This readme file was generated on [2024-10-23] by [Kaitlyn Chhe] GENERAL INFORMATION Title of Dataset: Circadian Effects of Melatonin Receptor-Targeting Molecules in vitro Author/Principal Investigator Information Name: Michelle E. Farkas ORCID: 0000-0001-5824-1243 Institution: University of Massachusetts Amherst Address: Department of Chemistry, 710 N. Pleasant St., Lederle Graduate Research Tower, Amherst MA 01003 Email: farkas@chem.umass.edu Author/Associate or Co-investigator Information Name: Kaitlyn Chhe ORCID:0009-0000-2165-9283 Institution: University of Massachusetts Amherst Address: Department of Chemistry, 710 N. Pleasant St., Lederle Graduate Research Tower, Amherst MA 01003 Email: kchhe@umass.edu Author/Alternate Contact Information Name: Stephanie R. Taylor ORCID: 0000-0003-3562=6479 Institution: Colby College Address: Department of Computer Science, 4000 Mayflower Hill Dr., Waterville ME 04901 Email: srtaylor@colby.edu Date of data collection: 2023-05-31 to 2024-07-12 Geographic location of data collection: Amherst, MA, USA Information about funding sources that supported the collection of the data: The research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under award number R35GM143016. SHARING/ACCESS INFORMATION Links to publications that cite or use the data: pending Links to other publicly accessible locations of the data: N/A Links/relationships to ancillary data sets: N/A DATA & FILE OVERVIEW File List: The dataset is first categorized into two folders (Bmal and Per2) based on the promoter reporter. The data is further separated by experiment date/treatment time of day (standard timing versus delayed timing, indicated as "standard" and "delayed," respectively). For the data labeled "standard" the cells were treated with small molecules immediately after synchronization. For data labeled "delayed" the cells were treated with molecules 12 h after synchronization. Each excel file will have the date the experiment started followed by the promoter gene, treatment time, and treatment type (MT = melatonin, NT = not treated, DMSO = vehicle, UCSF7447 = melatonin receptor-targeting molecule). Relationship between files, if important: N/A Additional related data collected that was not included in the current data package: N/A Are there multiple versions of the dataset? no If yes, name of file(s) that was updated: N/A Why was the file updated? N/A When was the file updated? N/A METHODOLOGICAL INFORMATION Description of methods used for collection/generation of data: Cells were plated in 35 mm dishes at a density of 4 x 105 cells per dish and synchro-nized when 90% confluent. Each experiment had 6 replicates per condition (N=6). The experiments were repeated twice for a total of 12 replicates per condition. For synchro-nization, cells were treated with 100 nM of dexamethasone (Sigma-Aldrich) diluted in cell culture media and incubated for 2 hours at 37 °C in a 5% CO2 atmosphere. After synchronization, cells were washed with PBS and then treated with 2 mL of luminometry recording media containing DMSO (vehicle control, 0.2%, MP Biomedicals), melatonin (1 mM, TCI America), or UCSF 7447 inverse agonist (10 μM or 50 nM, Sigma-Aldrich). Luminometry recording media was comprised of 11.25 mg/mL powdered DMEM (Sig-ma-Aldrich), 4 mM sodium bicarbonate (Fisher Scientific), 5% fetal bovine serum (Corn-ing), 10 mM HEPES (HyClone), 100 U/mL penicillin-streptomycin (Gibco), and 0.5 mM D-luciferin (Thermo Scientific) dissolved in autoclaved Millipore water. After dosing, the cells were transferred to a LumiCycle luminometer for data collection for 7 days at 37 °C. For the delayed treatments, synchronized cells were cultured in U2OS growth media for 12 hours (37 °C in 5% CO2 atmosphere) and then dosed with 2 mL of melatonin, UCSF7447, or vehicle control in recording media. After treatment, the cells were trans-ferred to a LumiCycle luminometer for data collection for 7 days at 37 °C. Methods for processing the data: Each time-series was pre-processed to exclude the initial 24-h transient, then de-trended by removing a 24-h moving average. To estimate circadian period and phase, the de-trended time series was fit (scipy.optimize.differential_evolution from Scipy v. 1.13.1) to a damped cosine curve with a linear baseline (Ae^(-λt)cos(2π/τ-θ)+c_0+c_1 t, where t is time in hours, τ is the period in hours, and θ is the phase in radians). A time-series was considered an outlier if the fit was poor (the coefficient of determination between the data and the fit was less than 0.9) or if its period or phase was more than 2 standard deviations from the mean of all time series for the same reporter and treatment condition. The circular mean and standard deviation measures were used for the phase (scipy.stats.circmean and scipy.stats.circstd). A two-sided permutation test was employed to determine whether the mean period or phase differed between treatment conditions (scipy.stats.permutation_test with 10000 re-samples). P-values were then adjusted using the Bonferroni correction to account for multiple comparisons. Instrument- or software-specific information needed to interpret the data: Microsoft Excel Standards and calibration information, if appropriate: Environmental/experimental conditions: Experiment conditions include non-treated (NT), vehicle control (DMSO), 1 mM Melatonin (MT), 50 nM UCSF7447, and 10 uM UCSF7447. Describe any quality-assurance procedures performed on the data: People involved with sample collection, processing, analysis and/or submission: Kaitlyn Chhe, Maya S. Hegde, Stephanie R. Taylor, and Michelle E. Farkas DATA-SPECIFIC INFORMATION FOR: Bmal and Per2 data sets Number of variables: All files have 5 columns Number of cases/rows: up to 1000 rows Variable List: Column 1 = reading number, column 2= time (hr:min), column 3 = time (days), column 4 = bioluminescence (counts/sec), column 5 = baseline Missing data codes: N/A Specialized formats or other abbreviations used: MT = melatonin , NT = non-treated