_8%sucrose_21Aug2019_PercentHourlySleep_processed.csv, Phase2_8%sucrose_21Aug2019SleepBout_MeanSB.csv
Variable list; all files contain values from piezoelectric sleep system measuring either avergae sleep bouts (i.e., MeanSB.csv) or percently hourly sleep (i.e., PercentHourlySleep-processed.csv):
Date - Date and time of when sleeo data is collected by piezo system (mm/dd/yyyy hh:mm)
Following columns specify an animals ID with corresponding values generated by piezoelectric system.
MicroBiome
Folder contains data files for microbiome statistics and generating PCOA plots
combined_otu_tax.tsv
GRP_20191213.metadata_AS.csv
GRP_20191213.metadata.csv
GRP_20191213.rarefied-class-feature-table.csv
Meta_litter_parents.csv
metadata_cut_for_shannon.csv
metadata.csv
otu_matrix.csv
otu_table.txt
shannon_vector.qza
taxonomy.csv
taxonomy.tsv
tree.nwk
unweighted_unifrac_pcoa_results.qza
--Information relevant to GRP_20191213.metadata_AS.csv and GRP_20191213.metadata.csv
Number of variables: 19
Number of rows: 193
Variable list:
SampleID - Unique animal identifier for microbiome analysis
Type - Tissue type taken, Int: Intestine sample; Fecal: Fecal sample
Daylength - Photoperiod treatment, Normal/Long or Short
Sample - Sample identifier A, B, C or D
Experimental.Trial - Treatment animals were under. 2wk acclim: 2 weeks of acclimation to Neutral/Long photoperiod; 4wk photoperiod: 4 weeks under Neutral/Long or Short photoperiods; 0% HCS: animals recieving no sugar solution; 8% HCS: animals recieving 8% sugar solution. NA specify animals not under any specific experimental trial and are disregarded in downstream analysis.
GrassRat_ID - Unique animal identifier
Trial - Which phase animals were in, 1 or 2
Sex - male (M) or female (F)
Sucrose - Animals given sugar (yes) or not (no)
Sugar_conc - Sugar concentration animals were given in bottle; 0 - no sugar, 0.08 - 8% sugar concentration
Photoperiod - Animals under Neutral/Long or Short photoperiod
Chamber - What experimental chamber animals were in
Plate - PCR plate identifier (A or B)
PCRRow - What row of the PCR plate sample was in
PCRCol - What column of the PCR plate sample was in
TrialA - Which phase animals were in, 1 or 2
LightDay - Numeric for if animals were under Neutral/Long photoperiod (12) or Short photoperiod (4)
TubeID - Microcentrifuge tube ID samples were in
--Information relevant to GRP_20191213.rarefied-class-feature-table.csv
Number of variables: 19
Number of rows: 193
Variable list:
OTU_ID - Contains concatenated identifier of a microbiome group, phylum, class, order, family, and genus\
D0 - column specifying microbiota group
D1 - column specifying microbiota phylum
D2 - column specifying microbiota class\
D3 - column specifying microbiota order\
D4 - column specifying microbiota family\
D5 - column specifying microbiota genus
The rest of the columns specify the animals ID and corresponding sequencing readcounts for the prior columns
--Information relevant to Meta_litter_parents.csv
Number of variables: 13
Number of rows: 47
Variable list:
GrassRat_ID - Unique animal identifier
Parent_Sire - Unique ID of animals biological father
Parent_Dame - Unique ID of animals biological mother\
ParentPair - Animals were obtained from 4 parental pairs (1- pair 1, 2- pair 2, 3 - pair 3, 4 - pair 4)
Litter - Litter that animal belonged to.
AgeAtDeath_days - Age in days (from birth (0), to death) animals died
Percent_liver_fat - Percent area of liver occupied by fat (NA values indicate no measurement taken)
Phase - specifies if animals were in phase 1 or phase 2 of the experiment
Chamber - Chamber room animals were located
Sex - male (M) or female (F)
Photoperiod - Photoperiod treatment animals were subjected too, Short or Long
Sugar_conc - Sugar concentration animals were given in bottle; 0 - no sugar, 0.02 - 2% sugar concentration, 0.04 - 4% sugar concentration, 0.06 - 6% sugar concentration, 0.08 - 8% sugar concentration
Sugar - Animals were under No sugar (0 sugar_conc) or High sugar (0.08 sugar_conc) treatment
--Information relevant to metadata_cut_for_shannon.csv and metadata.csv
Number of variables: 25
Number of rows: 159
Variable list:
SampleID - Unique animal identifier for microbiome analysis
Type - Tissue type taken, Int: Intestine sample; Fecal: Fecal sample
Daylength - Photoperiod treatment, Normal/Long or Short
Sample - Sample identifier A, B, C or D
Experimental.Trial - Treatment animals were under. 2wk acclim: 2 weeks of acclimation to Neutral/Long photoperiod; 4wk photoperiod: 4 weeks under Neutral/Long or Short photoperiods; 0% HCS: animals recieving no sugar solution; 8% HCS: animals recieving 8% sugar solution. NA specify animals not under any specific experimental trial and are disregarded in downstream analysis.
GrassRat_ID - Unique animal identifier
Trial - Which phase animals were in, 1 or 2
Sex - male (M) or female (F)
Sucrose - Animals given sugar (yes) or not (no)
Sugar_conc - Sugar concentration animals were given in bottle; 0 - no sugar, 0.08 - 8% sugar concentration
Photoperiod - Animals under Neutral/Long or Short photoperiod
Chamber - What experimental chamber animals were in
Plate - PCR plate identifier (A or B)
PCRRow - What row of the PCR plate sample was in
PCRCol - What column of the PCR plate sample was in
TrialA - Which phase animals were in, 1 or 2
LightDay - Numeric for if animals were under Neutral/Long photoperiod (12) or Short photoperiod (4)
TubeID - Microcentrifuge tube ID samples were in
Parent_Sire - Unique ID of animals biological father
Parent_Dame - Unique ID of animals biological mother\
ParentPair - Animals were obtained from 4 parental pairs (1- pair 1, 2- pair 2, 3 - pair 3, 4 - pair 4)
Litter - Litter that animal belonged to.
AgeAtDeath_days - Age in days (from birth (0), to death) animals died
Percent_liver_fat - Percent area of liver occupied by fat (NA values indicate no measurement taken)
--Information relevant to out_matrix.csv and otu_table.tsv
Number of variables: 161
Number of rows: 1711
Variable list:
OTUID - Unique identifier corresponding to the microbiota group, phylum, class, order, family, and genus\
The following columns contain microbiota readcount data for each sample
--Information relevant to taxonomy.csv and taxonomy.tsv
Number of variables: 3
Number of rows: 1711
Variable list:
OTUID - Unique identifier corresponding to the microbiota group, phylum, class, order, family, and genus\
Taxon - Contains concatenated character identifier of a microbiome group, phylum, class, order, family, and genus\
Confidence - Confidence value in placement of sample to the OTUID
--Information relevant to shannon_vector.qza and unweighted_unifrac_pcoa_results.qza
Files are in zipped qza format containing experimental metadata and shannon entropy
values for all samples (shannon_vector.qza) and PCOA eigenvalues for generating
PCOA plot.
Data file access: qza files can be unzipped with Archive Utility on Mac (and the
analogous software on Windows).
Contents: Unzipped shannon_vector.qza and unweighted_unifrac_pcoa_results.qza files
contain checksums.md5 file from sequencing, an alpha diversity file in .tsv format,
and a metadata.yaml file for appropriate downstream analysis in R. Files can be
read into R using the read_qza() as part of the qiime2R package.
--Information relevant to tree.nwk
Newick file to visualize tree network from microbiota sequencing data, and for
phylogenetic analysis using UniFrac package in R.
Contents: Files are non-readable for humans but can be viewed with a text editor
(in Mac or Windows) in Newick format, where parenthesis and commas represent
graph-theoretical trees with edge lengths. Files can be read into R using the
read_tree() function as part of the phyloseq package.
Code/Software
All uploaded data in Dryad is compatible for use with Excel and R.