Data for the effect of n-3 fatty acids on inflammatory neurodegenerative diseases. The experiment was located in New York, USA.

Contact Dr. Chuchun L. Chang (cc617@cumc.columbia.edu) with any questions.

Description of the data and file structure:

Quantitative Real-time PCR

Total ribonucleic acid (RNA) was isolated from the whole brain using Trizol reagent (Invitrogen). Single-stranded complementary deoxyribonucleic acid (cDNA) was synthesized using iScript reverse transcriptase (Bio-Rad). Relative quantification of messenger ribonucleic acid (mRNA) expression was determined by real-time qPCR with Fast SYBR Green PCR kit (Applied Biosystems) normalized to a housekeeping gene GAPDH on Thermal Cyclers (Bio-Rad). The difference between the target gene and the housekeeping gene Ct value (ΔΔCt) was calculated for all experiments. The expression of the target gene (linear value) was normalized to the housekeeping gene, which was determined by 2- (ΔΔCt)50.

Open Fields

We performed the Open Field tests to assess the spontaneous exploratory behavior of n-3-treated mice in a new environment, including locomotion and anxiety-related behaviors57. Each 4- to 5-month-old mouse had a 30-minute session monitored by Activity Monitor Version 7 software (Med Associates Inc.). It was then placed in the center of a Plexiglas arena (27.31 x 27.31 x 20.32 cm, Med Associates ENV-510) under dim light (~5 lux) for free exploration. Infrared beams along the arena's axes tracked movement, stereotypies, and time in the center zone (14.29 x 14.29 cm). Data were analyzed in six 5-minute intervals. Arenas were cleaned with 70% ethanol and dried between trials. We performed the Y-Maze to assess short-term spatial memory in 4-month-old mice by leveraging their innate exploration behavior58. In the Y-maze experiment, mice were put to explore three arms with equal dimensions (35 cm long, 5 cm wide, 10 cm high), each marked with a different sticker (equal sign, bus, plane)59. During Trial 1, mice were familiarized with two arms for 10 minutes, separated by an opaque door, then placed in a holding cage for 10 minutes. In Trial 2, mice explored all three arms for 5 minutes. The movement was recorded using Ethovision XT 12 software. The preference score, indicating memory performance, is calculated as: Preference score = (time in novel arm / (time in novel arm + time in the familiar arm)) x 100.

Y-maze

In the Y-maze experiment, mice were put to explore three arms with equal dimensions (35 cm long, 5 cm wide, 10 cm high), each marked with a different sticker (equal sign, bus, plane)59. During Trial 1, mice were familiarized with two arms for 10 minutes, separated by an opaque door, then placed in a holding cage for 10 minutes. In Trial 2, mice explored all three arms for 5 minutes. The movement was recorded using Ethovision XT 12 software. The preference score, indicating memory performance, is calculated as: Preference score = (time in novel arm / (time in novel arm + time in the familiar arm)) x 100.

Lipidomic

The employed lipidomic investigation and analytical workflow utilized a state-of-the-art LC-MS/MS platform, integrating an Agilent 6490 Triple Quadrupole (QQQ) MS with an Agilent 1260 Infinity LC system at the Columbia Biomarker Core Laboratory65. Briefly, lipid extracts were prepared from cell lysates using a chloroform-methanol extraction method and spiked with appropriate internal standards and analyzed on a platform comprising Agilent 1260 Infinity HPLC integrated to Agilent 6490A QQQ mass spectrometer controlled by Masshunter v 7.0 (Agilent Technologies) as described before66. Tree panels, scanning for either positive lipids, negative lipids or neutral lipids (under positive mode), were analyzed. Equal amounts of internal standards with known concentrations were spiked into each extract. Each standard was later used to calculate the concentrations of corresponding lipid classes by first calculating the ratio between the measured intensities of a lipid species and that of the corresponding internal standard multiplied by the known concentration of the internal standard. Lipid levels for each sample were calculated as nmol normalized for protein concentration (nmol/mg protein).

Data files include:

qPCR 7day.csv

This file contains data on the expression of inflammatory cytokines in 7-day-old 5xFAD mice treated with and without omega-3 fatty acids. All data were collected by the authors. Blank cells indicate missing data.

qPCR 4-5m.csv

This file contains data on the expression of inflammatory cytokines in 4-5-month-old 5xFAD mice treated with and without omega-3 fatty acids. All data were collected by the authors. Blank cells indicate missing data.

Open Field Summary.csv

This file contains data on locomotor activity and exploratory behavior in WT and 5xFAD mice, assessed across various activity zones. All data were collected by the authors. Blank cells indicate missing data.

Y-Maze-Summary.csv

This file contains data on the Y-maze test conducted on 4-10-month-old 5xFAD mice with and without omega-3 fatty acid treatment. The dataset includes information on spontaneous alternation, zone alternation, and arm entry behavior. All data were collected by the authors. Blank cells indicate missing data.

Lipidomic-nmole.csv

This file contains data on the lipid concentration profiles in 5xFAD mice, with a focus on lipid species and classes following omega-3 fatty acid treatment. All data were collected by the authors.

All numerical values in this dataset represent lipid concentrations, measured in nmol/mg, normalized to protein concentration.