title: cyc8.man

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

institute: RIKEN

description: RNA-seq

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.3.4.2
Alignment with TopHat v2.0.9
Read quantitation using custom scripts
Genome_build: sacCer3
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Yeast cells were grown in YPGlc (2% peptone, 1% yeast extract, and 2% glucose) medium. For the generation of FOGs, yeast cells were grown in YPMan (2% peptone, 1% yeast extract, and 2% mannose) medium for 3 hr.

extract_protocol:
Yeast cells were harvested using membrane filters (mixed cellulose esters, 0.45 µm, Merck), and transferred into liquid nitrogen directly. Frozen cells were mixed with frozen droplets of 600 µL lysis buffer (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, and 1% Triton X-100), and lysed by Multi-beads Shocker (Yasui Kikai). Lysates were treated with 25 U of TURBO DNase (Thermo Fisher Scientific) and cleared by centrifugation at 20,000 × g for 10 min at 4˚C. TRIzol LS reagent (Thermo Fisher Scientific) and Direct-zol RNA Kit (Zymo research, Irvine, CA) were used for the extraction of total RNA.
RNA extraction, rRNA depeletion (Ribo-zero Gold (yeast), illumina), and TruSeq stranded mRNA library prep kit (illumina)

tag: genetic background

value: BY4741 cyc8[delta]::kanMX4

tag: growth protocol

value: YPMan for 3 hr


title: Bcl11b monoallelic trial 1

status: Public on Jul 24 2019

type: SRA

city: Seattle

first: Nicholas

last: Pease

state: WA

address: 3720 15th Ave NE

country: USA

institute: University of Washington

description: primary cells

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Paired-end sequencing reads were aligned separately to mouse (NCBI37/mm9) and yeast (SacCer_Apr2011/sacCer3)  genomes using Bowtie2 (Langmead and Salzberg, 2012) with the following setting: --local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 700 as suggested for mapping CUT&RUN sequencing data (Skene et al., 2018).
The resulting alignments were converted to BAM files with SAMtools and then converted to BED files with BEDTools.
Reads were sorted and filtered to remove random chromosomes using custom python script, see supplementary files.
BEDTools genomecov was used to generate histograms for the mapped reads using a scaling factor that is the product of the number of spiked-in yeast reads and the number of input cells.
Genome_build: mm9, yeast
Supplementary_files_format_and_content: bedgraph

molecule: genomic DNA

organism: Mus musculus

source_name: cKit enriched bone marrow hematopoietic progenitor cells

growth_protocol: Cultured on OP9-DL1 stromal cells with 5ng/mL of IL-7 and Flt3l

extract_protocol:
CUT&RUN experiments were carried out as previously described (Skene et al, 2018) with the following modifications: 1-2.5x10^5 cells were isolated by FACS as described in sections above, bound to Concanavalin A coated magnetic beads (Bangs Laboratories), and  permeabilized with 0.025% (wt/vol) digitonin. Permeabilized cells were incubated overnight at 4C with 5ug of anti-H3K27me3 (Active Motif 39156) and then washed before incubating with protein A-MNase fusion protein (a gift from Steven Henikoff) for 15 minutes at room temperature. After washing, cells were incubated in CaCl2 to induce MNase cleavage activity for 30 minutes at 0oC. The reaction was stopped with 2XSTOP buffer (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 mg/mL RNase A and 40 mg/mL glycogen) with 2pg of yeast spike-in DNA per sample. Histone-DNA complexes were isolated from insoluble nuclear chromatin by centrifugation and DNA was extracted with a NucleoSpin PCR Clean-up kit (Macherey-Nagel).
Library preparation from CUT&RUN products was completed with KAPA Hyper Prep Kit (KAPA Biosystems) following standard protocol with PCR amplification settings adjusted so that annealing and extension steps are combined into one step at 60oC for 10s. Library products were size selected to be within 200 - 300 bp range using AMPure beads (Agencourt). Libraries were sequenced using an Illumina MiSeq system with paired-end 25 bp sequencing read length and TruSeq primer standard for approximately 5 millions reads per sample.

tag: cell type

tag: bcl11b expression

value: monoallelic Bcl11b expression

tag: days in culture

tag: antibody

value: H3K27me3 (Active Motif, 39425)

tag: number of cells


title: Bcl11b monoallelic trial 2

description: primary cells

value: cKit enriched bone marrow hematopoietic progenitor cells


title: Macrophages in a co-culture system with BMSCs, MSR1 WT_3

city: Nanjing

first: Shujie

last: Zhao

address: longmian street

country: China

institute: Department of Orthopedic, The First Affiliated Hospital of Nanjing Medical University

library_source: transcriptomic

data_processing:
fastp version 0.17.1
HISAT2 version 2.1.0
String Tie v1.3.4d
DESEQ2 v1.18.1
R version 3.4.3
Genome_build: gencode v27
Supplementary_files_format_and_content: comma-delimited text file including RPKM values and counts for each Sample

molecule: total RNA

source_name: Macrophages

growth_protocol: To obtain primary bone marrow-derived macrophages, bone marrow cells first underwent lysis of red blood cells and were then resuspended in complete RPMI-1640 medium consisting of 25 ng/ml macrophage colony-stimulating factor (M-CSF) and cultured for 7 days.

extract_protocol:
Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) .  RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA).
Quality RNA samples were converted into cDNA libraries using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (NR601, Vazyme, NanJing, China). VAHTSTM DNA Clean Beads (Vazyme #N411) in this study was used to purify the fragments during the process of library constructing. The purified products were enriched with 12-15 cycles of PCR to create the final cDNA library. Finally, libraries were sequenced on the Illumina Hiseq X Ten according the manufacturer's protocols.

treatment_protocol: Further, macrophages from MSR1 KO or WT mice were co-cultured with BMSCs via a transwell system for 48h.

tag: strain

value: BMM derived macrophages

tag: genotype

value: MSR1 WT


title: cyc8.glc_2

country: Japan

description: RNA-seq

value: YPGlc for 3 hr


title: cyc8.glc_1

description: RNA-seq


title: without ASP, biological rep1

type: RNA

city: Bei Jing

first: Xin

address: West 3rd Ring Road, Haidian District

institute: Capital Normal University

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Affy packages in R.

data_processing: The data were analyzed using Affymetrix default analysis settings and global scaling as normalization method.

label: botin

organism: Arabidopsis thaliana

source_name: seedlings grown on 1/2 MS medium without ASP

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip  3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US)followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Seeds of A. thaliana (Columbia 0) were surface sterilized, germinated on 1/2 MS medium supplemented with 0.1% sucrose and 0.7% plant agar, and grown at 22°C-24°C with a light/dark cycle of 16/8 h.

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: seedlings grown on 1/2 MS medium with or without ASP for 5 days

tag: cultivar

value: Columbia 0

tag: age

tag: tissue

value: seedlings


title: with ASP, biological rep2

source_name: seedlings grown on 1/2 MS medium with ASP


title: with ASP, biological rep1


title: without ASP, biological rep2


title: No Enzyme Control 3

type: other

city: Boston

first: Suzanne

last: Walker

state: MA

address: 4 Blackfan Circle

department: Microbiology and Immunobiology

institute: Harvard Medical School

description:
Array barcode 91430, batch HA20446
cont3
raw data file: cont3.gpr

hyb_protocol: The arrays were washed four times with TBST (5 mL × 5 min/wash) and incubated with 200 μL 270 µM iodoacetoamide and 1 µM 2,9-dimethyl-5,6,11,12-tetrahydro-dibenzocyclooctene in PBS buffer under a coverslip for 30 min. After the incubation, the arrays were washed again and incubated with 200 μL 1 µM ADIBO-biotin in PBS buffer under a coverslip for 30 min. The arrays were washed with TBS containing 0.5% SDS three times (5 mL × 5 min/wash) and twice with TBST (5 mL × 5 min/wash). The arrays were incubated with 200 μL 0.5 µg/mL streptavidin-Alexa Fluor 647 for 30 min at 4 °C. Finally, the arrays were washed again as above and dipped in water three times, spin-dried (200 ×g, 5 min), and scanned.

scan_protocol: Arrays were scanned with an axon GenePix 4000B using GenePix 5.0 or a GenePix 4300 scanner using GenePix 7.2.

data_processing: Un-normalized data were read into R using limma with normal-exponential background correction. For activity normalized data, a robust linear fit was obtained of the control series of V5-biotin control proteins on each block of each array was obtained, and the fluorescent values of all protein spots on each block was divided by the slope of the linear fit on the corresponding control block. The OGT-treated arrays (both wild-type and D2A) were then normalized for activity measurement by comparing the median staining-normalized signal for the control Estrogen Receptor alpha spots on every block. All proteins that showed evidence of OGT activity on blocks were scaled based upon the difference in staining-normalized Estrogen Receptor alpha between a given array block and the median of control arrays. Detailed methods are available in the supplemental information of the associated publication. The mean for each protein from each array was calculated for the resulting staining-and-activity normalized data and reported as the ActivityNorm samples, with the control samples being only normalized for staining. For comparisons between control arrays and OGT-treated arrays directly, we further median-normalized the staining and activity normalized groups of OGT-treated arrays (wild-type treated or D2A treated), so that each group of arrays had the same log2-transformed median. Values reported in the MedianNorm samples are these protein-level, median-normalized data, and are compared to the control arrays.

label: Alex Fluor 647 conjugated streptavidin

molecule: other

organism: Homo sapiens

source_name: No enzymatic reaction

label_protocol: Human ProtoArray microarrays were warmed from -20 °C to 4 °C for 20 min and washed twice (5 mL × 5 min/wash) with TBS containing 0.04% Tween 20 (TBST) in a four-well array incubation plate on a circular shaker at 50 rpm. Microarrays were then blocked for 1.5 hours at 4 °C with Microarray Blocking buffer (ArrayIt) and washed again with TBST buffer (5 mL × 5 min/wash) three time. The microarrays were then incubated with 200 μL 3 µM OGT and 290 µM UDP-GlcNAz in PBS buffer under a coverslip for 2 hours at room temperature. Control arrays lacked OGT, while D2A arrays had the mutant enzyme at 3 µM instead of wild-type OGT.

growth_protocol: OGT was produced recombinantly from E. coli as described in the associated publication and purified by metal affinity and size exclusion chromatography. UDP-GlcNAz was synthesized as described by Vocadlo et al. Proc. Natl. Acad. Sci. USA 2003, 100, 9116–21.

extract_protocol: Not applicable- arrays were treated enzymatically with recombinant protein. Label protocol describes treatment of array with sugar donor. hyb protocol describes washing and staining.

treatment_protocol: see associated publication

tag: sugar donor

value: UDP-GlcNAz

tag: ogt variant

tag: detection method

value: Chemoenzymatic Biotin Tagging

tag: normalization

value: None (pre-ratio)


title: wt.man

description: RNA-seq

value: WT


title: cKit positive Bcl11b inactive trial 2

description: primary cells


title: wt.glc_2

description: RNA-seq


title: wt.glc_1

description: RNA-seq


title: No Enzyme Control 2

description:
Array barcode 91412, batch HA20446
cont2
raw data file: cont2.gpr


title: Macrophages in a co-culture system with BMSCs, MSR1 KO_3

value: MSR1 KO


title: cKit positive Bcl11b inactive trial 1

description: primary cells


title: gc-CTRL rep3 [miRNA]

city: Changchun

first: Yun

state: Jilin

address: Xi'an Road

department: College of Animal Sciences

institute: Jilin University

data_processing:
Primary sequencing data produced using the Illumina HiSeqTM 2500 system were considered raw reads
Raw sequencing data generally feature clean reads, reads with a sequencing primer, tags containing N, and adapter sequences. Raw reads were filtered into clean reads, and low-quality regional data were removed for downstream analysis (quality control)
When the alignment results passed quality control, downstream analysis was performed, including analyses of gene expression levels, miRNAs, Gene Ontology (GO) enrichment, and pathway enrichment. Gene expression levels were calculated by fragments per kilo bases per million mapped reads (FPKM).
Supplementary_files_format_and_content: Excel files include RPKM values for each sample

organism: Sus scrofa

source_name: ovary

growth_protocol: The GCs were seeded at an initial density of 1 × 106 cells/mL in six-well plates. The culture medium consisted of DMEM/F12 with 10% FBS and 1% penicillin-streptomycin. The cells were incubated under humidified atmosphere containing 5% CO2 at 37°C for 24 h, and then washed with PBS to remove any unattached cells.

extract_protocol:
Total RNA was extracted from GCs of the pLVX-RBP4 group and the CTRL group with TRIzol reagent according to manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GCs were infected with lentiviral particles for 72 h, and the medium was replaced every 24 h.

value: landraces

value: ovary

value: granulosa cell


title: No Enzyme Control 1

description:
Array barcode 74616, batch HA20358
cont1
raw data file: cont1.gpr


title: gc-CTRL rep1 [miRNA]


title: Input_background

city: Beltsville

first: George

middle: E.

last: Liu

state: Maryland (MD)

address: 10300 Baltimore Ave Bldg 306

institute: USDA-ARS

data_processing:
we removed contaminating adapter molecules, reads containing ploy-N, and low-quality reads using Trim_Galore (version 0.4.1)
We then mapped clean reads to the cattle reference genome (UMD3.1.1) using BWA algorithm with default settings. We only kept reads uniquely aligned with less than two mismatches for the subsequent analysis. We employed MACS2.1.1 for peak-calling with default parameter settings by looking for significant enrichment in the studied samples when compared to the input data file (i.e., random background)
Genome_build: UMD 3.1.1
Supplementary_files_format_and_content: xlsx

organism: Bos taurus

extract_protocol:
Genomic DNA was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA).
CTCF-seq and ChIP-Seq of H3K27ac, H3K27m3, H3K4m1, H3K4m3, of rumen primary epithelial cells (RPEC) were performed at Active Motif according to proprietary methods. For ChIP-seq, CTCF-seq, the 75-nt sequence reads

tag: breed

value: Hostein

tag: treatmnet

value: Input background

value: Rumen Epithelial Primary Cells (REPC)

tag: chip antibody

value: none (input)


title: H3K4m3_BT

description: 10_03P4_00GMUSDA_Rumen-BT_H3K4me3_Btau_i80

value: 24h postButyrate treatment

tag: cell type

tag: chip antibody vendor

value: Active Motif

tag: chip antibody cat. #

tag: chip antibody lot/batch #


title: gc-RBP4 rep3 [miRNA]


title: H3K4m1_CO

description: 07_03OR_00GMUSDA_Rumen-primC_H3K4me1_Btau_i95

value: Control


title: gc-RBP4 rep2 [miRNA]


title: H3K4m1_BT

description: 08_03OS_00GMUSDA_Rumen-BT_H3K4me1_Btau_i96


title: H3K27m3_CO

description: 05_03OP_00GMUSDA_Rumen-primC_H3K27me3_Btau_i93


title: gc-RBP4 rep1 [miRNA]


title: H3K27m3_BT

description: 06_03OQ_00GMUSDA_Rumen-BT_H3K27me3_Btau_i94


title: ARF19k_pos_4

city: St. Louis

first: Lucia

last: Strader

state: MO

address: One Brookings Drive, CB-1137

department: Biology

institute: Washington University in St. Louis

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultipler written in python
Technical replicate fastq files were combined and aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart
Genome_build: Ensembl Release 23 (TAIR 10)
Supplementary_files_format_and_content: Gene counts in tab-delimitted text MS Excel format

source_name: UBQ10:YFP-ARF19k line treated with 10 µM IAA for 2h, replicate 4

growth_protocol: Seeds were surface-sterilized, suspended in 0.1% agar, and stratified for 2 d at 4°C to promote uniform germination. After stratification, seeds were plated on plant nutrient (PN) media solidified with 0.6% agar and supplemented with 0.5% (w/v) sucrose (PNS) at 22°C under continuous illumination.

extract_protocol:
RNA was extracted using Qiagen Rneasy Plant Mini Kit.
Epicentre Ribo-Zero Gold

treatment_protocol: After 5 days, seedlings were transferred to liquid PN supplemented with either ethanol (Mock) or 10 µM IAA for 2h. These treatments were repeated in quadruplicate for each line.

tag: ecotype

value: Columbia

value: Whole seedlings, 5 days old

value: Whole seedlings

tag: growth media

value: PNS


title: H3K4m3_CO

description: 09_03P3_00GMUSDA_Rumen-primC_H3K4me3_Btau_i78


title: gc-CTRL rep2 [miRNA]

tag: strain


title: H3K27ac_CO

description: 03_03OG_00GMUSDA_Rumen-primC_H3K27Ac_Btau_i70


title: H3K27ac_BT

description: 04_03OO_00GMUSDA_Rumen-BT_H3K27Ac_Btau_i92


title: ARF19k_pos_3

source_name: UBQ10:YFP-ARF19k line treated with 10 µM IAA for 2h, replicate 3


title: ARF19k_pos_2

source_name: UBQ10:YFP-ARF19k line treated with 10 µM IAA for 2h, replicate 2


title: MELA12R

type: genomic

city: Bronx

first: Amit

last: Verma

state: NY

address: 1300 Morris Park Ave

department: Medicine

institute: Albert Einstein College of Medicine

hyb_protocol: Amplified fractions were submitted to Roche-NimbleGen, Inc. (Madison, WI) for labeling and hybridization onto a human hg17 custom-designed oligonucleotide array (50-mers) covering 25,626 HpaII amplifiable fragments (HAF) located at gene promoters.

scan_protocol: Each fragment on the array is represented by 15 individual probes distributed randomly spatially across the microarray slide. Thus the microarray covers 50,000 CpGs corresponding to 14,000 gene promoters.

data_processing: The log2(HpaII/MspI) was used as a representative for methylation and analyzed as a continuous variable

source_name: MELA12R mspi

label_protocol: One microgram of genomic DNA was digested overnight with either HpaII or MspI followed by LM-PCR and labelling.

growth_protocol: Melanoma samples from patients were obtained as snap frozen tissue and used to isolate genomic DNA.

extract_protocol: Genomic DNA was extracted by a standard phenol-chloroform protocol followed by an ethanol precipitation and resuspension in 10 mM Tris-HCl pH 8.0

treatment_protocol: MSPI restriction digestions were performed as described in the HELP assay protocol

value: Melanoma

tag: treatment

value: MSPI restriction digestions

source_name: MELA12R HPAII

treatment_protocol: HPAII restriction digestions were performed as described in the HELP assay protocol

value: HPAII restriction digestions


title: MELA21

source_name: MELA21 mspi

source_name: MELA21 HPAII


title: MELA18R

source_name: MELA18R mspi

source_name: MELA18R HPAII


title: MELA22

source_name: MELA22 mspi

source_name: MELA22 HPAII


title: NHEMP3

description: Normal Melanocyte Control

source_name: NHEMP3 mspi

value: Normal Melanocyte Control

source_name: NHEMP3 HPAII


title: MELA23

source_name: MELA23 mspi

source_name: MELA23 HPAII


title: ARF19k_pos_1

source_name: UBQ10:YFP-ARF19k line treated with 10 µM IAA for 2h, replicate 1

tag: age


title: MELA19

source_name: MELA19 mspi

tag: tissue

source_name: MELA19 HPAII


title: CTCF_BT

value: CTCF


title: MELA40

source_name: MELA40 mspi

source_name: MELA40 HPAII


title: CTCF_CO

description: 01_03OE_00GMUSDA_Rumen-primC_CTCF_Btau_i68


title: MELA41

source_name: MELA41 mspi

source_name: MELA41 HPAII


title: MELA39

source_name: MELA39 mspi

source_name: MELA39 HPAII


title: MELA17

source_name: MELA17 mspi

source_name: MELA17 HPAII


title: MELA44

source_name: MELA44 mspi

source_name: MELA44 HPAII


title: MELA36

source_name: MELA36 mspi

source_name: MELA36 HPAII


title: MELA43

source_name: MELA43 mspi

source_name: MELA43 HPAII


title: MELA38

source_name: MELA38 mspi

source_name: MELA38 HPAII


title: NHEMP4

description: Normal Melanocyte Control

source_name: NHEMP4 mspi

source_name: NHEMP4 HPAII


title: MELA42

source_name: MELA42 mspi

source_name: MELA42 HPAII


title: MELA20

source_name: MELA20 mspi

source_name: MELA20 HPAII


title: ARF19k_4

source_name: UBQ10:YFP-ARF19k line, replicate 4


title: MELA35

source_name: MELA35 mspi

source_name: MELA35 HPAII


title: ARF19k_3

source_name: UBQ10:YFP-ARF19k line, replicate 3


title: CO1_ATAC-seq

data_processing:
we removed contaminating adapter molecules, reads containing ploy-N, and low-quality reads using Trim_Galore (version 0.4.1)
We mapped clean reads to the cattle reference genome (UMD3.1.1) using BWA algorithm with default settings. We only kept reads uniquely aligned with less than two mismatches for the subsequent analysis. We employed MACS2.1.1 for peak-calling with default parameter settings by looking for significant enrichment in the studied samples when compared to the input data file (i.e., random background)
Genome_build: UMD 3.1.1
Supplementary_files_format_and_content: xlsx

extract_protocol:
Genomic DNA was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA).
The library construction was performed at Active Motif according to proprietary methods. The paired-end 42-nt sequencing reads were generated using NextSeq 500 (Active Motif, Inc. Carlsbad, CA, USA).

tag: replicate


title: ARF19k_2

source_name: UBQ10:YFP-ARF19k line, replicate 2


title: CO2_ATAC-seq


title: BT2_ATAC-seq

value: 24h post-Butyrate treatment


title: MELA34

source_name: MELA34 mspi

source_name: MELA34 HPAII


title: BT1_ATAC-seq

value: Hostein


title: mir396ef developing uppermost internode [C75PS]_3

city: Nanchang

first: Dong

last: Wang

state: JiangXi

address: Hong Gu Tan New Road, No. 999

institute: Nanchang University

description:
WTPSvsC75PS.DiffExpGene.xlsx
WTPSvsC75PS.DiffExpGene.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptor and low quality sequences were trimmed with SOAPnuke1.3.0; Clean reads were aligned to reference genomes (MSU rice genome release 7) using Hisat2 with default parameters.
Mapped reads from three biological replicates for rice were merged and then assembled with Cufflinks (v2.2.1).
Genome_build: MSU rice genome release 7 http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/
Supplementary_files_format_and_content: FPKM and Annotation of DEGs

organism: Oryza sativa

source_name: developing uppermost internode

growth_protocol: All of the seeds of the rice materials were sowed in early June in the paddy field on natural condition in Hangzhou of the year 2017

extract_protocol:
Total RNAs were extracted with RNAprep pure Plant kit (TIANGEN, Cat. no. DP432).
Libraries were constructed through applying TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) in accordance with the manufacturer’s instruction.

tag: background cultivar

value: XiuShui 134 (XS134)

tag: genotype

tag: line id

value: developing uppermost internode

value: heading stage


title: mir396ef developing uppermost internode [C75PS]_2


title: MELA32

source_name: MELA32 mspi

source_name: MELA32 HPAII


title: mir396ef developing uppermost internode [C75PS]_1


title: T1

source_name: T1 mspi

source_name: T1 HPAII


title: ARF19_pos_1

source_name: UBQ10:YFP-ARF19 line treated with 10 µM IAA for 2h, replicate 1


title: ARF19_pos_2

source_name: UBQ10:YFP-ARF19 line treated with 10 µM IAA for 2h, replicate 2


title: wild-type developing uppermost internode [WTPS]_3

value: wildtype


title: ARF19_pos_3

source_name: UBQ10:YFP-ARF19 line treated with 10 µM IAA for 2h, replicate 3


title: ARF19_pos_4

source_name: UBQ10:YFP-ARF19 line treated with 10 µM IAA for 2h, replicate 4


title: MELA33

source_name: MELA33 mspi

source_name: MELA33 HPAII


title: ARF19k_1

source_name: UBQ10:YFP-ARF19k line, replicate 1


title: T10

source_name: T10 mspi

source_name: T10 HPAII


title: MELA31

source_name: MELA31 mspi

source_name: MELA31 HPAII


title: DSS&C188-9 colon, biological rep 3

city: Houston

first: Prema

last: Robinson

state: Texas

address: 6767 Bertner Ave

department: Infectious Diseases

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: Samples were reversed transcribed to generate amplified, fragmented and biotinylated sense-strand cDNA, according to manufacturer’s standard protocol. The fragmented and labeled sscDNA (5.2 µg) was then hybridized to Affymetrix Mouse Transcriptome Array 1.0 ST at 45ºC for 16h and subsequently washed and stained using Affymetrix proprietary reagents in the GeneChip Fluidics Station 450 (FS450).

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G scanner (Affymetrix) and quantified into .CEL files with image and signal intensities.

data_processing: Transcriptome Analysis Console software v4.0 (Affymetrix) was used for probe set summarization and robust multiarray average (RMA) normalization procedures.

label: biotin

source_name: Mus musculus WT colon

label_protocol: One hundred nanograms (100ng) of Total RNA was used to process the samples for Whole Transcriptome Expression Analysis with the WT Plus assay (Affymetrix).

growth_protocol: Total RNA was isolated from colonic tissues by homogenization in QIAzol lysis reagent (Qiagen) using a Tissue Lyser LT (Cat No./ID: 69980, Qiagen) to disrupt the tissue. The quality and quantity of the RNA were assessed by gel electrophoresis and a NanoDrop spectrophotometer (Thermo Fisher Scientific).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 8 week old BALB/C mice were randomly assigned to one of three  groups: 1) no DSS ; 2) DSS ; 3) DSS plus C188-9 (C188-9, a small-molecule inhibitor of STAT3).

tag: agent

value: DSS plus C188-9

value: 8 week

value: BALB/C

value: Colon

value: WT


title: MELA26

source_name: MELA26 mspi

source_name: MELA26 HPAII


title: MELA29

source_name: MELA29 mspi

source_name: MELA29 HPAII


title: MELA30

source_name: MELA30 mspi

source_name: MELA30 HPAII


title: wild-type developing uppermost internode [WTPS]_2

source_name: developing uppermost internode


title: MELA27

source_name: MELA27 mspi

source_name: MELA27 HPAII


title: ARF19_4

source_name: UBQ10:YFP-ARF19 line, replicate 4

value: Columbia

value: Whole seedlings, 5 days old

value: Whole seedlings

value: PNS


title: no DSS colon, biological rep 4

value: no DSS


title: ARF19_3

source_name: UBQ10:YFP-ARF19 line, replicate 3


title: no DSS colon, biological rep 3


title: DSS&C188-9 colon, biological rep 1


title: MELA24

source_name: MELA24 mspi

value: Melanoma

value: MSPI restriction digestions

source_name: MELA24 HPAII

value: HPAII restriction digestions


title: no DSS colon, biological rep 2


title: DSS&C188-9 colon, biological rep 2


title: wild-type developing uppermost internode [WTPS]_1

value: XiuShui 134 (XS134)


title: ARF19_2

source_name: UBQ10:YFP-ARF19 line, replicate 2


title: no DSS colon, biological rep 5


title: no DSS colon, biological rep 1


title: mir396ef seedling shoot [D389]_3

description:
XS134vsD389.DiffExpGene.xlsx
XS134vsD389.DiffExpGene.xlsx

source_name: seedling shoot

value: seedling shoot

value: 20 days


title: Col_pos_4

source_name: Col-0 treated with 10 µM IAA for 2h, replicate 4


title: ARF19_1

source_name: UBQ10:YFP-ARF19 line, replicate 1


title: mir396ef seedling shoot [D389]_2


title: Col_pos_3

source_name: Col-0 treated with 10 µM IAA for 2h, replicate 3


title: mir396ef seedling shoot [D389]_1


title: mir396ef seedling shoot [D371]_3

description:
XS134vsD371.DiffExpGene.xlsx
XS134vsD371.DiffExpGene.xlsx


title: Col_pos_2

source_name: Col-0 treated with 10 µM IAA for 2h, replicate 2


title: mir396ef seedling shoot [D371]_2


title: Col_4

source_name: Col-0, replicate 4


title: MELA14

source_name: MELA14 mspi

source_name: MELA14 HPAII


title: Col_3

source_name: Col-0, replicate 3


title: DSS colon, biological rep 4

source_name: Mus musculus WT colon

value: DSS


title: DSS colon, biological rep 1


title: MELA13

source_name: MELA13 mspi

source_name: MELA13 HPAII


title: normoglycemic-rep2

city: Paris

first: Christophe

last: Helary

address: 4, place Jussieu

department: Chemistry

country: France

institute: Sorbonne University

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix)

scan_protocol: GeneChip 3000 7G Scanner with Affymetrix GeneChip Command Console Software (AGCC).

data_processing: alternative CDF (MBNI Custom CDF;hgu133plus2hsentrezgenecdf, version 13.0.0) and signal intensities called using gcrma preprocessed data

source_name: THP-1 cells (1g/L glucose)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip® 3’ IVT Express Kit User Manual, Affymetrix).

growth_protocol: THP-1 cells cultivated in hyperglycemia or normoglycemia, hypoxia and differentiated into macrophages by PMA. Macrophages activated by LPS

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Qiagen Rneasy mini kit).

treatment_protocol: No treatment before the RNA extraction

value: normoglycemia

value: macrophage

tag: cell line

value: THP-1 cells


title: MELA15

source_name: MELA15 mspi

source_name: MELA15 HPAII


title: MELA7

source_name: MELA7 mspi

source_name: MELA7 HPAII


title: MELA9

source_name: MELA9 mspi

source_name: MELA9 HPAII


title: DSS colon, biological rep 3

value: 8 week

value: BALB/C

value: Colon


title: MELA5

source_name: MELA5 mspi

source_name: MELA5 HPAII


title: wild-type seedling shoot [XS134]_3

description:
XS134vsD371.DiffExpGene.xlsx, XS134vsD389.DiffExpGene.xlsx
XS134vsD371.DiffExpGene.xlsx, XS134vsD389.DiffExpGene.xlsx

source_name: seedling shoot

value: wildtype


title: DSS colon, biological rep 2

value: WT


title: Col_2

source_name: Col-0, replicate 2

value: Columbia

value: Whole seedlings, 5 days old

value: Whole seedlings

value: PNS


title: wild-type seedling shoot [XS134]_2


title: Col_pos_1

source_name: Col-0 treated with 10 µM IAA for 2h, replicate 1


title: wild-type seedling shoot [XS134]_1


title: MELA11

source_name: MELA11 mspi

value: Melanoma

value: MSPI restriction digestions

source_name: MELA11 HPAII

value: HPAII restriction digestions


title: Col_1

source_name: Col-0, replicate 1


title: normoglycemic-rep3


title: normoglycemic-rep1


title: hyperglycemia-rep3

source_name: THP-1 cells (4.5g/L glucose)

value: hyperglycemia


title: POOLED

description: Normal Melanocyte Control

source_name: POOLED mspi

value: Normal Melanocyte Control

source_name: POOLED HPAII


title: MELA3

source_name: MELA3 mspi

source_name: MELA3 HPAII


title: hyperglycemia-rep2


title: KK3

description: Normal Melanocyte Control

source_name: KK3 mspi

source_name: KK3 HPAII


title: MELA1

source_name: MELA1 mspi

source_name: MELA1 HPAII


title: FF2

description: Normal Melanocyte Control

source_name: FF2 mspi

source_name: FF2 HPAII


title: hyperglycemia-rep1


title: NT141_W18D2T60_CR

status: Public on Jul 23 2019

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Samples were hybridized to Affymetrix GeneChip Human Gene 1.1 ST array plates (Santa Clara, CA) according to manufacturer's instructions.

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' (v1.30.0).

source_name: Peripheral blood mononuclear cells isolated from subject 141, W18 = after intervention, Day 2 = OGTT, T60 = 60 minutes

label_protocol: One hundred nanogram of total RNA was used for whole transcript cDNA synthesis with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Included in this study were 72 healthy, overweight, Caucasian men and women, aged 50-65, with a BMI 25-35kg/m2, that were recruited from London (UK) and surroundings. Exclusion criteria included: weight change of ≥ 3kg in the preceding 3 months, current smokers, substance abuse, excess alcohol intake, pregnancy, diabetes, cardiovascular disease, cancer, gastrointestinal disease e.g. inflammatory bowel disease or irritable bowel syndrome, kidney disease, liver disease, pancreatitis, use of medications likely to interfere with energy metabolism, appetite regulation and hormonal balance (including: anti-inflammatory drugs or steroids, antibiotics, androgens, phenytoin, erythromycin or thyroid hormones), having any metallic or magnetic implants such as pacemakers, and claustrophobia. Before participating in the study, exach subject provided written informed consent. The study was approved by the Brent Ethics Committee (REC ref: 12/LO/0139) and was registered at clinicaltrials.gov as NCT01684917.

extract_protocol: RNA was isolated (RNeasy Micro kit, Qiagen, Venlo, the Netherlands), quantified (Nanodrop ND 1000, Nanodrop technologies, Wilmington, Delaware USA) and integrity was checked by an Agilent 2100 Bioanalyser with RNA 6000 microchips (Agilent Technologies, South Queensferry, UK). Samples were included for microarray analysis if the RNA integrity number (RIN) was > 7.

treatment_protocol: Intervention diets: Subjects were randomly assigned to either a 20% energy restriction (ER) diet  (n=40), or to a control diet (n=32) for 12 weeks. The ER diet consisted of 50% calories from carbohydrates, 35% from fat and 15% from protein, >18g of fibre, and at least five portions of fruit and vegetables a day. The control diet consisted of 40% calories from carbohydrates, 45% from fat and 15% from protein, and at least three portions of fruit and vegetables a day. Both groups completed a seven-day food diary the first and last week of the study. Diets were based on dietary advice. Compliance was assessed via a weekly telephone interview. Exercise was kept at the habitual level. Nutritional challenge tests: Before and after the intervention, all subjects were subjected to an oral glucose tolerance test (OGTT) and the next day to a mixed meal test (MMT). Peripheral blood mononuclear cells (PBMCs) were sampled at fasting, and postprandially during the OGTT at 30, 60, and 120 min and during MMT at 60, 120, 240, and 360 min. PBMCs were isolated from whole blood using BD Vacutainer Cell Preparation Tubes according to the manufacturer’s instructions.

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: OGTT

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: after intervention

tag: intervention group assignment (er/control)

value: ER

tag: age (yrs)

tag: gender

value: Female

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: III


title: NT022_W18D3T240_CR

source_name: Peripheral blood mononuclear cells isolated from subject 022, W18 = after intervention, Day 3 = MMT, T240 = 240 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: MMT

value: Approvel 150mg

value: I


title: NT022_W18D3T60_CR

source_name: Peripheral blood mononuclear cells isolated from subject 022, W18 = after intervention, Day 3 = MMT, T60 = 60 minutes

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)


title: NT041_W18D2T60_Control

source_name: Peripheral blood mononuclear cells isolated from subject 041, W18 = after intervention, Day 2 = OGTT, T60 = 60 minutes

value: control

tag: age (yrs)

tag: gender

value: Male

tag: body weight (kg)

value: II


title: NT142_W18D2T30_Control

source_name: Peripheral blood mononuclear cells isolated from subject 142, W18 = after intervention, Day 2 = OGTT, T30 = 30 minutes

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

value: Cod liver oil

value: IV


title: NT142_W5D2T120_Control

source_name: Peripheral blood mononuclear cells isolated from subject 142, W5 = before intervention, Day 2 = OGTT, T120 = 120 minutes

value: before intervention

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)


title: NT142_W18D2T60_Control

source_name: Peripheral blood mononuclear cells isolated from subject 142, W18 = after intervention, Day 2 = OGTT, T60 = 60 minutes

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use


title: NT142_W18D2T0_Control

source_name: Peripheral blood mononuclear cells isolated from subject 142, W18 = after intervention, Day 2 = OGTT, T0 = Fasting sample

tag: subject

tag: % body fat

tag: microarray plate batch


title: NT142_W18D2T120_Control

source_name: Peripheral blood mononuclear cells isolated from subject 142, W18 = after intervention, Day 2 = OGTT, T120 = 120 minutes

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)


title: NT041_W18D2T30_Control

source_name: Peripheral blood mononuclear cells isolated from subject 041, W18 = after intervention, Day 2 = OGTT, T30 = 30 minutes

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender


title: NT141_W18D2T30_CR

source_name: Peripheral blood mononuclear cells isolated from subject 141, W18 = after intervention, Day 2 = OGTT, T30 = 30 minutes

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)


title: NT141_W18D2T120_CR

source_name: Peripheral blood mononuclear cells isolated from subject 141, W18 = after intervention, Day 2 = OGTT, T120 = 120 minutes

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)


title: NT041_W18D2T0_Control

source_name: Peripheral blood mononuclear cells isolated from subject 041, W18 = after intervention, Day 2 = OGTT, T0 = Fasting sample

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)


title: NT141_W18D2T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 141, W18 = after intervention, Day 2 = OGTT, T0 = Fasting sample

tag: subject

tag: % body fat

tag: medication/supplement/diet use


title: mir396ef seedling shoot [D371]_1

source_name: seedling shoot

tag: background cultivar

value: XiuShui 134 (XS134)

tag: genotype

tag: line id

tag: tissue

value: seedling shoot

tag: age

value: 20 days


title: NT022_W18D3T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 022, W18 = after intervention, Day 3 = MMT, T0 = Fasting sample

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: microarray plate batch


title: NT041_W18D2T120_Control

source_name: Peripheral blood mononuclear cells isolated from subject 041, W18 = after intervention, Day 2 = OGTT, T120 = 120 minutes

value: OGTT

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)


title: NT022_W18D3T120_CR

source_name: Peripheral blood mononuclear cells isolated from subject 022, W18 = after intervention, Day 3 = MMT, T120 = 120 minutes

tag: subject

tag: % body fat

value: after intervention

tag: medication/supplement/diet use


title: NT041_W5D2T120_Control

source_name: Peripheral blood mononuclear cells isolated from subject 041, W5 = before intervention, Day 2 = OGTT, T120 = 120 minutes

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)


title: NT022_W18D3T360_CR

source_name: Peripheral blood mononuclear cells isolated from subject 022, W18 = after intervention, Day 3 = MMT, T360 = 360 minutes

tag: intervention group assignment (er/control)

value: ER

tag: age (yrs)

tag: gender


title: NT141_W5D2T120_CR

source_name: Peripheral blood mononuclear cells isolated from subject 141, W5 = before intervention, Day 2 = OGTT, T120 = 120 minutes

value: Female

tag: body weight (kg)

tag: body height (m)

tag: microarray plate batch


title: NT141_W5D2T60_CR

source_name: Peripheral blood mononuclear cells isolated from subject 141, W5 = before intervention, Day 2 = OGTT, T60 = 60 minutes

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

value: III


title: NT041_W5D2T60_Control

source_name: Peripheral blood mononuclear cells isolated from subject 041, W5 = before intervention, Day 2 = OGTT, T60 = 60 minutes

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)


title: NT148_W18D3T360_CR

source_name: Peripheral blood mononuclear cells isolated from subject 148, W18 = after intervention, Day 3 = MMT, T360 = 360 minutes

tag: subject

tag: % body fat

value: MMT

tag: heart rate (beats/min)

value: Nothing

value: XIII


title: NT141_W5D2T30_CR

source_name: Peripheral blood mononuclear cells isolated from subject 141, W5 = before intervention, Day 2 = OGTT, T30 = 30 minutes

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: medication/supplement/diet use


title: NT133_W18D3T360_Control

source_name: Peripheral blood mononuclear cells isolated from subject 133, W18 = after intervention, Day 3 = MMT, T360 = 360 minutes

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: control

tag: age (yrs)

value: XII


title: NT142_W5D2T30_Control

source_name: Peripheral blood mononuclear cells isolated from subject 142, W5 = before intervention, Day 2 = OGTT, T30 = 30 minutes

tag: gender

value: Male

tag: body weight (kg)

tag: body height (m)


title: NT125_W18D3T360_Control

source_name: Peripheral blood mononuclear cells isolated from subject 125, W18 = after intervention, Day 3 = MMT, T360 = 360 minutes

tag: bmi (kg/m2)

tag: hip circumference (cm)

value: thyroxine

tag: microarray plate batch

value: XI


title: NT022_W5D3T360_CR

source_name: Peripheral blood mononuclear cells isolated from subject 022, W5 = before intervention, Day 3 = MMT, T360 = 360 minutes

value: before intervention

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

value: Approvel 150mg

value: I


title: NT106_W18D3T360_CR

source_name: Peripheral blood mononuclear cells isolated from subject 106, W18 = after intervention, Day 3 = MMT, T360 = 360 minutes

tag: subject

tag: % body fat

tag: systolic blood pressure (mm hg)

value: X


title: NT076_W18D3T360_Control

source_name: Peripheral blood mononuclear cells isolated from subject 076, W18 = after intervention, Day 3 = MMT, T360 = 360 minutes

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: heart rate (beats/min)

value: HRT

value: VIII


title: NT044_W18D3T360_CR

source_name: Peripheral blood mononuclear cells isolated from subject 044, W18 = after intervention, Day 3 = MMT, T360 = 360 minutes

tag: moment of sampling / challenge test (before/after intervention)

value: after intervention

tag: intervention group assignment (er/control)

value: ER

tag: medication/supplement/diet use

value: V


title: NT041_W5D2T30_Control

source_name: Peripheral blood mononuclear cells isolated from subject 041, W5 = before intervention, Day 2 = OGTT, T30 = 30 minutes

value: OGTT

tag: age (yrs)

tag: gender

tag: body weight (kg)

value: II


title: NT065_W18D3T360_Control

source_name: Peripheral blood mononuclear cells isolated from subject 065, W18 = after intervention, Day 3 = MMT, T360 = 360 minutes

value: MMT

value: Female

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

value: cod liver oil, folic acid, multivitamins, vitamin c

value: VII


title: NT055_W18D3T360_Control

source_name: Peripheral blood mononuclear cells isolated from subject 055, W18 = after intervention, Day 3 = MMT, T360 = 360 minutes

value: control

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

value: fluoxetine

tag: microarray plate batch

value: VI


title: NT142_W5D2T0_Control

source_name: Peripheral blood mononuclear cells isolated from subject 142, W5 = before intervention, Day 2 = OGTT, T0 = Fasting sample

tag: subject

tag: % body fat

value: before intervention

value: Male

tag: diastolic blood pressure (mm hg)

value: Cod liver oil

value: IV


title: NT084_W18D3T360_Control

source_name: Peripheral blood mononuclear cells isolated from subject 084, W18 = after intervention, Day 3 = MMT, T360 = 360 minutes

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: systolic blood pressure (mm hg)

value: amlodipine

value: IX


title: NT141_W5D2T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 141, W5 = before intervention, Day 2 = OGTT, T0 = Fasting sample

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: ER

tag: heart rate (beats/min)

value: III


title: SkeletalMuscle_Indian_09S1-261_Rep2

city: Singapore

first: E Shyong

last: Tai

address: 1E Kent Ridge Road

country: Singapore

institute: National University of Singapore, Yong Loo Lin School of Medicine

hyb_protocol: According to the manufacturer's instructions.

scan_protocol: iScan system (Illumina)

data_processing: The data were normalised using quantile normalisation with limma in R

label: Biotin

source_name: Skeletal Muscle Biopsy

label_protocol: Samples were labelled with the Encore BiotinIL Module kit (NuGEN Technologies).

extract_protocol: Total RNA was extracted from patient's skeletal muscle tissue using a combination of TRIzol® Reagent (Invitrogen) and RNeasy Mini Kit (Qiagen). RNA was then amplified using the Ovation PicoSL WTA System (NuGEN Technologies) and purified using the Agencourt RNAClean XP Kit (Beckman Coulter).

tag: ethnicity

value: Indian

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: SkeletalMuscle_Indian_09S1-268_Rep2

tag: ethnicity


title: NT022_W5D3T240_CR

source_name: Peripheral blood mononuclear cells isolated from subject 022, W5 = before intervention, Day 3 = MMT, T240 = 240 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: Approvel 150mg

tag: microarray plate batch

value: I


title: NT148_W18D3T240_CR

source_name: Peripheral blood mononuclear cells isolated from subject 148, W18 = after intervention, Day 3 = MMT, T240 = 240 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: MMT

value: after intervention

value: Nothing

value: XIII


title: SkeletalMuscle_Malay_09S1-257_NoRep

tag: ethnicity

value: Malay

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT125_W18D3T240_Control

source_name: Peripheral blood mononuclear cells isolated from subject 125, W18 = after intervention, Day 3 = MMT, T240 = 240 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: control

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: thyroxine

tag: microarray plate batch

value: XI


title: SkeletalMuscle_Indian_09S1-255_Rep1

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT076_W18D3T240_Control

source_name: Peripheral blood mononuclear cells isolated from subject 076, W18 = after intervention, Day 3 = MMT, T240 = 240 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

value: Female

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: HRT

tag: microarray plate batch

value: VIII


title: SkeletalMuscle_Indian_09S1-255_Rep2

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT106_W18D3T240_CR

source_name: Peripheral blood mononuclear cells isolated from subject 106, W18 = after intervention, Day 3 = MMT, T240 = 240 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: X


title: SkeletalMuscle_Indian_09S1-268_Rep1

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT044_W18D3T240_CR

source_name: Peripheral blood mononuclear cells isolated from subject 044, W18 = after intervention, Day 3 = MMT, T240 = 240 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: ER

tag: age (yrs)

tag: gender

value: Male

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: V


title: NT041_W5D2T0_Control

source_name: Peripheral blood mononuclear cells isolated from subject 041, W5 = before intervention, Day 2 = OGTT, T0 = Fasting sample

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: OGTT

value: before intervention

value: II


title: NT084_W18D3T240_Control

source_name: Peripheral blood mononuclear cells isolated from subject 084, W18 = after intervention, Day 3 = MMT, T240 = 240 minutes

value: MMT

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: after intervention

tag: intervention group assignment (er/control)

value: amlodipine

value: IX


title: SkeletalMuscle_Malay_09S1-253_Rep2

tag: ethnicity

value: Malay

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT055_W18D3T240_Control

source_name: Peripheral blood mononuclear cells isolated from subject 055, W18 = after intervention, Day 3 = MMT, T240 = 240 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: control

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: fluoxetine

tag: microarray plate batch

value: VI


title: NT065_W18D3T240_Control

source_name: Peripheral blood mononuclear cells isolated from subject 065, W18 = after intervention, Day 3 = MMT, T240 = 240 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: Female

value: cod liver oil, folic acid, multivitamins, vitamin c

value: VII


title: SkeletalMuscle_Malay_09S1-250_Rep2

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT148_W18D3T120_CR

source_name: Peripheral blood mononuclear cells isolated from subject 148, W18 = after intervention, Day 3 = MMT, T120 = 120 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: ER

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: Nothing

tag: microarray plate batch

value: XIII


title: NT140_W18D3T360_CR

source_name: Peripheral blood mononuclear cells isolated from subject 140, W18 = after intervention, Day 3 = MMT, T360 = 360 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: IV


title: SkeletalMuscle_Indian_09S1-249_Rep1

tag: ethnicity

value: Indian

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: SkeletalMuscle_Indian_09S1-248_Rep2

tag: ethnicity


title: NT106_W18D3T120_CR

source_name: Peripheral blood mononuclear cells isolated from subject 106, W18 = after intervention, Day 3 = MMT, T120 = 120 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: X


title: NT133_W18D3T120_Control

source_name: Peripheral blood mononuclear cells isolated from subject 133, W18 = after intervention, Day 3 = MMT, T120 = 120 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: MMT

value: XII


title: NT022_W5D3T120_CR

source_name: Peripheral blood mononuclear cells isolated from subject 022, W5 = before intervention, Day 3 = MMT, T120 = 120 minutes

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: before intervention

tag: intervention group assignment (er/control)

value: Approvel 150mg

value: I


title: SkeletalMuscle_Malay_09S1-253_Rep1

tag: ethnicity

value: Malay

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: SkeletalMuscle_Indian_09S1-244_Rep2

tag: ethnicity


title: SkeletalMuscle_Indian_09S1-248_Rep1

tag: age


title: NT084_W18D3T120_Control

source_name: Peripheral blood mononuclear cells isolated from subject 084, W18 = after intervention, Day 3 = MMT, T120 = 120 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: after intervention

tag: intervention group assignment (er/control)

value: control

tag: age (yrs)

tag: gender

value: Male

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: amlodipine

tag: microarray plate batch

value: IX


title: SkeletalMuscle_Indian_09S1-247_NoRep

source_name: Skeletal Muscle Biopsy

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: SkeletalMuscle_Malay_09S1-250_Rep1

tag: ethnicity


title: NT125_W18D3T120_Control

source_name: Peripheral blood mononuclear cells isolated from subject 125, W18 = after intervention, Day 3 = MMT, T120 = 120 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: thyroxine

tag: microarray plate batch

value: XI


title: NT055_W18D3T120_Control

source_name: Peripheral blood mononuclear cells isolated from subject 055, W18 = after intervention, Day 3 = MMT, T120 = 120 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: Female

value: fluoxetine

value: VI


title: NT076_W18D3T120_Control

source_name: Peripheral blood mononuclear cells isolated from subject 076, W18 = after intervention, Day 3 = MMT, T120 = 120 minutes

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: HRT

value: VIII


title: SkeletalMuscle_Indian_09S1-249_Rep2

tag: ethnicity

value: Indian

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT065_W18D3T120_Control

source_name: Peripheral blood mononuclear cells isolated from subject 065, W18 = after intervention, Day 3 = MMT, T120 = 120 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: MMT

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: cod liver oil, folic acid, multivitamins, vitamin c

tag: microarray plate batch

value: VII


title: SkeletalMuscle_Indian_09S1-244_Rep1

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT044_W18D3T120_CR

source_name: Peripheral blood mononuclear cells isolated from subject 044, W18 = after intervention, Day 3 = MMT, T120 = 120 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: ER

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: V


title: SkeletalMuscle_Malay_09S1-243_Rep2

tag: ethnicity

value: Malay

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: SkeletalMuscle_Malay_09S1-243_Rep1

tag: ethnicity


title: SkeletalMuscle_Indian_09S1-242_Rep2

tag: age


title: NT060_W18D3T360_CR

source_name: Peripheral blood mononuclear cells isolated from subject 060, W18 = after intervention, Day 3 = MMT, T360 = 360 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: after intervention

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: III


title: SkeletalMuscle_Malay_09S1-240_NoRep

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT148_W18D3T60_CR

source_name: Peripheral blood mononuclear cells isolated from subject 148, W18 = after intervention, Day 3 = MMT, T60 = 60 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

value: Male

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: Nothing

tag: microarray plate batch

value: XIII


title: SkeletalMuscle_Indian_09S1-242_Rep1

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT022_W5D3T60_CR

source_name: Peripheral blood mononuclear cells isolated from subject 022, W5 = before intervention, Day 3 = MMT, T60 = 60 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: before intervention

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

value: Female

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: Approvel 150mg

tag: microarray plate batch

value: I


title: NT140_W18D3T240_CR

source_name: Peripheral blood mononuclear cells isolated from subject 140, W18 = after intervention, Day 3 = MMT, T240 = 240 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: IV


title: NT125_W18D3T60_Control

source_name: Peripheral blood mononuclear cells isolated from subject 125, W18 = after intervention, Day 3 = MMT, T60 = 60 minutes

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: control

value: thyroxine

value: XI


title: NT033_W18D3T360_CR

source_name: Peripheral blood mononuclear cells isolated from subject 033, W18 = after intervention, Day 3 = MMT, T360 = 360 minutes

value: MMT

tag: age (yrs)

tag: gender

tag: body weight (kg)

value: II


title: NT133_W18D3T240_Control

source_name: Peripheral blood mononuclear cells isolated from subject 133, W18 = after intervention, Day 3 = MMT, T240 = 240 minutes

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

value: XII


title: SkeletalMuscle_Malay_09S1-237_Rep2

tag: ethnicity

value: Malay

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT133_W18D3T60_Control

source_name: Peripheral blood mononuclear cells isolated from subject 133, W18 = after intervention, Day 3 = MMT, T60 = 60 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: after intervention

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch


title: SkeletalMuscle_Malay_09S1-236_Rep1

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT084_W18D3T60_Control

source_name: Peripheral blood mononuclear cells isolated from subject 084, W18 = after intervention, Day 3 = MMT, T60 = 60 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: amlodipine

tag: microarray plate batch

value: IX


title: SkeletalMuscle_Malay_09S1-234_NoRep

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT055_W18D3T60_Control

source_name: Peripheral blood mononuclear cells isolated from subject 055, W18 = after intervention, Day 3 = MMT, T60 = 60 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: fluoxetine

tag: microarray plate batch

value: VI


title: NT065_W18D3T60_Control

source_name: Peripheral blood mononuclear cells isolated from subject 065, W18 = after intervention, Day 3 = MMT, T60 = 60 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: cod liver oil, folic acid, multivitamins, vitamin c

value: VII


title: NT142_W5D2T60_Control

source_name: Peripheral blood mononuclear cells isolated from subject 142, W5 = before intervention, Day 2 = OGTT, T60 = 60 minutes

value: OGTT

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: before intervention

tag: intervention group assignment (er/control)

value: Male

value: Cod liver oil


title: SkeletalMuscle_Malay_09S1-237_Rep1

source_name: Skeletal Muscle Biopsy

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT044_W18D3T60_CR

source_name: Peripheral blood mononuclear cells isolated from subject 044, W18 = after intervention, Day 3 = MMT, T60 = 60 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: ER

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: V


title: SkeletalMuscle_Indian_09S1-230_Rep2

tag: ethnicity

value: Indian

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: SkeletalMuscle_Indian_09S1-230_Rep1

tag: ethnicity


title: NT106_W18D3T60_CR

source_name: Peripheral blood mononuclear cells isolated from subject 106, W18 = after intervention, Day 3 = MMT, T60 = 60 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: MMT

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

value: Female

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: X


title: SkeletalMuscle_Malay_09S1-239_NoRep

tag: ethnicity

value: Malay

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT076_W18D3T60_Control

source_name: Peripheral blood mononuclear cells isolated from subject 076, W18 = after intervention, Day 3 = MMT, T60 = 60 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: after intervention

tag: intervention group assignment (er/control)

value: control

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: HRT

tag: microarray plate batch

value: VIII


title: SkeletalMuscle_Malay_09S1-238_NoRep

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: SkeletalMuscle_Indian_09S1-231_Rep1

tag: ethnicity


title: SkeletalMuscle_Indian_09S1-231_Rep2

tag: age


title: SkeletalMuscle_Malay_09S1-236_Rep2

tag: tsh


title: NT060_W18D3T240_CR

source_name: Peripheral blood mononuclear cells isolated from subject 060, W18 = after intervention, Day 3 = MMT, T240 = 240 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: III


title: SkeletalMuscle_Indian_09S1-214_NoRep

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: SkeletalMuscle_Malay_09S1-224_NoRep

tag: ethnicity


title: NT140_W18D3T120_CR

source_name: Peripheral blood mononuclear cells isolated from subject 140, W18 = after intervention, Day 3 = MMT, T120 = 120 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: IV


title: SkeletalMuscle_Indian_09S1-212_Rep2

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: SkeletalMuscle_Malay_09S1-209_NoRep

tag: ethnicity


title: SkeletalMuscle_Malay_09S1-210_Rep2

tag: age


title: NT148_W18D3T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 148, W18 = after intervention, Day 3 = MMT, T0 = Fasting sample

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: Nothing

tag: microarray plate batch

value: XIII


title: SkeletalMuscle_Malay_09S1-210_Rep1

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: SkeletalMuscle_Malay_09S1-207_NoRep

tag: ethnicity


title: NT133_W18D3T0_Control

source_name: Peripheral blood mononuclear cells isolated from subject 133, W18 = after intervention, Day 3 = MMT, T0 = Fasting sample

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: XII


title: SkeletalMuscle_Indian_09S1-212_Rep1

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT033_W18D3T240_CR

source_name: Peripheral blood mononuclear cells isolated from subject 033, W18 = after intervention, Day 3 = MMT, T240 = 240 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: II


title: NT084_W18D3T0_Control

source_name: Peripheral blood mononuclear cells isolated from subject 084, W18 = after intervention, Day 3 = MMT, T0 = Fasting sample

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: Male

value: amlodipine

value: IX


title: NT076_W18D3T0_Control

source_name: Peripheral blood mononuclear cells isolated from subject 076, W18 = after intervention, Day 3 = MMT, T0 = Fasting sample

value: MMT

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)


title: NT125_W18D3T0_Control

source_name: Peripheral blood mononuclear cells isolated from subject 125, W18 = after intervention, Day 3 = MMT, T0 = Fasting sample

tag: age (yrs)

tag: gender

tag: body weight (kg)

value: thyroxine

value: XI


title: SkeletalMuscle_Malay_09S1-205_Rep1

tag: ethnicity

value: Malay

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: SkeletalMuscle_Malay_09S1-205_Rep2

tag: ethnicity


title: SkeletalMuscle_Indian_09S1-204_Rep3

value: Indian

tag: age


title: NT055_W18D3T0_Control

source_name: Peripheral blood mononuclear cells isolated from subject 055, W18 = after intervention, Day 3 = MMT, T0 = Fasting sample

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: after intervention

tag: intervention group assignment (er/control)

value: control

tag: age (yrs)

tag: gender

value: Female

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: fluoxetine

tag: microarray plate batch

value: VI


title: SkeletalMuscle_Malay_09S1-201_NoRep

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT106_W18D3T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 106, W18 = after intervention, Day 3 = MMT, T0 = Fasting sample

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: ER

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: X


title: NT065_W18D3T0_Control

source_name: Peripheral blood mononuclear cells isolated from subject 065, W18 = after intervention, Day 3 = MMT, T0 = Fasting sample

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: cod liver oil, folic acid, multivitamins, vitamin c

value: VII


title: NT060_W18D3T120_CR

source_name: Peripheral blood mononuclear cells isolated from subject 060, W18 = after intervention, Day 3 = MMT, T120 = 120 minutes

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: III


title: NT022_W5D3T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 022, W5 = before intervention, Day 3 = MMT, T0 = Fasting sample

value: before intervention

tag: age (yrs)

tag: gender

tag: body weight (kg)

value: Approvel 150mg

value: I


title: NT022_W18D2T60_CR

source_name: Peripheral blood mononuclear cells isolated from subject 022, W18 = after intervention, Day 2 = OGTT, T60 = 60 minutes

value: OGTT

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)


title: SkeletalMuscle_Indian_09S1-200_Rep2

source_name: Skeletal Muscle Biopsy

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT033_W18D3T120_CR

source_name: Peripheral blood mononuclear cells isolated from subject 033, W18 = after intervention, Day 3 = MMT, T120 = 120 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: MMT

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: II


title: SkeletalMuscle_Malay_09S1-206_NoRep

tag: ethnicity

value: Malay

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT044_W18D3T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 044, W18 = after intervention, Day 3 = MMT, T0 = Fasting sample

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: after intervention

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

value: Male

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: V


title: SkeletalMuscle_Indian_09S1-204_Rep1

tag: ethnicity

value: Indian

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: SkeletalMuscle_Indian_09S1-261_Rep1

tag: ethnicity


title: SkeletalMuscle_Indian_09S1-204_Rep2

tag: age


title: SkeletalMuscle_Malay_09S1-199_Rep2

tag: tsh


title: SkeletalMuscle_Indian_09S1-200_Rep1

tag: mstn


title: SkeletalMuscle_Malay_09S1-197_Rep2

tag: ldh


title: NT133_W5D3T360_Control

source_name: Peripheral blood mononuclear cells isolated from subject 133, W5 = before intervention, Day 3 = MMT, T360 = 360 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: control

tag: age (yrs)

tag: gender

value: Female

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: XII


title: NT125_W5D3T360_Control

source_name: Peripheral blood mononuclear cells isolated from subject 125, W5 = before intervention, Day 3 = MMT, T360 = 360 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: thyroxine

value: XI


title: SkeletalMuscle_Indian_09S1-196_NoRep

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT084_W5D3T360_Control

source_name: Peripheral blood mononuclear cells isolated from subject 084, W5 = before intervention, Day 3 = MMT, T360 = 360 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: amlodipine

tag: microarray plate batch

value: IX


title: NT106_W5D3T360_CR

source_name: Peripheral blood mononuclear cells isolated from subject 106, W5 = before intervention, Day 3 = MMT, T360 = 360 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: before intervention

value: ER

value: X


title: NT140_W18D3T0_CR

source_name: Peripheral blood mononuclear cells isolated from subject 140, W18 = after intervention, Day 3 = MMT, T0 = Fasting sample

value: MMT

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: IV


title: NT060_W18D3T60_CR

source_name: Peripheral blood mononuclear cells isolated from subject 060, W18 = after intervention, Day 3 = MMT, T60 = 60 minutes

tag: age (yrs)

tag: gender

tag: body weight (kg)

value: III


title: NT022_W18D2T30_CR

source_name: Peripheral blood mononuclear cells isolated from subject 022, W18 = after intervention, Day 2 = OGTT, T30 = 30 minutes

value: OGTT

value: after intervention

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

value: Approvel 150mg

value: I


title: NT044_W5D3T360_CR

source_name: Peripheral blood mononuclear cells isolated from subject 044, W5 = before intervention, Day 3 = MMT, T360 = 360 minutes

value: Male

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

value: V


title: NT033_W18D3T60_CR

source_name: Peripheral blood mononuclear cells isolated from subject 033, W18 = after intervention, Day 3 = MMT, T60 = 60 minutes

value: Female

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: II


title: NT065_W5D3T360_Control

source_name: Peripheral blood mononuclear cells isolated from subject 065, W5 = before intervention, Day 3 = MMT, T360 = 360 minutes

tag: subject

tag: % body fat

value: control

value: cod liver oil, folic acid, multivitamins, vitamin c

tag: microarray plate batch

value: VII


title: SkeletalMuscle_Malay_09S1-199_Rep1

tag: ethnicity

value: Malay

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: SkeletalMuscle_Indian_09S1-195_Rep1

tag: ethnicity

value: Indian


title: SkeletalMuscle_Indian_09S1-190_NoRep

tag: age


title: SkeletalMuscle_Malay_09S1-193_Rep1

tag: tsh


title: SkeletalMuscle_Indian_09S1-191_NoRep

tag: mstn


title: NT055_W5D3T360_Control

source_name: Peripheral blood mononuclear cells isolated from subject 055, W5 = before intervention, Day 3 = MMT, T360 = 360 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

value: before intervention

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: fluoxetine

tag: microarray plate batch

value: VI


title: SkeletalMuscle_Indian_09S1-189_Rep2

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT148_W5D3T240_CR

source_name: Peripheral blood mononuclear cells isolated from subject 148, W5 = before intervention, Day 3 = MMT, T240 = 240 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

value: MMT

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: ER

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: Nothing

tag: microarray plate batch

value: XIII


title: SkeletalMuscle_Malay_09S1-192_NoRep

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: SkeletalMuscle_Malay_09S1-194_NoRep

tag: ethnicity


title: SkeletalMuscle_Malay_09S1-193_Rep2

tag: age


title: NT140_W5D3T360_CR

source_name: Peripheral blood mononuclear cells isolated from subject 140, W5 = before intervention, Day 3 = MMT, T360 = 360 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: IV


title: SkeletalMuscle_Malay_09S1-197_Rep1

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: SkeletalMuscle_Indian_09S1-195_Rep2

tag: ethnicity


title: NT076_W5D3T360_Control

source_name: Peripheral blood mononuclear cells isolated from subject 076, W5 = before intervention, Day 3 = MMT, T360 = 360 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

value: HRT

tag: microarray plate batch

value: VIII


title: SkeletalMuscle_Indian_09S1-189_Rep1

source_name: Skeletal Muscle Biopsy

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT133_W5D3T240_Control

source_name: Peripheral blood mononuclear cells isolated from subject 133, W5 = before intervention, Day 3 = MMT, T240 = 240 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

tag: age (yrs)

tag: gender

value: Female

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch

value: XII


title: SkeletalMuscle_Indian_09S1-188_NoRep

tag: ethnicity

tag: age

tag: tsh

tag: mstn

tag: ldh

tag: alt

tag: ast

tag: hdl

tag: percentagesmclefat

tag: weight

tag: hipcir

tag: waistcir

tag: percentagebf

tag: bmi

tag: leptin

tag: fpg

tag: isi


title: NT076_W5D3T240_Control

source_name: Peripheral blood mononuclear cells isolated from subject 076, W5 = before intervention, Day 3 = MMT, T240 = 240 minutes

tag: subject

tag: % body fat

tag: type of challenge study (ogtt/mmt)

tag: sampling time challenge test (h)

tag: moment of sampling / challenge test (before/after intervention)

tag: intervention group assignment (er/control)

value: control

tag: age (yrs)

tag: gender

tag: body weight (kg)

tag: body height (m)

tag: bmi (kg/m2)

tag: hip circumference (cm)

tag: waist circumference (cm)

tag: waist hip ratio (ratio)

tag: diastolic blood pressure (mm hg)

tag: systolic blood pressure (mm hg)

tag: heart rate (beats/min)

tag: medication/supplement/diet use

tag: microarray plate batch