DOI: 10.5061/dryad.n2z34tn3g
title: Effects of short photoperiod and carbohydrate consumption on sleep, liver steatosis, and the gut microbiome in diurnal grass rats

description: 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.
description: # 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: ) 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.