title: ESQ-36059

description: clozapine treated sample

source_name: peripheral blood leukocytes

tag: gender

tag: treatment status

value: Clozapine

value: peripheral blood leukocytes


title: WAT, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P108

status: Public on Feb 23 2022

type: RNA

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'oligo' (v1.58.0).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P108

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: The study population consisted of 110 healthy abdominally obese men and women, aged 40-70 years at time of recruitment. Subjects were recruited from the NQPlus cohort, a database of the Wageningen University, and local advertisements. Abdominal obesity was defined as a BMI >27kg/m2 or a waist circumference >88cm (women) or >102cm (men). Exclusion criteria were: earlier diagnosed with diabetes or diagnosed during our screening (OGTT, fasting glucose >7mmol/L, after 2h >11.1mmol/L), daily alcohol intake of >20g (women) or 30g (men), smoking, unstable body weight (weight gain or loss of >3kg in the past three months), diagnosed with a long-term medical condition, using medication known to interfere with glucose or lipid homeostasis, being allergic to fish oil or restricted to a vegetarian dietary regime. All subjects gave written informed consent. The study was approved by the Medical Ethics Committee of Wageningen University and registered at ClinicalTrials.gov, identifier: NCT02194504.

extract_protocol: RNA from frozen adipose tissue samples was isolated using a TRIzol/chloroform extraction (Thermo Fisher Scientific, Waltham, USA) and purified using the Qiagen Mini column kit according to manufacturers’ protocol (Qiagen, Hilden, Germany). RNA yield was quantified on a NanoDrop ND 1000 spectrophotometer (NanoDrop Technologies, Wilmington, USA) while RNA integrity was measured on an Agilent 2100 BioAnalyzer with RNA 6000 Nanochips (Agilent Technologies, Santa Clara, USA). Samples with RNA integrity (RIN) score of 6.2 and higher were included, average RIN-score was 8.0.

treatment_protocol: This study was a parallel-designed randomized 12-week intervention that examined the effects of a 25% energy restriction (ER) high nutrient quality diet; a 25% ER low nutrient quality diet; or a habitual diet on cardiometabolic risk factors by using an array of outcome measures, including subcutaneous adipose tissue (AT) transcriptomics. AT transcriptomics were determined at the fasted state, and 4 hrs postprandial of a standardized mixed meal shake challenge, both before (0 wk) and after the intervention (12 wk). An energy restriction of 25% was applied to the calculate estimated energy requirement (EER) of each participant. The two ER diets were iso-caloric and matched for alcohol, sodium, and total fat. The differences between the two ER diets was that the high nutrient quality ER diet was, compared to the low nutrient quality ER diet, enriched in monounsaturated fatty acids (MUFA; 13.4 vs. 9.3 En%), n-3 polyunsaturated fatty acids (PUFA; 7.7 vs. 4.1 En%), fiber (3.1 vs. 2.2 En%) and plant protein (10.3 vs. 5.7 En%), and reduced in fructose content (3.4 vs. 7.0 En%). The composition of the diets formed the basis of daily meal plans provided to the participant during the intervention. To increase the intake of n-3 PUFA in the high nutrient quality ER diet, a daily capsule providing 400 mg EPA and 300 mg DHA was included in the meal plan. Participants visited the facility weekly for an individual session with a qualified dietician, after which the key food products were provided for the following week. Adherence to the diet was determined based on the collection of leftovers of the supplied products, and on the participant's food diary, in which deviations from the protocol were reported. To calculate reported intake of energy and nutrients, the meal plans with reported deviations were used. Additional consumed food items were added to the intake while leftovers were subtracted. Metabolizable energy of the two diets was calculated using specific Atwater values. On a separate study day at the start of the study and after the 12 week intervention, measurements on metabolic health were conducted before and during a mixed meal shake challenge at Wageningen University, The Netherlands. Prior to this day, participants were asked to refrain from alcohol, avoid strenuous exercise, ensure a sufficient night's rest, and consume a low-fat standardized meal before 8pm, after which they had to fast. Subcutaneous adipose tissue biopsies were taken caudally from the umbilicus under local anesthesia (1% lidocaine) using a small liposuction cannula in the fasted state, as well as 4 hrs after consumption of a mixed meal shake. The mixed meal was a shake consisting of 320g water, 20g protifar, 83.5g dextrose, 60g palm olein, and 20 drops vanilla oil, equalling to 3833kJ and 76.3g carbohydrates, 17.6g protein, and 60g fat. Adipose tissue biopsies were taken by trained nurses on sagittal different locations to prevent analysis of acute inflammation and wound healing mediators. Biopsies were rinsed with phosphate-buffered saline to eliminate blood and immediately frozen in liquid nitrogen and stored at -80 ºC until RNA isolation.

tag: Sex

value: Female

tag: intervention

tag: specification intervention diet

value: habitual diet

tag: moment of adipose tissue sampling

value: 0 weeks (baseline)

tag: time of adipose tissue sampling

value: 0 hours (before/fasted)

tag: tissue

value: subcutaneous white adipose tissue (WAT)


title: Max-null ESCs Dox untreated

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

country: Japan

institute: Saitama Medical University

description: Reference sample for Max-null ES cells Dox-treated for 6 days

hyb_protocol: Affymetrix Standard WT Plus Protocol.

scan_protocol: AGCC Standard Protocol.

data_processing: The data were background-subtracted and normalized using the Transcriptome Analysis Console Software (TAC4.0, ThermoFisher, https://www.thermofisher.com/jp/en/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-software/affymetrix-transcriptome-analysis-console-software.html).

organism: Mus musculus

source_name: Max-null ESCs Dox untreated

label_protocol: Affymetrix WT Plus Kit.

growth_protocol: Culture under conventional ES culture condition with LIF (1000 units/ml) and 10% serum.

extract_protocol: Total RNAs were isolated from ESCs with RNeasy Mini Kit (QUIAGEN, 74106)

value: Male

tag: strain

tag: cell type

value: ES cells


title: Max-null ESCs Dox-treated (6day)

source_name: Max-null ESCs Dox-treated (6day)


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P111

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P111

value: 25% energy restricted (ER), high nutrient quality

value: 4 hours after a mixed-meal challenge (postprandial)


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P107

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P107

value: 12 weeks after intervention


title: WAT, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P108

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P108


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P106

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P106


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P106

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P106


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P106

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P106


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P103

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P103


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P106

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P106


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P104

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P104


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P104

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P104


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P099

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P099

value: 25% energy restricted (ER), low nutrient quality


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P104

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P104


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P104

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P104


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P101

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P101


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P103

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P103


title: ESQ-32832

status: Public on Feb 24 2022

type: genomic

city: Mexico City

first: José Jaime

last: Martínez Magaña

state: Mexico City

address: Av. Insurgentes Sur 3877, La Fama, Tlalpan,

country: Mexico

institute: Instituto Nacional de Medicina Genómica

description: clozapine treated sample

hyb_protocol: The bisulfite-converted DNA was amplified, fragmented, and hybridized with the Infinium MethylationEPIC BeadChip, Illumina using the standard Illumina protocol.

scan_protocol: Standard Illumina iScan settings for Methylation EPIC

data_processing:
Raw data was read by minfi package (version 3.14) from IDAT files and converted to rgset from this we calculate the methylated and unmethylated intensities for each sample and probe.
Unmethylated and methylated signal intensities

label: cy3, cy5

molecule: genomic DNA

source_name: peripheral blood leukocytes

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from peripheral blood leukocytes was entered using standard techniques.


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P100

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P100


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P101

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P101


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P103

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P103


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P099

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P099


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P103

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P103


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P101

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P101


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P101

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P101


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P100

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P100


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P100

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P100


title: WAT, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P098

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P098


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P099

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P099


title: control ES cells

description: Reference sample for bHLHZ-deleted Mga expressing ES cells and T-box-deleted Mga expressing ES cells

source_name: control ES cells


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P100

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P100


title: WAT, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P098

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P098


title: WAT, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P098

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P098


title: WAT, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P098

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P098


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P099

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P099


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P097

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P097


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P097

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P097


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P097

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P097


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P111

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P111


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P095

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P095


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P095

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P095


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P096

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P096


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P097

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P097


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P092

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P092


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P095

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P095


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P092

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P092


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P093

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P093


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P091

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P091


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P091

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P091


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P092

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P092


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P092

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P092


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P096

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P096


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P091

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P091


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P089

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P089


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P093

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P093


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P093

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P093


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P096

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P096


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P091

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P091


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P096

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P096


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P093

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P093


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P089

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P089


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P089

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P089


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P088

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P088


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P087

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P087


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P088

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P088


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P087

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P087


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P089

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P089


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P087

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P087


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P084

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P084


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P095

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P095


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P088

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P088


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P084

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P084


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P081

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P081


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P081

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P081


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P081

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P081


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P083

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P083


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P084

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P084


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P080

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P080


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P079

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P079


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P079

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P079


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P080

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P080


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P087

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P087


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P079

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P079


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P081

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P081


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P079

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P079


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P083

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P083


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P080

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P080


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P084

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P084


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P080

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P080


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P083

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P083


title: WAT, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P077

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P077


title: WAT, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P077

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P077


title: WAT, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P077

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P077


title: WAT, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P076

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P076


title: WAT, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P076

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P076


title: WAT, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P077

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P077


title: WAT, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P076

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P076


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P083

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P083


title: WAT, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P076

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P076


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P075

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P075


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P075

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P075


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P075

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P075


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P075

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P075


title: WAT, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P071

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P071


title: WAT, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P074

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P074


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P073

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P073


title: WAT, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P071

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P071


title: WAT, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P071

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P071


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P073

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P073


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P068

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P068


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P068

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P068


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P073

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P073


title: WAT, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P074

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P074


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P068

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P068


title: WAT, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P074

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P074


title: WAT, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P067

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P067


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P064

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P064


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P065

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P065


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P065

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P065


title: WAT, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P074

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P074


title: WAT, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P071

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P071


title: WAT, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P067

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P067


title: WAT, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P067

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P067


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P065

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P065


title: WAT, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P067

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P067


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P068

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P068


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P065

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P065


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P088

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P088


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P064

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P064


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P060

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P060


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P059

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P059


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P060

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P060


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P064

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P064


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P073

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P073


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P064

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P064


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P060

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P060


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P059

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P059


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P060

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P060


title: WAT, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P055

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P055


title: WAT, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P055

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P055


title: WAT, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P055

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P055


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P059

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P059


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P059

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P059


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P052

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P052


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P051

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P051


title: WAT, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P054

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P054


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P052

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P052


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P052

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P052


title: WAT, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P054

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P054


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P051

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P051


title: WAT, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P050

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P050


title: WAT, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P050

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P050


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P052

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P052


title: WAT, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P054

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P054


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P051

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P051


title: WAT, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P054

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P054


title: WAT, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P050

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P050


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P051

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P051


title: WAT, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P055

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P055


title: WAT, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P047

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P047


title: WAT, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P047

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P047


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P049

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P049


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P049

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P049


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P049

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P049


title: WAT, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P050

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P050


title: WAT, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P045

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P045


title: WAT, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P045

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P045


title: WAT, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P045

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P045


title: WAT, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P047

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P047


title: WAT, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P047

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P047


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P049

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P049


title: WAT, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P041

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P041


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P037

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P037


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P035

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P035


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P037

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P037


title: WAT, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P041

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P041


title: WAT, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P045

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P045


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P038

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P038


title: WAT, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P041

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P041


title: WAT, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P041

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P041


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P038

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P038


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P035

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P035


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P035

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P035


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P038

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P038


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P037

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P037


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P037

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P037


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P035

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P035


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P034

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P034


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P038

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P038


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P034

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P034


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P033

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P033


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P034

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P034


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P034

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P034


title: WAT, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P031

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P031


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P033

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P033


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P033

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P033


title: WAT, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P031

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P031


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P030

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P030


title: WAT, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P031

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P031


title: WAT, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P031

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P031


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P033

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P033


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P030

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P030


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P030

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P030


title: WAT, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P028

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P028


title: WAT, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P026

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P026


title: WAT, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P026

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P026


title: WAT, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P028

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P028


title: WAT, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P028

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P028


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P024

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P024


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P024

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P024


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P030

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P030


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P024

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P024


title: WAT, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P026

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P026


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P021

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P021


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P021

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P021


title: WAT, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P028

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P028


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P017

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P017


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P021

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P021


title: WAT, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P016

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P016


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P017

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P017


title: WAT, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P016

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P016


title: WAT, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P026

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P026


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P019

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P019


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P019

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P019


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P017

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P017


title: WAT, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P016

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P016


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P019

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P019


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P024

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P024


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P019

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P019


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P017

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P017


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P015

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P015


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P014

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P014


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P012

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P012


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P014

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P014


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P015

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P015


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P015

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P015


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P014

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P014


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P014

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P014


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P015

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P015


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P012

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P012


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P011

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P011


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P012

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P012


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P011

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P011


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P012

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P012


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P011

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P011


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P010

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P010


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P010

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P010


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P010

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P010


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P009

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P009


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P009

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P009


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P009

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P009


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P010

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P010


title: WAT, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P008

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P008


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P011

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P011


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P021

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P021


title: WAT, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P008

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P008


title: WAT, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P006

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P006


title: WAT, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P008

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P008


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P009

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P009


title: stimulated airway macrophage -8wk post vaccination  rep5

type: SRA

city: Hamilton

first: Karen

last: Mossman

state: Ontario

address: 1280 Main St West

department: Department of Medicine

country: Canada

institute: McMaster University

library_source: transcriptomic

data_processing:
Raw sequence data were exported to FASTQ format and were filtered based on quality scores.
Next the reads were mapped to  the UCSC/HG38 reference version using HISAT2.
The counts were obtained by using ht-seq count with the “intersection-strict” option.
Counts were transformed with TMM transformation and then normalized with VOOM.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data file contains a matrix containing data from all samples.

growth_protocol: Frozen bronchoalveolar fluis cells were revived for 6h, and one million viable cells were seeded onto a 12-well plate and rested for 2h at 37C, 5%Co2. Airway macrophages were enriched by removal of non-adherent cells via extensive washing.

extract_protocol:
12h.  Total RNA was extracted using RNeasy Plus Mini Kit from Qiagen which includes gDNA eliminator columns
cDNA libraries were sequenced using an Illumina HiSeq machine (1x50 bp sequence reads)

treatment_protocol: Enriched airway macrophages were cultured for 12 h with or wothout stimulation with whole cell M.tb lysate.

value: airway macrophages

tag: vaccination state

value: After vaccination

tag: treatment

value: stimulated with M.tb whole cell lysate


title: stimulated airway macrophage -baseline rep3

value: Before vaccination


title: stimulated airway macrophage -8wk post vaccination rep2


title: stimulated airway macrophage -8 wk post vaccination rep1


title: stimulated airway macrophage -8wk post vaccination  rep4


title: stimulated airwayvmacrophage -8wk post vaccination  rep3


title: WAT, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P006

source_name: subcutaneous white adipose tissue, after (t=12wk) diet2 intervention, fasted state (t=0hr), subject P006


title: WAT, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P006

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P006


title: stimulated airway macrophage -baseline rep5


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P003

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P003


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P003

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P003


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P005

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P005


title: WAT, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P006

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet2 intervention, fasted state (t=0hr), subject P006


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P003

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P003


title: WAT, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P008

source_name: subcutaneous white adipose tissue, after (t=12wk) diet0 intervention, fasted state (t=0hr), subject P008


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P003

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P003


title: stimulated airway macrophage -baseline rep2


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P002

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P002


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P005

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P005


title: WAT, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P005

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P005


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P002

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P002


title: unstimulated airway macrophage -8wk post vaccination  rep5

value: unstimulated


title: stimulated airway macrophage -baseline rep1


title: unstimulated airway macrophage -8wk post vaccination  rep4


title: WAT, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P002

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, 4hr postprandial mixed-meal challenge (t=4hr), subject P002


title: WAT, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P002

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet1 intervention, fasted state (t=0hr), subject P002


title: WAT, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P005

source_name: subcutaneous white adipose tissue, after (t=12wk) diet1 intervention, fasted state (t=0hr), subject P005


title: unstimulated airway macrophage -8wk post vaccination  rep3


title: unstimulated airway macrophage -8wk post vaccination rep2


title: stimulated airway macrophage -baseline rep4


title: unstimulated airway macrophage -baseline rep5


title: unstimulated airway macrophage -baseline rep4


title: 3months_heart_96h_ISO_PE_male2

city: Mannheim

first: Christiane

last: Vettel

address: Ludolf-Krehlstr. 13-17

department: Experimentelle Pharmacologie Mannheim

country: Germany

institute: Heidelberg University

data_processing:
Trimmomatics was used to trim raw fastq reads.
Trimmed reads were aligned to the reference using the short read aligner STAR (https://code.google.com/p/rna-star/).
Genes were quantified by the use of featurecounts in R. Differential expression analysis was performed using Deseq2 from R. Differentially expressed Genes were selected with (0.75<FC>1.5 and FDR<0.05).).
Genome_build: mm10
Supplementary_files_format_and_content: Deseq2 output

molecule: polyA RNA

extract_protocol:
Total RNA was isolated using  guanidinium thiocyanate-phenol-chloroform extraction
BGI

treatment_protocol: Mice received osmotic minipumps containing either isoprenaline or isoprenaline and phenylephrine. Daily dosage of each substance: 30mg/kg for 96 h

value: male

value: heart

tag: age

tag: genotype

value: WT

value: ISO/PE treated


title: unstimulated airway macrophage -8 wk post vaccination rep1


title: 3months_heart_96h_ISO_PE_male1


title: 3months_heart_96h_ISO_PE_female2

value: female


title: unstimulated airway macrophage -baseline rep3


title: 3months_heart_96h_ISO_male2

value: ISO treated


title: unstimulated airway macrophage -baseline rep1


title: YS4F5

city: Gainesville

first: Thomas

middle: C

last: Foster

state: FL

address: 1149 S Newell Dr.

department: Neuroscience

country: USA

institute: University of Florida

description: microRNA

data_processing:
Data was analyzed using Partek Flow (Partek Inc.) Reads were trimmed based on size such that reads below 15 bp and reads above 35 bp were discarded. Following trimming, reads were aligned using Bowtie (version 1.0.0) against the mouse genome reference (mm10).
Gene annotation was completed with the miRBase mature microRNAs model (release version 22) and normalization was performed using the CPM method.  In order to consider genes that are not present in miRBase, gene annotation was also done using mm10-Ensembl Transcripts (release version 100) followed by  normalization.
Supplementary_files_format_and_content: comma separated values files which contain the normalized counts for each sample.

source_name: Hippocampus

extract_protocol:
Animals were sacrificed either 24 hours or 4 days following sepsis. Age and sex-matched control groups were sacrificed directly from the home cage, without receiving surgery or anesthesia. Mice were anesthetized with isoflurane and swiftly decapitated and mixed arteriovenous blood was collected in a heparinized vacutainer tube. The brains were rapidly removed and the hippocampi were dissected. All brain samples were flash frozen in liquid nitrogen and were stored at -80 C. One whole hippocampus was used for next-generation sequencing.
Sequencing libraries were constructed using the library preparation kit Ion Total RNA-Seq kit v2 (Thermo Fisher, Cat# 4475936). Ion Xpress barcodes (Thermo Fisher, catalog number4475485) were added for multiplex sequencing.

value: Female

value: Hippocampus

tag: treatment group

value: Female Young Sepsis - 4 days


title: 3months_heart_ctr_male1

value: control


title: 3months_heart_ctr_female2


title: 3months_heart_96h_ISO_female2


title: 3months_heart_96h_ISO_male1


title: unstimulated airway macrophage -baseline rep2


title: 3months_heart_ctr_female1


title: YS4F1

description: microRNA


title: YS4F3

description: microRNA


title: YS4F4

description: microRNA


title: YMS7F

description: microRNA

value: Female Young Sepsis -1 day


title: YMS5F

description: microRNA


title: YMS1F

description: microRNA


title: Gargle_samples

city: Tucson

first: Darren

middle: A.

last: Cusanovich

state: AZ

address: 1230 N Cherry Avenue, BSRL 421

department: Cellular and Molecular Medicine

institute: University of Arizona

description: Saline gargle samples containing viral and human RNA

data_processing:
Library strategy: Swab-Seq
BCL files converted to fastq files with bcl2fastq2.
Reads with appropriate barcodes demultiplexed with custom python script.
Fastq files mapped to reference sequences and concatenated by barcodes using kallisto and BUStools.
Further filtering, calculation of S2/Spike-in ratio, and data visualization performed in R.
Genome_build: Custom reference that includes SARS-CoV-2 S2 sequence, spike-in control sequence, and RPP30 gene.
Supplementary_files_format_and_content: Two kinds of processed data files are provided: *.data.txt and *.metadata.txt. *.data.txt files are tab-separated files with 4 columns. Column 1 is a barcode sequence that addresses a specific well in the experiment. Column 2 is a placeholder (represents a UMI sequence for BUStools) that lists "A" for all samples. Column 3 is an indicator of which target sequence is quantified (0 = S2, 1 = spike-in control, 4 = RPP30). Column 4 provides the counts of reads mapping to the indicated target sequence. *.metadata.txt are tab-separated files that provide information about the conditions of each well in the experiment. The first 5 columns of metadata files are standard. Column 1 is the well barcode (consistent with the well barcodes in the *.data.txt files). Column 2 is the i7 portion of the barcode. Column 2 is the i5 portion of the barcode. Column 4 indicates the plate ID (just "Plate1" if there was only one plate in the experiment). Column 5 indicates the well of the plate that the barcode represents (wells A01 through H12). A variable number of additional columns are provided, depending on the experiment. The column header indicates the information provided.

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: Saline gargle samples

extract_protocol: An extraction-free protocol for saline gargle samples was used to amplify viral RNA from inactivated particles in this experiment. Barcoded primers targeting human RPP30 and SARS-CoV-2 S genes amplify targets in parallel. Samples contain S spike-in control RNA for normalization.

tag: experimental design ("serial dilution" or "positive/negative")

value: Positive/negative

tag: pcr kit

value: TaqPath Multiplex

tag: pcr cycles

tag: viral inactivation

value: 65C for 30min


title: YMS6F

description: microRNA

tag: Sex


title: siPSMD14_2

city: XinXiang

first: Yang

last: Xiao

country: China

institute: XinXiang Medical Universtiy

data_processing:
Using BGISEQ-500 sequencing platform
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: xlsx files include FPKM values for each Sample

growth_protocol: MCF7 cells were plated in 12-well plates at 30% fusion per well

extract_protocol:
Lysis of cells with Trizol reagent and harvesting of RNA
RNA libraries were prepared for sequencing using BGISEQ-500 protocols

treatment_protocol: MCF-7 cells were transfected with siControl or siPSMD14.

tag: cell line

value: human breast cancer cell line

tag: genotype/variation


title: siControl_3

value: siControl


title: YMC6F

description: microRNA

value: Female Young Control


title: siPSMD14_1


title: siControl_2


title: YMC5F

description: microRNA


title: YMC3F

description: microRNA


title: siControl_1


title: YMC1F

description: microRNA


title: Stat_Rep3_F

city: Toulouse

first: Laurence

last: Girbal

address: 135 avenue de rangueil

country: France

institute: TBI

data_processing:
Reads were mapped onto the E. coli genome (version U0009.3, GenBank) using the Burrows-Wheeler alignment method (version 0.7.12-r1069). Counting was performed with HTSeq-count version 0.6.1p1 using the « intersection non empty » mode.
Supplementary_files_format_and_content: Matrix of read counts for every gene (in total for 4488 genes)

organism: Escherichia coli

source_name: Escherichia coli

growth_protocol: E. coli MG1655 was grown in batch cultures in a bioreactor at 37°C, pH 7.0 and 350 rpm, in M9 medium supplemented with 3 g/L glucose. All cultures were inoculated at an OD600nm of 0.1 after overnight preculture. The partial pressure of oxygen was continuously monitored during the culture and maintained above 30%. Cells were collected in the exponential phase at an OD600nm of ~1.3, and in the stationary phase 1 h after glucose depletion at an OD600nm of ~3.4.

extract_protocol:
Total RNA was extracted using the RNeasy Midi kit (Qiagen, Germantown, MD, USA) and quantified using a Nanodrop® spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). The 23S/16S and 16S/23S ratios in each subfraction were calculated using the Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) and used to pool the subfractions into seven fractions labelled A to G. Fraction A consisted of subfractions containing DNAs, free RNAs, and free small and large ribosomal subunits. In fractions B to G, the 23S/16S ratio was constant, at about 1.8, corresponding to entire ribosomes. The 1st peak (fraction B) was attributed to the monosome. The 2nd, 3rd, and 4th peaks were attributed to 2, 3, and 4 ribosomes, respectively.
Ribosomal RNA was removed using the Ribo-ZeroRM Magnetic Kit (Illumina, San Diego, CA, USA). Then 10 ng ribodepleted RNA was used to construct a sequencing library using the Ion Total RNA-Seq Kit v2 Kit and the Ion Xpress™ RNA-Seq Barcode 1-16 Kit (Thermo Fisher Scientific, Waltham, MA, USA). The library was constructed and (100 base pair [bp]) single-end sequencing on an Ion Torrent system equipped with an Ion P1 Chip Kit was performed by the GeT-BioPuces platform (http://get-biopuces.insa-toulouse.fr/). These experiments were repeated with three independent cultures.

treatment_protocol: Translation was arrested by adding 0.1 mg/mL chloramphenicol. Cells were harvested, washed twice, and resuspended in lysis buffer (20 mM Tris HCl pH 8, 140 mM KCl, 40 mM MgCl2, 0.5 mM DTT, 100 μg/ml chloramphenicol, 1 mg/ml heparin, 20 mM EGTA, 1% Triton X-100). Heparin was used as a RNase inhibitor. After mechanical cell disruption with glass beads, mRNA-ribosome complexes were size-separated on a sucrose gradient (10 to 50% (w/v) in polysome gradient buffer (same composition as lysis buffer except for heparin at a final concentration of 0.5 mg/ml)) into 24 subfractions.


title: OS4F7

description: microRNA

value: Female Old Sepsis - 4 days


title: Stat_Rep3_E


title: Stat_Rep3_G


title: Stat_Rep3_C


title: OMS4F

description: microRNA

value: Female Old Sepsis  -1 day


title: OS4F2

description: microRNA


title: siPSMD14_3


title: Stat_Rep3_B


title: OMS2F

description: microRNA


title: OMS3F

description: microRNA


title: Stat_Rep3_A


title: Stat_Rep3_D


title: OMS1F

description: microRNA


title: OMC3F

description: microRNA

value: Female Old Control


title: OMC4F

description: microRNA


title: Stat_Rep2_E


title: Stat_Rep2_G


title: Stat_Rep2_F


title: OMC2F

description: microRNA


title: Stat_Rep2_B


title: Stat_Rep2_C


title: OMC1F

description: microRNA


title: DOS4F4

description: microRNA


title: OS4F4

description: microRNA


title: YS4M4

description: microRNA

value: Male

value: Male Young Sepsis - 4 days


title: Stat_Rep1_G


title: Stat_Rep1_F


title: Stat_Rep1_E


title: YS4M1

description: microRNA


title: YS4M3

description: microRNA


title: YMS4M

description: microRNA

value: Male Young Sepsis -1 day


title: YS4M2

description: microRNA


title: Stat_Rep1_D


title: YMS3M

description: microRNA


title: Stat_Rep2_D


title: WAT, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P016

source_name: subcutaneous white adipose tissue, before (baseline; t=0wk) diet0 intervention, fasted state (t=0hr), subject P016

value: Female

tag: intervention

tag: specification intervention diet

value: habitual diet

tag: moment of adipose tissue sampling

value: 0 weeks (baseline)

value: 0 hours (before/fasted)

value: subcutaneous white adipose tissue (WAT)


title: 155615

city: Köln

first: Martin

last: Lukačišin

state: Deutschland

address: Zülpicher Straße 47a

department: Institute for Biological Physics

institute: Universität zu Köln

data_processing:
Adapters were removed using cutadapt; cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -a AGATCGGAAGAGCACACGTCTGAAC -a TGGAATTCTCGGGTGCCAAGG -a AGATCGGAAGAGCACACGTCT -a CTGTCTCTTATACACATCT -a AGATGTGTATAAGAGACAG -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -A AGATCGGAAGAGCGTCGTGTAGGGA -A TGGAATTCTCGGGTGCCAAGG -A AGATCGGAAGAGCACACGTCT -A CTGTCTCTTATACACATCT -A AGATGTGTATAAGAGACAG
The resulting reads were aligned to the annotated reference S. cerevisiae genome R64-2 using HISAT2
The reads mapping to introns or CDS of intron-containing genes were quantified using featureCounts using custom produced .saf files extracted from the reference .gff annotation file. featureCounts -T 8 -F SAF -p -a myAnnotation.saf -M -O -P
The intron retention rate was calculated as the ratio of intron counts normalised to the intron length over the CDS counts normalised to the length of the CDS region. For genes containing multiple introns, the introns were treated jointly for CDS introns and separately for 5′ UTR introns.
Genome_build: Saccharomyces cerevisiae R64-2
Supplementary_files_format_and_content: counts

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: RNA samples from treatments with single stressors were obtained from cultures with automated re-inoculation every 8 hours, with a total incubation time of 24 hours, to keep cultures in exponential phase and assure the drug effects have taken place

extract_protocol:
RNA was extracted using the Ribopure RNA Purification Kit, yeast from Thermo Scientific following the kit recommendations.
Libraries were prepared at the Cologne Center for Genomics (CCG). Ribodepleted libraries were prepared using QIAseq FastSelect - rRNA Yeast Kit. Both mRNA and total RNA libraries were prepared with the Illumina TrueSeq Stranded mRNA kit.  Libraries were sequenced using 2×100bp paired-end reads.

treatment_protocol: Strains were grown in YPD with a drug, either in a concentration gradient to select samples closest to 50% of growth inhibition (LiCl, Fenpropimorph, and Myriocin), or in a single concentration (0.4 M NaCl and glucose 20%). Fenpropimorph (Sigma Aldrich cat. No. 36772) was tested in a 0.5-1.5 µM gradient, sequenced samples were treated with 0.85 µM Fenpropimorph. Myriocin (Sigma Aldrich cat. No. 476300) gradient encompassed 0.25-0.75 µg/ml; 0.32 µg/ml Myriocin samples were sequenced.

value: LiCl IC50, sorted GFP low

tag: molecule subtype

value: Ribodepleted RNA


title: 155614

value: LiCl IC50, sorted GFP high


title: 155612

value: LiCl IC50

value: RPS22B-GFP 5'UTR intron deleted


title: YMS2M

description: microRNA

tag: tissue

value: Hippocampus


title: Stat_Rep1_A

tag: strain


title: Stat_Rep1_C


title: Stat_Rep1_B


title: YMS1M

description: microRNA


title: 155611

tag: treatment

value: Fenpropimorph IC50

value: WT


title: 155610

value: Myriocin IC50


title: 155608


title: Expo_Rep3_G


title: Stat_Rep2_A


title: 155589

value: polyA RNA


title: Expo_Rep3_F


title: YMC5M

description: microRNA

value: Male

value: Male Young Control


title: 155586


title: YMC4M

description: microRNA


title: 155613

value: NaCl 0.4 M


title: 154723


title: Expo_Rep3_E


title: 154727


title: 154725


title: YMC3M

description: microRNA


title: Expo_Rep3_D


title: 154721


title: OS4M8

description: microRNA

value: Male Old Sepsis - 4 days


title: YMC2M

description: microRNA


title: Fetal alcohol exposed, 5 months replicate 2, discarded array

city: Montreal

first: Roberta

middle: M

last: Palmour

state: Quebec

address: 1033 Pine West

department: Psychiatry

institute: McGill

description: mRNA expression data from the hippocampus of vervet green monkeys sacrificed at 5 months after birth

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan at the McGill Genome Center

data_processing: The data were analyzed with FlexArray software and the Bioconductor package in R. These data were normalized using the Robust Multi-Array (RMA) normalization method. Probe sets have been trimmed for present/absent calls, annotation, and where multiple probe sets were available for a single gene only the probe set showing the highest mean expression value was selected

organism: Chlorocebus aethiops

source_name: Fetal alcohol exposed, 5 months replicate 4 (discarded array)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: miRNeasy Qiazol extraction performed according to manufacturers specifications

treatment_protocol: Whole hippocampus was extracted and placed in a 1 ml sterile vial containing GITC

tag: age

value: Sacrificed at 5 months

tag: ethanol exposure

value: Pre Natal Alcohol Exposure


title: 155609

value: Glucose 20%

tag: genotype


title: OS4M5

description: microRNA

tag: treatment group


title: 154716


title: 154719


title: Expo_Rep3_A


title: Expo_Rep3_B


title: Expo_Rep2_G


title: OS4M2

description: microRNA


title: OS4M3

description: microRNA


title: Fetal alcohol exposed, 5 months replicate 6

source_name: Chlorocebus aethiops hippocampus sacrificed at 5 months after prenatal alcohol exposure


title: Expo_Rep2_F


title: Fetal alcohol exposed, 5 months replicate 5


title: Expo_Rep2_E


title: Fetal alcohol exposed, 2 years replicate 5, discarded array

description: mRNA expression data from the hippocampus of vervet green monkeys sacrificed at 2 years after birth

source_name: Chlorocebus aethiops hippocampus sacrificed at 2 years after prenatal alcohol exposure (discarded array)

value: Sacrificed at 2 years


title: Expo_Rep3_C


title: OMS2M

description: microRNA

value: Male Old Sepsis -1 day


title: Expo_Rep2_D


title: Fetal alcohol exposed, 5 months replicate 4


title: Expo_Rep2_B


title: OMS3M

description: microRNA


title: Expo_Rep2_C


title: OMS4M

description: microRNA


title: Expo_Rep2_A


title: Expo_Rep1_G


title: OMS1M

description: microRNA


title: OMC2M

description: microRNA

value: Male Old Control


title: Fetal alcohol exposed, 2 years replicate 6

source_name: Chlorocebus aethiops hippocampus sacrificed at 2 years after prenatal alcohol exposure


title: Fetal alcohol exposed, 5 months replicate 2


title: Fetal alcohol exposed, 2 years replicate 4


title: Control 5 months, replicate 3

source_name: Chlorocebus aethiops hippocampus sacrificed at 5 months post sucrose exposure

value: Pre Natal sucrose exposure


title: Fetal alcohol exposed, 2 years replicate 3


title: OMC1M

description: microRNA


title: OMC4M

description: microRNA


title: VhG4

city: Dalian

first: dongxu

last: gao

address: Heishijiao

institute: Dalian Ocean University

data_processing:
Illumina Casava1.8 software used for basecalling.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome (Takifugu_rubripes_Ensemble_92) using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Takifugu_rubripes_Ensemble_92
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for  all sample

organism: Takifugu rubripes

source_name: gill

growth_protocol: T. rubripes (average size 118 ± 7.5 g) were obtained from a local supplier (Tianzheng Industrial, Dalian, China) and acclimated for approximately 7 days in a temperature controlled room (19 ± 1 ◦C).

extract_protocol:
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Fish were put into the aquaria with the bacteria at concentration of 2.5×10e7 CFU/mL for 12 h of immersion exposure. At 12 h fish were transferred to clean seawater and maintained for 7 days. Control groups were maintained in the clean seawater all the time. Spleen and gill tissues were collected in both symptomatic treatment fish and control fish at 7 day.

tag: average size

value: Vibrio harveyi at concentration of 2.5x 10e7 CFU/mL

tag: infection

value: Vibrio harveyi infection

value: gill


title: Expo_Rep1_E


title: Control 5 months, replicate 5


title: Fetal alcohol exposed, 2 years replicate 1


title: Fetal alcohol exposed, 2 years replicate 2


title: OMC3M

description: microRNA

value: Hippocampus


title: Expo_Rep1_F


title: Control 5 months, replicate 2


title: Control 2 years, replicate 4

source_name: Chlorocebus aethiops hippocampus sacrificed at 2 years post sucrose exposure


title: Control 2 years, replicate 6


title: Control 2 years, replicate 5


title: Control 2 years, replicate 3


title: Control 5 months, replicate 6


title: Control 2 years, replicate 2


title: Control 2 years, replicate 1


title: VhG3


title: Expo_Rep1_C


title: VhG2


title: Expo_Rep1_B


title: VhG1


title: Mouse 10: T cells with combo

city: Gaithersburg

first: Eric

last: Tu

state: MD

address: 1 Medimmune way

institute: AstraZeneca

description:
RE807-RMS37481-45
Gene expression data from xenograft tumors of combo-treated mouse.

hyb_protocol: Biotin-labeled cRNA was fragmented and hybridized on Human Genome U133 Plus 2.0 GeneChip arrays (Affymetrix) according to manufacturer’s instruction.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Data capture and array quality assessments were performed with the GeneChip Operating Software tool. Normalization of gene expression profiles was performed by using robust multi-array average method. Probesets with highest sample variance among multiple probesets per gene were selected and used for downstream analyses. Differential gene expression analysis was carried out by R package LIMMA with linear modeling and empirical Bayes moderation.

source_name: Xenograft tumors from combo-treated mouse

label_protocol: RNA was converted to biotin-labeled cRNA using MessageAmp™ Premier RNA Amplification Kit (Thermo Fisher Scientific) according to manufacturer’s instruction.

growth_protocol: NSG mice at 6-8 weeks were used in the study. Mice were treated with antibodies for 17 days before the tumors were harvested.

extract_protocol: Total RNA was derived from cells using RNeasy Mini Kit (Qiagen) according to manufacturer’s instruction.

treatment_protocol: Tumors were cut into smaller fragments that were placed into tumor digestion enzyme buffer (RPMI + DNase + Collagenase) to process to single cell suspension using gentleMACS Dissociator (Miltenyi Biotec).

tag: mouse strain

value: NSG

value: NSCLC tumor

value: combo