title: maternal whole blood replicate 2

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

institute: BioChainBJ

description:
Sample name: NMB6-blo_cy5/cy3
Biological replicate 2 of 4 maternal whole blood
US10283824_252984210018_S01_CGH_107_Sep09_2_2.txt

hyb_protocol: According to the instructions of Agilent Oligo aCGH  Hybridization Kit

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent GeneSpring GX 11.5 was used for background subtraction and LOWESS normalization.Following global mean normalization, probes with an intensity <400 were discarded for further analysis.

source_name: methylated CpG-island recovery assay (MIRA) enriched, maternal whole blood, 2 of 4 mother-baby pairs

label_protocol: The products of whole genome amplification from the total input DNA without MBD enrichment and from methylation-enriched DNA were purified by using DNA purification kit, respectively. The purified DNA fragments were then labeled with cy3-dCTP or cy5-dCTP with Klenow enzyme (Takara) according to the instruction of the manufacturer.

extract_protocol: DNA was isolated from fresh frozen tissues using standard phenol/chloroform method.

tag: sample id

value: maternal whole blood

tag: gender

value: Female

tag: sample type

value: methylation-enriched DNA

source_name: input, maternal whole blood, 2 of 4 mother-baby pairs

value: total input DNA


title: Eed-null MLL-AF9 BM-cells, biological rep1

status: Public on Feb 22 2012

type: RNA

city: Boston

first: Amit

last: Sinha

state: MA

address: 44 Binney St

department: Pediatric Oncology

country: USA

institute: Dana-Farber Cancer Institute

hyb_protocol: 5 mcg of amplified, labeled cDNA was hybridized to the Affymetrix 430 2.0 microarray using standard conditions.

scan_protocol: GeneChip Scanner 3000, 7G. Standard Affymetrix protocol.

data_processing: RMA background correction and quantile normalization was done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/), which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al. Biostatistics (2003).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Sorted GFP+/YFP+ bone marrow cells, Eed-null

label_protocol: Amplified cDNA was labeled using the NuGEN Encore Biotin Module.

growth_protocol: Leukemia was generated by injecting sublethally irradiated (600cGy) C57B/6 recipient mice with 100,000 cells from replated leukemic colonies and administering pIpC 2-3 weeks after transplantation after to activate Cre expression.

extract_protocol: Total RNA was extracted using Trizol reagent. RNA was amplified using the NuGEN Ovation Pico WTA system (NuGEN, San Carlos, CA).

treatment_protocol: Bone marrow cells from leukemic mice were sorted based on Forward/Side Scatter, Propidium Iodide negativity and GFP/YFP double positivity. GFP indicates retroviral gene transfer of MLL-AF9-ires-GFP, and YFP indicates successful Cre activation.

tag: background strain

tag: disease state

value: MLL-AF9-induced acute myeloid leukemia (AML)

tag: genotype

value: Eed-null

tag: cell type

value: sorted GFP+/YFP+ bone marrow cells


title: maternal whole blood replicate 3

type: genomic

country: China

description:
Sample name: NMB7-blo_cy5/cy3
Biological replicate 3 of 4 maternal whole blood
US10283824_252984210018_S01_CGH_107_Sep09_2_3.txt

molecule: genomic DNA

organism: Homo sapiens

source_name: methylated CpG-island recovery assay (MIRA) enriched, maternal whole blood, 3 of 4 mother-baby pairs

tag: tissue

source_name: input, maternal whole blood, 3 of 4 mother-baby pairs


title: 24 day pre-tumor Dnmt3b-deficient thymocytes, biological replicate 2

city: Omaha

first: Ryan

last: Hlady

state: Nebraska

department: Eppley

institute: UNMC

description:
TEJ%F0F(v)v1 (3b24-2).CEL
gene expression data from Dnmt3b-deficient pre-tumor thymocytes

hyb_protocol: Following fragmentation and end labeling, 5.0 ug of end-labeled cDNA was hybridized to Affymetrix Mouse Gene 1.0 ST Arrays at 45°  for 16 hrs using an Affymetrix hybridization oven and stained using the Affmetrix 450 fluidics station per manufacturer’s recommendations.

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G.

data_processing: Intensities were imported into Partek Genomics Suite software using Robust Multi-chip Averaging (RMA) background correction and quantile normalization on a linear scale. Regularized t test analysis of control versus treatment comparisons was performed using a Bayesian approach to estimate the within treatment variation among replicates using Cyber-T software

source_name: Dnmt3b-deficient pre-tumor cells harvested from thymus of 24 day old Dnmt3b-deficient mice

label_protocol: Total RNA samples (300 ng) were processed using the Ambion WT Expression kit per manufacturer’s recommendations to generate sense cDNA (Ambion, Austin, TX). The cDNA was fragmented and end labeled using the GeneChip WT Terminal Labeling kit per Affymetrix instructions (Affymetrix, Santa Clara, CA).

growth_protocol: Th1, Th2, Th3, 3b24-1, 3b24-2 were harvested at 24 days. All Final tumor mice were harvested when lymphoma tumor burden became apparent.

extract_protocol: TRIzol extraction of RNA followed by column purification by Qiagen's RNEasy kit

treatment_protocol: Thymi from pre-tumor mice were  sorted for EGFP+ cells and placed directly into TRIzol. Final tumors were harvested and placed directly into TRIzol.

tag: strain

value: FVB

value: Thymus

value: thymocyte

tag: tumor stage

value: 24 day pre-tumor


title: 24 day pre-tumor Dnmt3b-deficient thymocytes, biological replicate 1

description:
TEJ%F0F(V)m3 (3b24-1).CEL
gene expression data from Dnmt3b-deficient pre-tumor thymocytes


title: maternal whole blood replicate 4

description:
Sample name: NMB8-blo_cy5/cy3
Biological replicate 4 of 4 maternal whole blood
US10283824_252984210018_S01_CGH_107_Sep09_2_4.txt

source_name: methylated CpG-island recovery assay (MIRA) enriched, maternal whole blood, 4 of 4 mother-baby pairs

source_name: input, maternal whole blood, 4 of 4 mother-baby pairs


title: maternal whole blood replicate 1

description:
Sample name: NMB5-blo_cy5/cy3
Biological replicate 1 of 4 maternal whole blood
US10283824_252984210018_S01_CGH_107_Sep09_2_1.txt

source_name: methylated CpG-island recovery assay (MIRA) enriched, maternal whole blood, 1 of 4 mother-baby pairs

source_name: input, maternal whole blood, 1 of 4 mother-baby pairs


title: Ezh2-null MLL-AF9 BM-cells, biological rep3

source_name: Sorted GFP+/YFP+ bone marrow cells, Ezh2-null


title: sars_mu_lung_STAT_Day5_rMA15_#2

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

description: US23502338_251486818921_S01_GE1-v5_95_Feb07_1_2.txt

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B).

data_processing:
Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.
Agilent Feature extractor software:
platform       x86_64-redhat-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
R version 2.12.2 (2011-02-25)
bioconductor packages: limma
Information on package 'limma'
Description:
Package:       limma
Version:       3.6.9
Date:          2010/12/01version
For the creation of the normalized data matrix, the limma package was used. Background correction was performed (method=normexp, offset=1).
Data was quantile normalized between arrays with the quantile normalization method and then log2 transformed.

source_name: lung

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: 10-week-old mice were infected intranasally with either phosphate-buffered saline (PBS) alone (Invitrogen, Carlsbad, CA) or 1 × 10^5 PFU rMA15-PBS. Lungs were harvested for microarray at 2, 5 and 9 days-post infection for microarray.

extract_protocol: All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: The left lobe of the lung from each animal was harvested, homogenized using TRIzol and stored at -80 degrees C prior to RNA extraction.

tag: genotype/variation

tag: virus infection

value: SARS rMA15

tag: sample collection time post infection

value: 5 days

tag: biological replicate

value: lung


title: sars_mu_lung_STAT_Day5_rMA15_#3

description: US23502338_251486818921_S01_GE1-v5_95_Feb07_1_4.txt


title: placental tissue replicate 3

description:
Sample name: NMB7-pla_cy5/cy3
Biological replicate 3 of 4 placental tissue
US10283824_252984210018_S01_CGH_107_Sep09_1_3.txt

source_name: methylated CpG-island recovery assay (MIRA) enriched,placental tissue, 3 of 4 mother-baby pairs

value: placental tissue

source_name: input, placental tissue, 3 of 4 mother-baby pairs


title: placental tissue replicate 4

description:
Sample name: NMB8-pla_cy5/cy3
Biological replicate 4 of 4 placental tissue
US10283824_252984210018_S01_CGH_107_Sep09_1_4.txt

source_name: methylated CpG-island recovery assay (MIRA) enriched, placental tissue, 4 of 4 mother-baby pairs

source_name: input, placental tissue, 4 of 4 mother-baby pairs


title: Ezh2-null MLL-AF9 BM-cells, biological rep2


title: Ezh2-null MLL-AF9 BM-cells, biological rep1


title: Dnmt3b-deficient Lymphoma, biological replicate 2

description:
TEJ%F0F(II)m8 (3b2).CEL
gene expression data from Dnmt3b-deficient tumors

source_name: Dnmt3b-deficient tumor cells harvested from thymic lymphoma of Dnmt3b-deficient tumor mice

value: lymphoma

value: Final Tumor


title: sars_mu_lung_STAT_Day5_rMA15_#1

description: US23502338_251486818920_S01_GE1-v5_95_Feb07_1_3.txt


title: Dnmt3b-deficient Lymphoma, biological replicate 1

description:
TEJ%F0Fy2 (3b1).CEL
gene expression data from Dnmt3b-deficient tumors


title: sars_mu_lung_STAT_Day2_rMA15_#2

description: US23502338_251486818922_S01_GE1-v5_95_Feb07_1_2.txt

value: 2 days


title: WT MLL-AF9 BM-cells, biological rep3

source_name: Sorted GFP+/YFP+ bone marrow cells, WT

value: WT


title: sars_mu_lung_STAT_Day2_rMA15_#1

description: US23502338_251486818856_S01_GE1-v5_95_Feb07_1_3.txt


title: WT MLL-AF9 BM-cells, biological rep2


title: sars_mu_lung_IFNAR_Day5_novirus_#2

description: US23502338_251486818856_S01_GE1-v5_95_Feb07_1_2.txt

value: mock-infected (PBS)


title: WT MLL-AF9 BM-cells, biological rep1


title: placental tissue replicate 1

description:
Sample name: NMB5-pla_cy5/cy3
Biological replicate 1 of 4 placental tissue
US10283824_252984210018_S01_CGH_107_Sep09_1_1.txt

source_name: methylated CpG-island recovery assay (MIRA) enriched,placental tissue, 1 of 4 mother-baby pairs

value: methylation-enriched DNA

source_name: input, placental tissue, 1 of 4 mother-baby pairs

value: total input DNA


title: Wild-Type Lymphoma, biological replicate 3

description:
TEb4 (WT3).CEL
gene expression data from Wild-Type Tumors

source_name: Tumor cells harvested from thymic lymphoma of Wild-Type Tumor mice


title: Dnmt3b-deficient Lymphoma, biological replicate 3

description:
TEJ%F0F(II)p4 (3b3).CEL
gene expression data from Dnmt3b-deficient tumors


title: sars_mu_lung_STAT_Day2_rMA15_#3

description: US23502338_251486818898_S01_GE1-v5_95_Feb07_1_4.txt


title: Normal Thymocytes, biological replicate 3

description:
FVB 14 (Th3).CEL
gene expression data from normal thymocytes

source_name: Normal thymocytes from FVB control


title: Normal Thymocytes, biological replicate 2

description:
FVB 13 (Th2).CEL
gene expression data from normal thymocytes


title: sars_mu_lung_IFNAR_Day5_novirus_#3

description: US23502338_251486818899_S01_GE1-v5_95_Feb07_1_2.txt


title: Epididymal adipose GPR120KO ND #720

city: Kyoto

first: Akira

last: Hirasawa

state: Kyoto

address: 46-29 Yoshida Shimoadachi-cho, Sakyo-ku

department: Genomic Drug Discovery Science

country: Japan

institute: Kyoto University Graduate School of Pharmaceutical Sciences

hyb_protocol: The labeled cDNA were then hybridized on Affimetrix gene chip and stained.

scan_protocol: The probe arrays were scanned with the GeneChip(R) Scanner.

data_processing: The data were analyzed with R software. The MAS 5.0 normalization were performed using the justMAS function in the simpleaffy package from Bioconductor.

source_name: EpiAdip GPR120KO ND

label_protocol: cDNA labeling was performed according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted by guanidine hydrochloride-phenol-chloroform method and transcribed to cDNA.

value: Epididymal adipose

value: GPR120 KO

tag: treatment

value: normal diet ND

tag: genetic background

value: mixed 129/Sv and C57BL/6

tag: subject

value: mouse 720


title: Wild-Type Lymphoma, biological replicate 1

description:
TEa2 (WT1).CEL
gene expression data from Wild-Type Tumors

value: FVB

value: Thymus


title: JB09

city: Baltimore

first: Kenneth

middle: W

last: Witwer

state: MD

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files and provided as an Excel spreadsheet.
Raw data were log2-transformed. Data were inverted to facilitate use of HTqPCR (R/Bioconductor) for subsequent analysis. Quantile normalization was performed, and data were inverted to approximate log2 of abundance.

source_name: PBMC

label_protocol:
none (detection probe is labeled with a proprietary molecular barcode)
RNA was not labeled; instead, RNA (33 ng/ul) was pre-processed following the NanoString manufacturer's protocol by the Johns Hopkins Microarray Core Facility

extract_protocol: Peripheral blood mononuclear cells (PBMC) were isolated from fresh blood using a standard Ficoll protocol. Total RNA was extracted from ten million PBMCs using the miRvana isolation kit (Ambion) per the manufacturer's protocol. RNA was eluted in 100 ul nuclease-free water.

value: PBMC

tag: infection status

value: HIV-1 Viremic


title: Wild-Type Lymphoma, biological replicate 2

description:
TEb1 (WT2).CEL
gene expression data from Wild-Type Tumors


title: sars_mu_lung_IFNAR_Day5_novirus_#1

description: US23502338_251486818896_S01_GE1-v5_95_Feb07_1_1.txt

value: 5 days

value: lung


title: sars_mu_lung_IFNAR_Day9_rMA15_#3

description: US23502338_251486818897_S01_GE1-v5_95_Feb07_1_4.txt

value: SARS rMA15

value: 9 days


title: Epididymal adipose WT ND #686

source_name: EpiAdip wildtype ND

value: wild-type

value: mouse 686


title: TOV112D cells_treated with NSC319726_biological rep3

city: New Brunswick

first: Alexei

last: Vazquez

state: NJ

address: 195 Little Albany St

institute: The Cancer Institute of New Jersey

description:
Drug3_B3_HG-U133_Plus_2
Gene expression data from TOV112 treated with NSC319726

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix HG-U133 plus 2.0 arrays.

scan_protocol: Arrays were scanned using a GenePix 4000B microarray scanner.

data_processing: The data was analyzed with Bioconductor, RMA normalization.

source_name: TOV112D cells_treated with NSC319726

label_protocol: Biotinylated cRNA was generated using standard Affymetrix protocols.

growth_protocol: TOV112D cells were cultured in DMEM + 10% FBS.

extract_protocol: RNA was extracted from the cells using Qiagen RNeasy kit.

treatment_protocol: When cell confluency reached 50-60% (1 day) the cells were treated with NSC319726 (1 µM) for 24 hours before harvested for RNA extraction.

tag: cell line

value: epithelial ovarian cancer cell

value: NSC319726 (1 µM) for 24 hrs


title: TOV112D cells_untreated_biological rep2

description:
CTL_A2_HG-U133_Plus_2
Gene expression data from TOV112 cells without treatment

source_name: TOV112D cells_untreated

value: Untreated


title: Normal Thymocytes, biological replicate 1

description:
FVB 12 (Th1).CEL
gene expression data from normal thymocytes

value: thymocyte


title: Liver GPR120KO ND #720

source_name: Liver GPR120KO ND

value: Liver

value: GPR120 KO

value: normal diet ND


title: TOV112D cells_treated with NSC319726_biological rep2

description:
Drug3_B2_HG-U133_Plus_2
Gene expression data from TOV112 treated with NSC319726


title: TOV112D cells_untreated_biological rep3

description:
CTL_A3_HG-U133_Plus_2
Gene expression data from TOV112 cells without treatment


title: Liver GPR120KO ND #719

value: mixed 129/Sv and C57BL/6

value: mouse 719


title: TOV112D cells_treated with NSC319726_biological rep1

description:
Drug3_B1_HG-U133_Plus_2
Gene expression data from TOV112 treated with NSC319726


title: sars_mu_lung_IFNAR_Day9_rMA15_#2

description: US23502338_251486818919_S01_GE1-v5_95_Feb07_1_4.txt

source_name: lung


title: sars_mu_lung_IFNAR_Day9_rMA15_#1

description: US23502338_251486818921_S01_GE1-v5_95_Feb07_1_3.txt


title: sars_mu_lung_IFNAR_Day5_rMA15_#2

description: US23502338_251486818919_S01_GE1-v5_95_Feb07_1_3.txt


title: Liver GPR120KO ND #718

value: mouse 718


title: SALL4 shRNA biological rep1

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

hyb_protocol: A total of 2.5µg of labelled cDNA was used for hybridization.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were summarized with the RMA and normalized with the Cross-correlation method.

source_name: HCC SNU-398_SALL4 knockdown

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

growth_protocol: SNU-398 human HCC cells were maintained in RPMI medium supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmostphere of 5% CO2

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

treatment_protocol: Cells were treated with scrambled or SALL4 shRNAs

value: Hepatocellular carcinoma (HCC)

value: SALL4 knockdown


title: sars_mu_lung_IFNAR_Day5_rMA15_#1

description: US23502338_251486818897_S01_GE1-v5_95_Feb07_1_1.txt

value: 5 days

value: lung


title: SALL4 shRNA biological rep3


title: SALL4 shRNA biological rep2


title: Epididymal adipose GPR120KO ND #719

value: Epididymal adipose


title: hMSC-senescent_donor5(#274)_Px_63yrs

city: Wuerzburg

first: Peggy

last: Benisch

country: Germany

institute: Orthopedic Center for Musculoskeletal Research

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133_Plus_2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit.

scan_protocol: Hybridization signals were detected with Affymetrix GeneChip Scanner 3000.

data_processing: Global scaling was performed by Affymetrix GeneChipOperatingSoftware 1.4 using the MAS5 algorithm.

source_name: hMSC-senescent

label_protocol: RNA was amplified and labeled according to the GeneChip One-Cycle cDNA Synthesis Kit starting from 2 µg RNA (Affymetrix, High Wycombe, United Kingdom).

growth_protocol: Cell culture medium, fetal calf serum (FCS), trypsin-EDTA and antibiotics were obtained from PAA Laboratories GmbH, Linz, Austria. Human MSC of bone marrow were selected by surface adherence and expanded in DMEM/Ham’s F-12 (1:1) medium supplemented with 10% heat-inactivated FCS, 1 U/ml penicillin, 100 µg/ml streptomycin and 50 µg/ml L-ascorbic acid 2-phosphate (Sigma Aldrich GmbH, Schnelldorf, Germany). Upon 70-90% confluence cells were reseeded in a ratio of 1:3. For hMSC-senescent, this procedure was repeated for up to x passages when the hMSC did not become confluent within 3 weeks due to replicative senescence. Control cells were reseeded until passage 1 and 2, respectively.

extract_protocol: At 80-90% confluence human MSC monolayers were lysed. Total RNA was isolated using the NucleoSpin RNA II Purification Kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions including DNase digestion.

tag: gender

value: male

tag: age

value: 63 yrs

value: bone marrow

value: mesenchymal stem cells

tag: passage

value: long term-cultivation (cellular senescence state)

tag: donor/sample id

value: donor 5 (MSC population #274)


title: hMSC-senescent_donor4(#277)_Px_54yrs

value: 54 yrs

tag: cell type

value: donor 4 (MSC population #277)


title: scrambled biological rep2

source_name: HCC SNU-398_control

value: scrambled control


title: hMSC-senescent_donor2(#278)_Px_59yrs

value: female

value: 59 yrs

tag: tissue

value: donor 2 (MSC population #278)


title: scrambled biological rep3

value: Hepatocellular carcinoma (HCC)


title: Epididymal adipose WT ND #690

tag: genotype

value: wild-type

value: normal diet ND

value: mixed 129/Sv and C57BL/6

value: mouse 690


title: Liver WT ND #690

source_name: Liver wildtype ND

value: Liver


title: sars_mu_lung_IFNAR_Day5_rMA15_#3

description: US23502338_251486818898_S01_GE1-v5_95_Feb07_1_1.txt

tag: strain

value: SARS rMA15

value: 5 days

value: lung


title: Epididymal adipose GPR120KO ND #718

value: Epididymal adipose

value: GPR120 KO

value: mouse 718


title: sars_mu_lung_IFNAR_Day2_rMA15_#2

description: US23502338_251486818897_S01_GE1-v5_95_Feb07_1_3.txt

tag: genotype/variation

value: 2 days


title: Liver WT ND #687

value: mouse 687


title: hMSC-senescent_donor1(#276)_Px_42yrs

value: female

value: 42 yrs

value: bone marrow

value: mesenchymal stem cells

value: long term-cultivation (cellular senescence state)

value: donor 1 (MSC population #276)


title: hMSC-senescent_donor3(#271)_Px_64yrs

value: 64 yrs

value: donor 3 (MSC population #271)


title: PKS_P34

city: Lucknow

first: Pankaj

middle: Kumar

last: Singh

state: Uttar Pradesh

address: Chowk

department: Radiotherapy

country: India

institute: Chhatrapati Shahuji Maharaj Medical University

description: Human Gene 1.0 ST Array

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 17 hr at 45C on Human Gene 1.0 ST Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using Affymetrix Scanner 7G

data_processing: The data were analyzed with Robust Multichip Average (RMA ) using 'affy' library of Bioconductor, followed by MAD Scaling

label: Biotin

source_name: Human Cancerous tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

tag: cancer type

value: Invasive


title: scrambled biological rep1

value: Hepatocellular carcinoma (HCC)

value: scrambled control


title: PKS_P33

description: Human Gene 1.0 ST Array


title: hMSC-osteopo_donor5(#573)_P1_89yrs

growth_protocol: Cell culture medium, fetal calf serum (FCS), trypsin-EDTA and antibiotics were obtained from PAA Laboratories GmbH, Linz, Austria. Human MSC of bone marrow were selected by surface adherence and expanded in DMEM/Ham’s F-12 (1:1) medium supplemented with 10% heat-inactivated FCS, 1 U/ml penicillin, 100 µg/ml streptomycin and 50 µg/ml L-ascorbic acid 2-phosphate (Sigma Aldrich GmbH, Schnelldorf, Germany). Upon 70-90% confluence cells were reseeded in a ratio of 1:3 at least once.

extract_protocol: At 80-90% confluence human MSC monolayers were lysed in P1 and P2, respectively. Total RNA was isolated using the NucleoSpin RNA II Purification Kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions including DNase digestion.

value: 89 yrs (elderly)

tag: diagnosis

value: primary osteoporosis

value: passage 1

tag: sample id

value: donor 5 with primary osteoporosis (MSC population #573)


title: sars_mu_lung_IFNAR_Day2_rMA15_#3

description: US23502338_251486818896_S01_GE1-v5_95_Feb07_1_2.txt

tag: virus infection

value: SARS rMA15

tag: sample collection time post infection

value: 2 days

tag: biological replicate

value: lung


title: PKS_M29

description: Human Gene 1.0 ST Array


title: sars_mu_lung_129_Day5_novirus_#2

description: US23502338_251486818899_S01_GE1-v5_95_Feb07_1_3.txt

value: wild-type

value: mock-infected (PBS)

value: 5 days


title: Epididymal adipose WT ND #687

value: Epididymal adipose

tag: treatment

value: normal diet ND

tag: genetic background

value: mixed 129/Sv and C57BL/6

tag: subject

value: mouse 687


title: Liver WT HFD #560

source_name: Liver wildtype HFD

value: Liver

value: high fat diet HFD

value: mouse 560


title: hMSC-osteopo_donor4(#572)_P1_82yrs

tag: gender

value: female

tag: age

value: 82 yrs (elderly)

value: bone marrow

value: mesenchymal stem cells

value: donor 4 with primary osteoporosis (MSC population #572)


title: PKS_P25

description: Human Gene 1.0 ST Array

value: Invasive


title: Liver WT HFD #547

value: mouse 547


title: Liver WT ND #686

value: wild-type

value: mouse 686


title: hMSC-osteopo_donor2(#547)_P1_94yrs

value: 94 yrs (elderly)

value: primary osteoporosis

tag: passage

value: passage 1

value: donor 2 with primary osteoporosis (MSC population #547)


title: sars_mu_lung_129_Day5_novirus_#3

description: US23502338_251486818920_S01_GE1-v5_95_Feb07_1_2.txt

value: mock-infected (PBS)

value: 5 days

value: lung


title: hMSC-osteopo_donor3(#558)_P2_87yrs

value: 87 yrs (elderly)

tag: cell type

value: passage 2

value: donor 3 with primary osteoporosis (MSC population #558)


title: PKS_UBcontrol

description: Human Gene 1.0 ST Array

source_name: Urinary Bladder control RNA

value: no carcinoma


title: sars_mu_lung_IFNAR_Day2_rMA15_#1

description: US23502338_251486818919_S01_GE1-v5_95_Feb07_1_2.txt

value: SARS rMA15

value: 2 days

tag: tissue


title: Epididymal adipose WT HFD #547

source_name: EpiAdip wildtype HFD

value: Epididymal adipose

tag: genotype

value: high fat diet HFD

value: mixed 129/Sv and C57BL/6


title: sars_mu_lung_129_Day9_rMA15_#3

description: US23502338_251486818899_S01_GE1-v5_95_Feb07_1_4.txt

tag: strain

value: wild-type

value: 9 days


title: PKS_M13

description: Human Gene 1.0 ST Array

value: Superficial


title: PKS_T18

description: Human Gene 1.0 ST Array


title: sars_mu_lung_129_Day5_novirus_#1

description: US23502338_251486818922_S01_GE1-v5_95_Feb07_1_1.txt

tag: genotype/variation


title: hMSC-old_donor4(#663)_P1_89yrs

label_protocol: RNA was labeled according to the GeneChip 3' IVT Express Kit (Affymetrix, High Wycombe, United Kingdom) starting from 200ng total RNA.

extract_protocol: At 80-90% confluence, human MSC monolayers were lysed. Total RNA was isolated using the NucleoSpin RNA II Purification Kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions including DNase digestion.

value: female

value: 89 yrs (elderly-aged)

value: bone marrow

value: mesenchymal stem cells

value: passage 1

value: donor 4 (MSC population #663)


title: PKS_M27

description: Human Gene 1.0 ST Array

tag: cancer type

value: Invasive


title: hMSC-osteopo_donor1(#535)_P1_79yrs

value: 79 yrs (elderly)

tag: diagnosis

value: primary osteoporosis

value: donor 1 with primary osteoporosis (MSC population #535)


title: sars_mu_lung_129_Day9_rMA15_#2

description: US23502338_251486818856_S01_GE1-v5_95_Feb07_1_1.txt

value: SARS rMA15

value: lung


title: Liver WT HFD #546

value: Liver

value: high fat diet HFD

value: mouse 546


title: Epididymal adipose WT HFD #560

value: Epididymal adipose

value: wild-type

value: mixed 129/Sv and C57BL/6

value: mouse 560


title: sars_mu_lung_129_Day9_rMA15_#1

description: US23502338_251486818897_S01_GE1-v5_95_Feb07_1_2.txt

value: 9 days


title: Epididymal adipose WT HFD #546


title: hMSC-old_donor2(#559)_P1_79yrs

value: male

value: 79 yrs (elderly-aged)

value: bone marrow

value: mesenchymal stem cells

tag: sample id

value: donor 2 (MSC population #559)


title: Liver GPR120KO HFD #429

source_name: Liver GPR120KO HFD

value: GPR120 KO

value: mouse 429


title: hMSC-old_donor1(#520)_P1_79yrs

value: female

value: passage 1

value: donor 1 (MSC population #520)


title: placental tissue replicate 2

description:
Sample name: NMB6-pla_cy5/cy3
Biological replicate 2 of 4 placental tissue
US10283824_252984210018_S01_CGH_107_Sep09_1_2.txt

source_name: methylated CpG-island recovery assay (MIRA) enriched,placental tissue, 2 of 4 mother-baby pairs

value: placental tissue

tag: sample type

value: methylation-enriched DNA

source_name: input, placental tissue, 2 of 4 mother-baby pairs

value: total input DNA


title: hMSC-C_donor5(#247)_P1_56yrs

label_protocol: RNA was amplified and labeled according to the GeneChip One-Cycle cDNA Synthesis Kit and the GeneChip 3’IVT Express Kit starting from 2 µg total RN , respectively (both from Affymetrix, High Wycombe, United Kingdom).

value: 56 yrs (middle-aged)

value: donor 5 (MSC population #247)


title: sars_mu_lung_129_Day5_rMA15_#3

description: US23502338_251486818898_S01_GE1-v5_95_Feb07_1_2.txt

value: wild-type

tag: virus infection

value: SARS rMA15

tag: sample collection time post infection

value: 5 days

value: lung


title: hMSC-old_donor3(#606)_P1_80yrs

value: 80 yrs (elderly-aged)

value: bone marrow

value: donor 3 (MSC population #606)


title: Epididymal adipose GPR120KO HFD #429

source_name: EpiAdip GPR120KO HFD

value: Epididymal adipose

value: GPR120 KO

tag: treatment

value: high fat diet HFD

value: mixed 129/Sv and C57BL/6


title: sars_mu_lung_129_Day2_rMA15_#3

description: US23502338_251486818920_S01_GE1-v5_95_Feb07_1_4.txt

value: 2 days

tag: biological replicate


title: sars_mu_lung_129_Day5_rMA15_#2

description: US23502338_251486818921_S01_GE1-v5_95_Feb07_1_1.txt


title: hMSC-C_donor4(#296)_P1_62yrs

value: female

value: 62 yrs (middle-aged)

value: mesenchymal stem cells

value: passage 1

value: donor 4 (MSC population #296)


title: Liver GPR120KO HFD #428

value: Liver

tag: genetic background

tag: subject

value: mouse 428


title: sars_mu_lung_129_Day5_rMA15_#1

description: US23502338_251486818856_S01_GE1-v5_95_Feb07_1_4.txt

value: wild-type

value: SARS rMA15

value: 5 days


title: hMSC-C_donor3(#295)_P1_61yrs

tag: gender

value: male

tag: age

value: 61 yrs (middle-aged)

value: bone marrow

value: donor 3 (MSC population #295)


title: G11

type: SAGE

anchor: NlaIII

city: hangzhou

first: liu

last: xiaoguang

address: yuhang road

institute: Zhejiang University

data_processing: Data analyzed with CLCGenomicsWorkbench_3_6_5 software.

organism: Pyricularia grisea

extract_protocol: Liquid nitrogen grinding method

value: Wild-Type

tag: incubation time

value: 3 days

tag: incubation temperature

tag: rotation speed


title: T146

source_name: T146- Tag_counts

tag: strain

value: temperature sensitive mutant


title: hMSC-C_donor2(#353)_P2_67yrs

value: female

value: 67 yrs (middle-aged)

tag: tissue

tag: cell type

tag: passage

value: passage 2

value: donor 2 (MSC population #353)


title: Liver GPR120KO HFD #427

tag: genotype

value: GPR120 KO

value: high fat diet HFD

value: mixed 129/Sv and C57BL/6

value: mouse 427


title: sars_mu_lung_129_Day2_rMA15_#2

description: US23502338_251486818922_S01_GE1-v5_95_Feb07_1_3.txt

tag: genotype/variation

value: wild-type

value: SARS rMA15

value: 2 days

value: lung


title: Epididymal adipose GPR120KO HFD #428

value: Epididymal adipose

value: mouse 428


title: sars_mu_lung_129_Day2_rMA15_#1

description: US23502338_251486818920_S01_GE1-v5_95_Feb07_1_1.txt

tag: virus infection


title: subject10_t=0h_MUFA_(baseline)

status: Public on Feb 21 2012

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.16.0).

source_name: vastus lateralis muscle, subject10, t=0h, MUFA (baseline)

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction. A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).

growth_protocol: Ten insulin resistant men (age 50–70 years; BMI 29-39 kg/m2; HOMAIR >2.5) participated in a single-blinded randomized, crossover study. Exclusion criteria were weight change of >3 kg within the last 3 months before the study; diabetes; chronic inflammatory conditions; kidney or liver dysfunction; use of hypolipidemic or anti-inflammatory medication; use of β-blockers; use of aspirin >1 per week; highly-trained athletes; and alcohol abuse. All subjects were informed about the nature of the study and written informed consent was obtained before study participation. The local Medical Ethical Committee of Maastricht University Medical Centre approved the study protocol.

extract_protocol: Skeletal muscle biopsies were taken at baseline (after placing the three catheters and before the background blood sampling) and at the end of the postprandial measurement period (t=240mins). Biopsies were obtained from the vastus lateralis muscle under local anesthesia of the skin and fascia using the Bergström method with suction, cleaned from any visible fat and blood, immediately frozen in isopentane at its melting point, and stored at −80ºC until analysis.

treatment_protocol: The design of the study was a randomized cross-over design with three different treatments. On four occasions, subjects arrived at the university after an overnight fast. On the first day, subjects completed anthropometric measurements, a fasting blood sample was collected, and a hyperinsulinaemic–euglycaemic clamp was performed to measure insulin sensitivity. On the other three days (2-3 weeks between measurements, in randomized order), subjects were studied under baseline conditions and for 4 hours after the ingestion of a liquid high-fat mixed-meal, which was high either in saturated fatty acids (SFA), mono-unsaturated fatty acids (MUFA),  or polyunsaturated fatty acids (PUFA).

tag: meal type

value: MUFA

tag: time

tag: background

value: Caucasian

value: male

value: 56 years


title: hMSC-C_donor1(#276)_P1_42yrs

value: female

value: 42 yrs (middle-aged)

value: bone marrow

value: mesenchymal stem cells

value: passage 1

tag: sample id

value: donor 1 (MSC population #276)


title: DKS5 at normoxia - sample 1

first: Daniel

last: Shue

address: 50 Blossom Street

department: GI Unit

institute: Massachusetts General Hospital

description:
K-ras mutant cells at normoxia (21% O2)
DKS5-Normoxia-1.CHP
DKS5-Normoxia-1.CEL

hyb_protocol: RNA samples were hybridized as described in the Nugen protocol in a Model 640 hybridisation oven, then washed in Model 450 fluidics stations using lab-made solutions.

scan_protocol: Microarray samples were scanned using the Model 3000 7G scanner, GCOS v1.4.

data_processing: Data was analyzed with Microarray Suite 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: K-ras mutant cells at normoxia (21% O2)

label_protocol: The Nugen Ovation RNA Amplification System V2 (60 rx)--Cat # 3100-60 was used for cDNA synthesis and amplification, and then the Nugen FL-Ovation cDNA Biotin Module V2 (60 rx)--Cat#  4200-60 was used for labelling.

growth_protocol: Two colon cancer cell lines, DKS-5 (K-ras mutant) and DKO-3 (K-ras wild-type), were grown in vitro and harvested @ 70% confluency under standard growth media

extract_protocol: Total RNA was extracted from these cell lines using the Qiagen RNeasy kit.

treatment_protocol: DKS-5 and DKO-3 cells were incubated under normoxic (21% O2) and 12-hr hypoxic (1% O2) conditions.

value: Colon

tag: cell line

value: colon cancer cell line DKS-5

value: K-ras mutant

tag: stress

value: normoxia

value: control


title: DKO3 at normoxia - sample 1

description:
K-ras knockout (WT) cells at normoxia (21% O2)
DKO3-Normoxia-1.CHP
DKO3-Normoxia-1.CEL

value: colon cancer cell line DKO-3

value: K-ras knockout (wild-type)


title: subject9_t=4h_MUFA_(post prandial)

source_name: vastus lateralis muscle, subject9, t=4h, MUFA (post prandial)

value: MUFA

tag: gender

tag: age

value: 62 years


title: subject10_t=0h_PUFA_(baseline)

source_name: vastus lateralis muscle, subject10, t=0h, PUFA (baseline)

value: PUFA

value: Caucasian

value: male


title: subject10_t=4h_MUFA_(post prandial)

source_name: vastus lateralis muscle, subject10, t=4h, MUFA (post prandial)

value: 56 years


title: subject10_t=0h_SFA_(baseline)

source_name: vastus lateralis muscle, subject10, t=0h, SFA (baseline)

value: SFA


title: subject9_t=4h_SFA_(post prandial)

source_name: vastus lateralis muscle, subject9, t=4h, SFA (post prandial)


title: DKS5 at normoxia - sample 2

description:
K-ras mutant cells at normoxia (21% O2)
DKS5-Normoxia-2.CHP
DKS5-Normoxia-2.CEL


title: DKO3 after 12h of hypoxia - sample 1

description:
K-ras knockout (WT) cells after 12h of hypoxia (1% O2)
DKO3-Hypoxia12h-1.CHP
DKO3-Hypoxia12h-1.CEL

value: hypoxia


title: DKS5 after 12h of hypoxia - sample 1

description:
K-ras mutant cells after 12h of hypoxia (1% O2)
DKS5-Hypoxia12h-1.CHP
DKS5-Hypoxia12h-1.CEL


title: subject10_t=4h_SFA_(post prandial)

source_name: vastus lateralis muscle, subject10, t=4h, SFA (post prandial)


title: Epididymal adipose GPR120KO HFD #427

value: Epididymal adipose

value: GPR120 KO

tag: treatment

value: high fat diet HFD

tag: genetic background

value: mixed 129/Sv and C57BL/6

tag: subject

value: mouse 427


title: DKO3 at normoxia - sample 2

description:
K-ras knockout (WT) cells at normoxia (21% O2)
DKO3-Normoxia-2.CHP
DKO3-Normoxia-2.CEL

tag: tissue

value: Colon

value: normoxia


title: TOV112D cells_untreated_biological rep1

description:
CTL_A1_HG-U133_Plus_2
Gene expression data from TOV112 cells without treatment

source_name: TOV112D cells_untreated

tag: cell type

value: epithelial ovarian cancer cell

value: Untreated


title: subject9_t=0h_MUFA_(baseline)

source_name: vastus lateralis muscle, subject9, t=0h, MUFA (baseline)

value: MUFA


title: DKS5 after 12h of hypoxia - sample 2

description:
K-ras mutant cells after 12h of hypoxia (1% O2)
DKS5-Hypoxia12h-2.CHP
DKS5-Hypoxia12h-2.CEL

value: colon cancer cell line DKS-5

value: K-ras mutant


title: DKO3 after 12h of hypoxia - sample 2

description:
K-ras knockout (WT) cells after 12h of hypoxia (1% O2)
DKO3-Hypoxia12h-2.CHP
DKO3-Hypoxia12h-2.CEL

value: colon cancer cell line DKO-3

value: K-ras knockout (wild-type)


title: subject10_t=4h_PUFA_(post prandial)

source_name: vastus lateralis muscle, subject10, t=4h, PUFA (post prandial)

value: PUFA

value: Caucasian

value: male

value: 56 years


title: subject9_t=0h_SFA_(baseline)

source_name: vastus lateralis muscle, subject9, t=0h, SFA (baseline)

value: SFA

value: 62 years


title: subject8_t=4h_MUFA_(post prandial)

source_name: vastus lateralis muscle, subject8, t=4h, MUFA (post prandial)

value: 70 years


title: subject8_t=0h_PUFA_(baseline)

source_name: vastus lateralis muscle, subject8, t=0h, PUFA (baseline)


title: subject8_t=0h_MUFA_(baseline)

source_name: vastus lateralis muscle, subject8, t=0h, MUFA (baseline)


title: subject8_t=4h_PUFA_(post prandial)

source_name: vastus lateralis muscle, subject8, t=4h, PUFA (post prandial)


title: T4_Post_Female_Old (81449)

city: Indianapolis

first: Shawn

middle: T.

last: Estrem

address: Lilly Corporate Center

institute: Eli Lilly and Company

description:
EA08017_81449_AGEX_OF_T4_23_H133+.CHP
EA08017_81449_AGEX_OF_T4_23_H133+.CEL

hyb_protocol: Affymetrix Fluidics Station 400

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1500.

source_name: Vastus lateralis muscle

label_protocol: 40ng of total RNA was labeled using NuGen WT-Ovation RNA Amp v2 kit and protocol

extract_protocol: Homogenize the muscle tissue in TRI reagent and extracted RNA according to manufacturer's protocol, and then purified using Rneasy Micro Kit (Qiagen).

value: Old

value: Female

tag: training state

value: Trained

tag: time point

value: 4hrs post exercise

value: Vastus lateralis muscle


title: subject8_t=0h_SFA_(baseline)

source_name: vastus lateralis muscle, subject8, t=0h, SFA (baseline)


title: T4_Post_Female_Old (81402)

description:
EA08017_81402_AGEX_OF_T4_12_H133+.CHP
EA08017_81402_AGEX_OF_T4_12_H133+.CEL


title: subject8_t=4h_SFA_(post prandial)

source_name: vastus lateralis muscle, subject8, t=4h, SFA (post prandial)


title: T4_Post_Female_Old (81440)

description:
EA08017_81440_AGEX_OF_T4_21_H133+.CHP
EA08017_81440_AGEX_OF_T4_21_H133+.CEL


title: T4_Post_Female_Old (81383)

description:
EA08017_81383_AGEX_OF_T4_7_H133+.CHP
EA08017_81383_AGEX_OF_T4_7_H133+.CEL


title: T4_Post_Female_Old (81426)

description:
EA08017_81426_AGEX_OF_T4_18_H133+.CHP
EA08017_81426_AGEX_OF_T4_18_H133+.CEL


title: subject7_t=4h_PUFA_(post prandial)

source_name: vastus lateralis muscle, subject7, t=4h, PUFA (post prandial)

value: 63 years


title: T3_Pre_Female_Old (81427)

description:
EA08017_81427_AGEX_OF_T3_18_H133+.CHP
EA08017_81427_AGEX_OF_T3_18_H133+.CEL

value: Basal


title: T3_Pre_Female_Old (81438)

description:
EA08017_81438_AGEX_OF_T3_21_H133+.CHP
EA08017_81438_AGEX_OF_T3_21_H133+.CEL


title: subject7_t=0h_SFA_(baseline)

source_name: vastus lateralis muscle, subject7, t=0h, SFA (baseline)


title: T3_Pre_Female_Old (81403)

description:
EA08017_81403_AGEX_OF_T3_12_H133+.CHP
EA08017_81403_AGEX_OF_T3_12_H133+.CEL


title: T3_Pre_Female_Old (81385)

description:
EA08017_81385_AGEX_OF_T3_7_H133+.CHP
EA08017_81385_AGEX_OF_T3_7_H133+.CEL


title: subject6_t=4h_PUFA_(post prandial)

source_name: vastus lateralis muscle, subject6, t=4h, PUFA (post prandial)

value: 67 years


title: subject7_t=4h_MUFA_(post prandial)

source_name: vastus lateralis muscle, subject7, t=4h, MUFA (post prandial)

value: MUFA


title: T3_Pre_Female_Old (81448)

description:
EA08017_81448_AGEX_OF_T3_23_H133+.CHP
EA08017_81448_AGEX_OF_T3_23_H133+.CEL


title: subject7_t=0h_MUFA_(baseline)

source_name: vastus lateralis muscle, subject7, t=0h, MUFA (baseline)


title: T2_Post_Female_Old (81447)

description:
EA08017_81447_AGEX_OF_T2_23_H133+.CHP
EA08017_81447_AGEX_OF_T2_23_H133+.CEL

value: Untrained


title: subject7_t=4h_SFA_(post prandial)

source_name: vastus lateralis muscle, subject7, t=4h, SFA (post prandial)


title: T2_Post_Female_Old (81441)

description:
EA08017_81441_AGEX_OF_T2_21_H133+.CHP
EA08017_81441_AGEX_OF_T2_21_H133+.CEL


title: subject6_t=0h_SFA_(baseline)

source_name: vastus lateralis muscle, subject6, t=0h, SFA (baseline)


title: subject6_t=4h_SFA_(post prandial)

source_name: vastus lateralis muscle, subject6, t=4h, SFA (post prandial)


title: T2_Post_Female_Old (81428)

description:
EA08017_81428_AGEX_OF_T2_18_H133+.CHP
EA08017_81428_AGEX_OF_T2_18_H133+.CEL


title: T4_Post_Female_Old (81361)

description:
EA08017_81361_AGEX_OF_T4_1_H133+.CHP
EA08017_81361_AGEX_OF_T4_1_H133+.CEL


title: subject5_t=4h_MUFA_(post prandial)

source_name: vastus lateralis muscle, subject5, t=4h, MUFA (post prandial)


title: subject6_t=4h_MUFA_(post prandial)

source_name: vastus lateralis muscle, subject6, t=4h, MUFA (post prandial)


title: subject7_t=0h_PUFA_(baseline)

source_name: vastus lateralis muscle, subject7, t=0h, PUFA (baseline)

value: PUFA


title: T2_Post_Female_Old (81382)

description:
EA08017_81382_AGEX_OF_T2_7_H133+.CHP
EA08017_81382_AGEX_OF_T2_7_H133+.CEL


title: T2_Post_Female_Old (81404)

description:
EA08017_81404_AGEX_OF_T2_12_H133+.CHP
EA08017_81404_AGEX_OF_T2_12_H133+.CEL


title: subject5_t=0h_PUFA_(baseline)

source_name: vastus lateralis muscle, subject5, t=0h, PUFA (baseline)

value: Caucasian


title: subject6_t=0h_MUFA_(baseline)

source_name: vastus lateralis muscle, subject6, t=0h, MUFA (baseline)

value: male


title: T2_Post_Female_Old (81359)

description:
EA08017_81359_AGEX_OF_T2_1_H133+.CHP
EA08017_81359_AGEX_OF_T2_1_H133+.CEL


title: T1_Pre_Female_Old (81429)

description:
EA08017_81429_AGEX_OF_T1_18_H133+.CHP
EA08017_81429_AGEX_OF_T1_18_H133+.CEL


title: T1_Pre_Female_Old (81405)

description:
EA08017_81405_AGEX_OF_T1_12_H133+.CHP
EA08017_81405_AGEX_OF_T1_12_H133+.CEL


title: subject5_t=0h_MUFA_(baseline)

source_name: vastus lateralis muscle, subject5, t=0h, MUFA (baseline)


title: T1_Pre_Female_Old (81439)

description:
EA08017_81439_AGEX_OF_T1_21_H133+.CHP
EA08017_81439_AGEX_OF_T1_21_H133+.CEL

source_name: Vastus lateralis muscle


title: subject5_t=4h_PUFA_(post prandial)

source_name: vastus lateralis muscle, subject5, t=4h, PUFA (post prandial)


title: T1_Pre_Female_Old (81446)

description:
EA08017_81446_AGEX_OF_T1_23_H133+.CHP
EA08017_81446_AGEX_OF_T1_23_H133+.CEL


title: T3_Pre_Female_Old (81360)

description:
EA08017_81360_AGEX_OF_T3_1_H133+.CHP
EA08017_81360_AGEX_OF_T3_1_H133+.CEL


title: subject4_t=4h_PUFA_(post prandial)

source_name: vastus lateralis muscle, subject4, t=4h, PUFA (post prandial)


title: subject6_t=0h_PUFA_(baseline)

source_name: vastus lateralis muscle, subject6, t=0h, PUFA (baseline)


title: subject4_t=0h_PUFA_(baseline)

source_name: vastus lateralis muscle, subject4, t=0h, PUFA (baseline)


title: subject4_t=0h_MUFA_(baseline)

source_name: vastus lateralis muscle, subject4, t=0h, MUFA (baseline)


title: subject4_t=4h_SFA_(post prandial)

source_name: vastus lateralis muscle, subject4, t=4h, SFA (post prandial)


title: subject3_t=0h_SFA_(baseline)

source_name: vastus lateralis muscle, subject3, t=0h, SFA (baseline)

value: 55 years


title: subject3_t=4h_SFA_(post prandial)

source_name: vastus lateralis muscle, subject3, t=4h, SFA (post prandial)

value: SFA


title: subject4_t=4h_MUFA_(post prandial)

source_name: vastus lateralis muscle, subject4, t=4h, MUFA (post prandial)

value: 62 years


title: T4_Post_Female_Young (81418)

description:
EA08017_81418_AGEX_YF_T4_16_H133+.CHP
EA08017_81418_AGEX_YF_T4_16_H133+.CEL

value: Young


title: T4_Post_Female_Young (81463)

description:
EA08017_81463_AGEX_YF_T4_27_H133+.CHP
EA08017_81463_AGEX_YF_T4_27_H133+.CEL


title: T4_Post_Female_Young (81457)

description:
EA08017_81457_AGEX_YF_T4_25_H133+.CHP
EA08017_81457_AGEX_YF_T4_25_H133+.CEL


title: T1_Pre_Female_Old (81358)

description:
EA08017_81358_AGEX_OF_T1_1_H133+.CHP
EA08017_81358_AGEX_OF_T1_1_H133+.CEL

value: Old


title: T1_Pre_Female_Old (81384)

description:
EA08017_81384_AGEX_OF_T1_7_H133+.CHP
EA08017_81384_AGEX_OF_T1_7_H133+.CEL

value: Female


title: T4_Post_Female_Young (81394)

description:
EA08017_81394_AGEX_YF_T4_10_H133+.CHP
EA08017_81394_AGEX_YF_T4_10_H133+.CEL

value: Trained


title: subject3_t=4h_MUFA_(post prandial)

source_name: vastus lateralis muscle, subject3, t=4h, MUFA (post prandial)


title: subject3_t=0h_MUFA_(baseline)

source_name: vastus lateralis muscle, subject3, t=0h, MUFA (baseline)


title: T4_Post_Female_Young (81387)

description:
EA08017_81387_AGEX_YF_T4_8_H133+.CHP
EA08017_81387_AGEX_YF_T4_8_H133+.CEL

value: 4hrs post exercise


title: subject4_t=0h_SFA_(baseline)

source_name: vastus lateralis muscle, subject4, t=0h, SFA (baseline)


title: T4_Post_Female_Young (81444)

description:
EA08017_81444_AGEX_YF_T4_22_H133+.CHP
EA08017_81444_AGEX_YF_T4_22_H133+.CEL

value: Vastus lateralis muscle


title: T4_Post_Female_Young (81369N2)

description:
EA08017_81369N2_AGEX_YF_T4_3_H133+.CHP
EA08017_81369N2_AGEX_YF_T4_3_H133+.CEL


title: T4_Post_Female_Young (81408)

description:
EA08017_81408_AGEX_YF_T4_13_H133+.CHP
EA08017_81408_AGEX_YF_T4_13_H133+.CEL


title: subject3_t=4h_PUFA_(post prandial)

source_name: vastus lateralis muscle, subject3, t=4h, PUFA (post prandial)


title: T3_Pre_Female_Young (81456)

description:
EA08017_81456_AGEX_YF_T3_25_H133+.CHP
EA08017_81456_AGEX_YF_T3_25_H133+.CEL


title: subject2_t=0h_SFA_(baseline)

source_name: vastus lateralis muscle, subject2, t=0h, SFA (baseline)

value: 54 years


title: T3_Pre_Female_Young (81442)

description:
EA08017_81442_AGEX_YF_T3_22_H133+.CHP
EA08017_81442_AGEX_YF_T3_22_H133+.CEL

value: Basal


title: subject3_t=0h_PUFA_(baseline)

source_name: vastus lateralis muscle, subject3, t=0h, PUFA (baseline)


title: subject2_t=4h_PUFA_(post prandial)

source_name: vastus lateralis muscle, subject2, t=4h, PUFA (post prandial)


title: T2_Post_Female_Young (81462)

description:
EA08017_81462_AGEX_YF_T2_27_H133+.CHP
EA08017_81462_AGEX_YF_T2_27_H133+.CEL

source_name: Vastus lateralis muscle


title: T3_Pre_Female_Young (81465)

description:
EA08017_81465_AGEX_YF_T3_27_H133+.CHP
EA08017_81465_AGEX_YF_T3_27_H133+.CEL


title: subject2_t=4h_SFA_(post prandial)

source_name: vastus lateralis muscle, subject2, t=4h, SFA (post prandial)


title: subject2_t=4h_MUFA_(post prandial)

source_name: vastus lateralis muscle, subject2, t=4h, MUFA (post prandial)


title: subject2_t=0h_PUFA_(baseline)

source_name: vastus lateralis muscle, subject2, t=0h, PUFA (baseline)


title: T3_Pre_Female_Young (81419)

description:
EA08017_81419_AGEX_YF_T3_16_H133+.CHP
EA08017_81419_AGEX_YF_T3_16_H133+.CEL


title: T3_Pre_Female_Young (81368)

description:
EA08017_81368_AGEX_YF_T3_3_H133+.CHP
EA08017_81368_AGEX_YF_T3_3_H133+.CEL


title: T3_Pre_Female_Young (81406)

description:
EA08017_81406_AGEX_YF_T3_13_H133+.CHP
EA08017_81406_AGEX_YF_T3_13_H133+.CEL


title: subject2_t=0h_MUFA_(baseline)

source_name: vastus lateralis muscle, subject2, t=0h, MUFA (baseline)


title: subject1_t=4h_SFA_(post prandial)

source_name: vastus lateralis muscle, subject1, t=4h, SFA (post prandial)

value: 64 years


title: T2_Post_Female_Young (81409)

description:
EA08017_81409_AGEX_YF_T2_13_H133+.CHP
EA08017_81409_AGEX_YF_T2_13_H133+.CEL


title: subject1_t=4h_PUFA_(post prandial)

source_name: vastus lateralis muscle, subject1, t=4h, PUFA (post prandial)


title: subject1_t=0h_SFA_(baseline)

source_name: vastus lateralis muscle, subject1, t=0h, SFA (baseline)


title: subject1_t=0h_PUFA_(baseline)

source_name: vastus lateralis muscle, subject1, t=0h, PUFA (baseline)


title: T2_Post_Female_Young (81445)

description:
EA08017_81445_AGEX_YF_T2_22_H133+.CHP
EA08017_81445_AGEX_YF_T2_22_H133+.CEL


title: T2_Post_Female_Young (81455)

description:
EA08017_81455_AGEX_YF_T2_25_H133+.CHP
EA08017_81455_AGEX_YF_T2_25_H133+.CEL


title: T2_Post_Female_Young (81420)

description:
EA08017_81420_AGEX_YF_T2_16_H133+.CHP
EA08017_81420_AGEX_YF_T2_16_H133+.CEL


title: T3_Pre_Female_Young (81395)

description:
EA08017_81395_AGEX_YF_T3_10_H133+.CHP
EA08017_81395_AGEX_YF_T3_10_H133+.CEL


title: subject1_t=4h_MUFA_(post prandial)

source_name: vastus lateralis muscle, subject1, t=4h, MUFA (post prandial)

value: MUFA


title: subject1_t=0h_MUFA_(baseline)

source_name: vastus lateralis muscle, subject1, t=0h, MUFA (baseline)


title: Tdrd7 null P30 mouse lens rep2

first: Anton

last: Aboukhalil

address: 77 Avenue Louis Pasteur, 464

institute: Massachusetts Institute of Technology

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using rank invariant normalization using Illumina's GenomeStudio2010.2 v 1.7.0

source_name: P30 Mouse lens

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion) for Illumina arrays

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. DNAse treatment was performed according to Qiagen kit instructions. Quality control was performed with Agilent Bioanalyser.

tag: strain

value: C57BL/6J and C3A.Blia mix

tag: genotype/variation

value: Tdrd7 null

value: Lens


title: Tdrd7 heterozygous P4 mouse lens rep1

description: replicate 1

source_name: P4 Mouse lens

value: Tdrd7 heterozygous


title: Tdrd7 null P4 mouse lens rep3

description: replicate 3


title: T2_Post_Female_Young (81367)

description:
EA08017_81367_AGEX_YF_T2_3_H133+.CHP
EA08017_81367_AGEX_YF_T2_3_H133+.CEL

value: Untrained


title: Tdrd7 heterozygous P4 mouse lens rep2

description: replicate 2


title: T1_Pre_Female_Young (81464)

description:
EA08017_81464_AGEX_YF_T1_27_H133+.CHP
EA08017_81464_AGEX_YF_T1_27_H133+.CEL


title: T2_Post_Female_Young (81396)

description:
EA08017_81396_AGEX_YF_T2_10_H133+.CHP
EA08017_81396_AGEX_YF_T2_10_H133+.CEL


title: T1_Pre_Female_Young (81407)

description:
EA08017_81407_AGEX_YF_T1_13_H133+.CHP
EA08017_81407_AGEX_YF_T1_13_H133+.CEL


title: Tdrd7 null P4 mouse lens rep1

description: replicate 1


title: T2_Post_Female_Young (81386)

description:
EA08017_81386_AGEX_YF_T2_8_H133+.CHP
EA08017_81386_AGEX_YF_T2_8_H133+.CEL


title: Tdrd7 heterozygous P30 mouse lens rep2

description: replicate 2


title: T4_Post_Male_Old (81435)

description:
EA08017_81435_AGEX_OM_T4_20_H133+.CHP
EA08017_81435_AGEX_OM_T4_20_H133+.CEL

value: Male


title: Tdrd7 null P30 mouse lens rep3

description: replicate 3


title: Tdrd7 null P30 mouse lens rep1

description: replicate 1


title: T4_Post_Male_Old (81401)

description:
EA08017_81401_AGEX_OM_T4_11_H133+.CHP
EA08017_81401_AGEX_OM_T4_11_H133+.CEL


title: T1_Pre_Female_Young (81454)

description:
EA08017_81454_AGEX_YF_T1_25_H133+.CHP
EA08017_81454_AGEX_YF_T1_25_H133+.CEL


title: Tdrd7 null P4 mouse lens rep2

description: replicate 2


title: T1_Pre_Female_Young (81388)

description:
EA08017_81388_AGEX_YF_T1_8_H133+.CHP
EA08017_81388_AGEX_YF_T1_8_H133+.CEL


title: T4_Post_Male_Old (81417)

description:
EA08017_81417_AGEX_OM_T4_15_H133+.CHP
EA08017_81417_AGEX_OM_T4_15_H133+.CEL


title: Tdrd7 heterozygous P30 mouse lens rep1

description: replicate 1


title: Tdrd7 heterozygous P30 mouse lens rep3

description: replicate 3


title: Tdrd7 heterozygous P4 mouse lens rep3

description: replicate 3


title: Lentiviral construct containing Tdrd7 shRNA rep 3

description: replicate 3

source_name: 21EM15 mouse lens epithelial cell line

value: lens epithelial cell line


title: T1_Pre_Female_Young (81397)

description:
EA08017_81397_AGEX_YF_T1_10_H133+.CHP
EA08017_81397_AGEX_YF_T1_10_H133+.CEL

value: Young


title: T4_Post_Male_Old (81376)

description:
EA08017_81376_AGEX_OM_T4_5_H133+.CHP
EA08017_81376_AGEX_OM_T4_5_H133+.CEL

value: Old


title: T1_Pre_Female_Young (81443)

description:
EA08017_81443_AGEX_YF_T1_22_H133+.CHP
EA08017_81443_AGEX_YF_T1_22_H133+.CEL

value: Female


title: T4_Post_Male_Old (81458)

description:
EA08017_81458_AGEX_OM_T4_26_H133+.CHP
EA08017_81458_AGEX_OM_T4_26_H133+.CEL

value: Trained


title: T1_Pre_Female_Young (81366)

description:
EA08017_81366_AGEX_YF_T1_3_H133+.CHP
EA08017_81366_AGEX_YF_T1_3_H133+.CEL


title: T4_Post_Male_Old (81362)

description:
EA08017_81362_AGEX_OM_T4_2_H133+.CHP
EA08017_81362_AGEX_OM_T4_2_H133+.CEL

value: 4hrs post exercise


title: Lentiviral construct containing Tdrd7 shRNA rep 2

description: replicate 2


title: control20_PBMC

city: Santa Clara

first: Radha

last: Duttagupta

state: CA

address: 3450 Central Expressway

department: Applied Research

institute: Affymetrix

description: 20101117_RD_Lankenau_c20_PBMC_RNA_1ug_B1_T1.CEL

hyb_protocol: The totol amount of RNA was hybridized to the arrays for 16 hours at 480C with rotation at 60rpm.

scan_protocol: Samples were scanned using the GCS 3000 7G Scanner and processed using miRNA_1-0_2xgain library files.

data_processing:
The data was preprocessed using Affymetrix miRNA QC tool where Individual feature intensities were background subtracted, transformed through addition of small constant (value equal to 16) quantile normalized and median summarized, then log2 transformed.
Background subtracted, transformation of values through addition of small constant (16) ,all negative values set to 1, quantile normalized and median summarized, log2 data.

source_name: PBMC

label_protocol: A total of 1-3ug of total RNA was labelled using the Genisphere HSR Labelling Kit (http://www.genisphere.com/array_detection_flashtag_biotin.html)

growth_protocol: Blood was drawn in sodium EDTA tubes.

extract_protocol: Total RNA was extracted using Trizol procedure and Low molecular weight RNAs isolated by Microcon YM-100 columns (Millipore) and concentrated with Microcon YM-3 columns (Millipore)

treatment_protocol: All samples were diluted with PBS, layered on Ficoll and spun at 400g for 30-40 minutes at room tempertaure (RT) to separate the plasma, Peripheral Blood Mononuclear Cells (PBMC)/platelet and Red Blood Cells. The plasma was re-centrifuged at 100,000g for 60 minutes at 40C to obtain the microvesicular (mv) fraction. The PBMC/platelet fraction was centrifuged twice at 65g for 15min at RT and the resultant pellet pooled to yield the enriched PMBC (pmbc) fraction. The supernatant fraction from these two rounds were pooled and centrifuges at 450 g for 20 min at RT to isolate the platelet fraction.

value: Blood

value: PBMC

tag: disease status

value: healthy control


title: control19_PBMC

description: 20101117_RD_Lankenau_c19_PBMC_RNA_1ug_B1_T1.CEL


title: control9a_PBMC

description: 20101117_RD_Lankenau_c9a_PBMC_RNA_1ug_B1_T1.CEL


title: control17_PBMC

description: 20101117_RD_Lankenau_c17_PBMC_RNA_1ug_B1_T1.CEL


title: control9c_PBMC

description: 20101117_RD_Lankenau_c9c_PBMC_RNA_1ug_B1_T1.CEL


title: Lentiviral construct containing GFP rep 3

description: replicate 3

value: Lentiviral construct containing GFP


title: T3_Pre_Male_Old (81400)

description:
EA08017_81400_AGEX_OM_T3_11_H133+.CHP
EA08017_81400_AGEX_OM_T3_11_H133+.CEL

value: Basal

value: Vastus lateralis muscle


title: Lentiviral construct containing Tdrd7 shRNA rep 1

description: replicate 1


title: T2_Post_Male_Old (81460)

description:
EA08017_81460_AGEX_OM_T2_26_H133+.CHP
EA08017_81460_AGEX_OM_T2_26_H133+.CEL


title: control18_PBMC

description: 20101117_RD_Lankenau_c18_PBMC_RNA_1ug_B1_T1.CEL


title: control9b_PBMC

description: 20101117_RD_Lankenau_c9b_PBMC_RNA_1ug_B1_T1.CEL


title: Lentiviral construct containing GFP rep 2

description: replicate 2


title: T3_Pre_Male_Old (81459)

description:
EA08017_81459_AGEX_OM_T3_26_H133+.CHP
EA08017_81459_AGEX_OM_T3_26_H133+.CEL


title: T3_Pre_Male_Old (81416)

description:
EA08017_81416_AGEX_OM_T3_15_H133+.CHP
EA08017_81416_AGEX_OM_T3_15_H133+.CEL


title: control16_PBMC

description: 20101117_RD_Lankenau_c16_PBMC_RNA_1ug_B1_T1.CEL


title: T3_Pre_Male_Old (81437)

description:
EA08017_81437_AGEX_OM_T3_20_H133+.CHP
EA08017_81437_AGEX_OM_T3_20_H133+.CEL


title: control13_PBMC

description: 20101117_RD_Lankenau_c13_PBMC_RNA_1ug_B1_T1.CEL


title: control14_PBMC

description: 20101117_RD_Lankenau_c14_PBMC_RNA_1ug_B1_T1.CEL


title: T3_Pre_Male_Old (81363)

description:
EA08017_81363_AGEX_OM_T3_2_H133+.CHP
EA08017_81363_AGEX_OM_T3_2_H133+.CEL


title: T2_Post_Male_Old (81415)

description:
EA08017_81415_AGEX_OM_T2_15_H133+.CHP
EA08017_81415_AGEX_OM_T2_15_H133+.CEL


title: T2_Post_Male_Old (81434)

description:
EA08017_81434_AGEX_OM_T2_20_H133+.CHP
EA08017_81434_AGEX_OM_T2_20_H133+.CEL


title: T1_Pre_Male_Old (81436)

description:
EA08017_81436_AGEX_OM_T1_20_H133+.CHP
EA08017_81436_AGEX_OM_T1_20_H133+.CEL


title: T2_Post_Male_Old (81377)

description:
EA08017_81377_AGEX_OM_T2_5_H133+.CHP
EA08017_81377_AGEX_OM_T2_5_H133+.CEL


title: Lentiviral construct containing GFP rep 1

description: replicate 1


title: T2_Post_Male_Old (81399)

description:
EA08017_81399_AGEX_OM_T2_11_H133+.CHP
EA08017_81399_AGEX_OM_T2_11_H133+.CEL


title: T2_Post_Male_Old (81364)

description:
EA08017_81364_AGEX_OM_T2_2_H133+.CHP
EA08017_81364_AGEX_OM_T2_2_H133+.CEL


title: T3_Pre_Male_Old (81374)

description:
EA08017_81374_AGEX_OM_T3_5_H133+.CHP
EA08017_81374_AGEX_OM_T3_5_H133+.CEL


title: T1_Pre_Male_Old (81461)

description:
EA08017_81461_AGEX_OM_T1_26_H133+.CHP
EA08017_81461_AGEX_OM_T1_26_H133+.CEL


title: control15_PBMC

description: 20101117_RD_Lankenau_c15_PBMC_RNA_1ug_B1_T1.CEL


title: T1_Pre_Male_Old (81414)

description:
EA08017_81414_AGEX_OM_T1_15_H133+.CHP
EA08017_81414_AGEX_OM_T1_15_H133+.CEL


title: control5_PBMC

description: 20101117_RD_Lankenau_c5_PBMC_RNA_1ug_B1_T1.CEL


title: control12_PBMC

description: 20101117_RD_Lankenau_c12_PBMC_RNA_1ug_B1_T1.CEL


title: control7_PBMC

description: 20101117_RD_Lankenau_c7_PBMC_RNA_1ug_B1_T1.CEL


title: control6_PBMC

description: 20101117_RD_Lankenau_c6_PBMC_RNA_1ug_B1_T1.CEL


title: control11_PBMC

description: 20101117_RD_Lankenau_c11_PBMC_RNA_1ug_B1_T1.CEL


title: control8_PBMC

description: 20101117_RD_Lankenau_c8_PBMC_RNA_1ug_B1_T1.CEL


title: control3_PBMC

description: 20101117_RD_Lankenau_c3_PBMC_RNA_1ug_B1_T1.CEL


title: control4_PBMC

description: 20101117_RD_Lankenau_c4_PBMC_RNA_1ug_B1_T1.CEL


title: control10_PBMC

description: 20101117_RD_Lankenau_c10_PBMC_RNA_1ug_B1_T1.CEL


title: control1_PBMC

description: 20101117_RD_Lankenau_c1_PBMC_RNA_1ug_B1_T1.CEL


title: patient7c_PBMC

description: 20101117_RD_Lankenau_p7c_PBMC_RNA_1ug_B1_T1.CEL

value: ulcerative colitis


title: control2_PBMC

description: 20101117_RD_Lankenau_c2_PBMC_RNA_1ug_B1_T1.CEL


title: patient7a_PBMC

description: 20101117_RD_Lankenau_p7a_PBMC_RNA_1ug_B1_T1.CEL


title: T1_Pre_Male_Old (81375)

description:
EA08017_81375_AGEX_OM_T1_5_H133+.CHP
EA08017_81375_AGEX_OM_T1_5_H133+.CEL


title: patient7b_PBMC

description: 20101117_RD_Lankenau_p7b_PBMC_RNA_1ug_B1_T1.CEL


title: T4_Post_Male_Young (81450)

description:
EA08017_81450_AGEX_YM_T4_24_H133+.CHP
EA08017_81450_AGEX_YM_T4_24_H133+.CEL


title: T1_Pre_Male_Old (81365)

description:
EA08017_81365_AGEX_OM_T1_2_H133+.CHP
EA08017_81365_AGEX_OM_T1_2_H133+.CEL


title: T3_Pre_Male_Young (81466)

description:
EA08017_81466_AGEX_YM_T3_28_H133+.CHP
EA08017_81466_AGEX_YM_T3_28_H133+.CEL


title: T4_Post_Male_Young (81393)

description:
EA08017_81393_AGEX_YM_T4_9_H133+.CHP
EA08017_81393_AGEX_YM_T4_9_H133+.CEL


title: T1_Pre_Male_Old (81398)

description:
EA08017_81398_AGEX_OM_T1_11_H133+.CHP
EA08017_81398_AGEX_OM_T1_11_H133+.CEL


title: T4_Post_Male_Young (81425)

description:
EA08017_81425_AGEX_YM_T4_17_H133+.CHP
EA08017_81425_AGEX_YM_T4_17_H133+.CEL


title: T3_Pre_Male_Young (81433)

description:
EA08017_81433_AGEX_YM_T3_19_H133+.CHP
EA08017_81433_AGEX_YM_T3_19_H133+.CEL


title: T4_Post_Male_Young (81380)

description:
EA08017_81380_AGEX_YM_T4_6_H133+.CHP
EA08017_81380_AGEX_YM_T4_6_H133+.CEL


title: T4_Post_Male_Young (81431)

description:
EA08017_81431_AGEX_YM_T4_19_H133+.CHP
EA08017_81431_AGEX_YM_T4_19_H133+.CEL


title: T4_Post_Male_Young (81370)

description:
EA08017_81370_AGEX_YM_T4_4_H133+.CHP
EA08017_81370_AGEX_YM_T4_4_H133+.CEL


title: T3_Pre_Male_Young (81451)

description:
EA08017_81451_AGEX_YM_T3_24_H133+.CHP
EA08017_81451_AGEX_YM_T3_24_H133+.CEL


title: T4_Post_Male_Young (81468)

description:
EA08017_81468_AGEX_YM_T4_28_H133+.CHP
EA08017_81468_AGEX_YM_T4_28_H133+.CEL


title: T4_Post_Male_Young (81411)

description:
EA08017_81411_AGEX_YM_T4_14_H133+.CHP
EA08017_81411_AGEX_YM_T4_14_H133+.CEL


title: patient14_PBMC

description: 20101117_RD_Lankenau_p14_PBMC_RNA_1ug_B1_T1.CEL


title: patient18_PBMC

description: 20101117_RD_Lankenau_p18_PBMC_RNA_1ug_B1_T1.CEL


title: patient20_PBMC

description: 20101117_RD_Lankenau_p20_PBMC_RNA_1ug_B1_T1.CEL


title: patient17_PBMC

description: 20101117_RD_Lankenau_p17_PBMC_RNA_1ug_B1_T1.CEL


title: patient16_PBMC

description: 20101117_RD_Lankenau_p16_PBMC_RNA_1ug_B1_T1.CEL


title: patient21_PBMC

description: 20101117_RD_Lankenau_p21_PBMC_RNA_1ug_B1_T1.CEL


title: T3_Pre_Male_Young (81424)

description:
EA08017_81424_AGEX_YM_T3_17_H133+.CHP
EA08017_81424_AGEX_YM_T3_17_H133+.CEL


title: patient19_PBMC

description: 20101117_RD_Lankenau_p19_PBMC_RNA_1ug_B1_T1.CEL


title: T3_Pre_Male_Young (81378)

description:
EA08017_81378_AGEX_YM_T3_6_H133+.CHP
EA08017_81378_AGEX_YM_T3_6_H133+.CEL


title: patient15_PBMC

description: 20101117_RD_Lankenau_p15_PBMC_RNA_1ug_B1_T1.CEL


title: T2_Post_Male_Young (81469)

description:
EA08017_81469_AGEX_YM_T2_28_H133+.CHP
EA08017_81469_AGEX_YM_T2_28_H133+.CEL


title: patient13_PBMC

description: 20101208_RD_Lankenau_p13_PBMC_RNA_200ng_B2_T1


title: T2_Post_Male_Young (81452)

description:
EA08017_81452_AGEX_YM_T2_24_H133+.CHP
EA08017_81452_AGEX_YM_T2_24_H133+.CEL


title: tdp-1(ok803) 3

first: Jiou

last: Wang

address: 615 N. Wolfe St.

institute: Johns Hopkins University

hyb_protocol: 15 µg of  the labeled aRNA was  fragmented and hybridized to the Affymetrix C. elegans genome array. Affymetrix Fluidics Station 450 was used to wash and stain the chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated aRNA. The staining was further amplified using a biotinilated anti-streptavidin antibody, followed by a second staining step with a streptavidin-phycoerythrin conjugate.

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was perfomed through the Affymetrix GeneChip Command Console version 3.4 (AGCC v3.4) software from Affymetrix.

data_processing: Data were extracted from the  CEL files, RMA normalized and converted to Log2 notation with Partek Genomics Suite (Partek, Missouri, USA).  These values were labeled as to genotype and the groups compared with a standard 1-way ANOVA, Student's t-test.

organism: Caenorhabditis elegans

source_name: mixed stages of C. elegans

label_protocol: The RNAs were labeled using the 3’ IVT Express Labeling protocol described by Affymetrix.

growth_protocol: N2 and outcrossed tdp-1(ok803lf) C. elegans were grown under standard conditions, and mixed stages of worms  were harvested.

extract_protocol: Total RNAs were extracted with TRIzol (Invitrogen) from triplicates of C. elegans and purified with the RNeasy kit (Qiagen).

tag: genotype


title: T3_Pre_Male_Young (81392)

description:
EA08017_81392_AGEX_YM_T3_9_H133+.CHP
EA08017_81392_AGEX_YM_T3_9_H133+.CEL


title: patient12_PBMC

description: 20101117_RD_Lankenau_p12_PBMC_RNA_1ug_B1_T1.CEL


title: tdp-1(ok803) 2


title: tdp-1(ok803)


title: T3_Pre_Male_Young (81413)

description:
EA08017_81413_AGEX_YM_T3_14_H133+.CHP
EA08017_81413_AGEX_YM_T3_14_H133+.CEL


title: wild-type 3

value: wild-type


title: T2_Post_Male_Young (81430)

description:
EA08017_81430_AGEX_YM_T2_19_H133+.CHP
EA08017_81430_AGEX_YM_T2_19_H133+.CEL


title: T3_Pre_Male_Young (81371)

description:
EA08017_81371_AGEX_YM_T3_4_H133+.CHP
EA08017_81371_AGEX_YM_T3_4_H133+.CEL


title: T2_Post_Male_Young (81410)

description:
EA08017_81410_AGEX_YM_T2_14_H133+.CHP
EA08017_81410_AGEX_YM_T2_14_H133+.CEL


title: T2_Post_Male_Young (81423)

description:
EA08017_81423_AGEX_YM_T2_17_H133+.CHP
EA08017_81423_AGEX_YM_T2_17_H133+.CEL


title: T2_Post_Male_Young (81391)

description:
EA08017_81391_AGEX_YM_T2_9_H133+.CHP
EA08017_81391_AGEX_YM_T2_9_H133+.CEL


title: T2_Post_Male_Young (81372)

description:
EA08017_81372_AGEX_YM_T2_4_H133+.CHP
EA08017_81372_AGEX_YM_T2_4_H133+.CEL


title: T2_Post_Male_Young (81381)

description:
EA08017_81381_AGEX_YM_T2_6_H133+.CHP
EA08017_81381_AGEX_YM_T2_6_H133+.CEL


title: T1_Pre_Male_Young (81453)

description:
EA08017_81453_AGEX_YM_T1_24_H133+.CHP
EA08017_81453_AGEX_YM_T1_24_H133+.CEL


title: T1_Pre_Male_Young (81467)

description:
EA08017_81467_AGEX_YM_T1_28_H133+.CHP
EA08017_81467_AGEX_YM_T1_28_H133+.CEL


title: patient11_PBMC

description: 20101117_RD_Lankenau_p11_PBMC_RNA_1ug_B1_T1.CEL


title: wild-type 2


title: wild-type 1


title: patient8_PBMC

description: 20101117_RD_Lankenau_p8_PBMC_RNA_1ug_B1_T1.CEL


title: patient6_PBMC

description: 20101117_RD_Lankenau_p6_PBMC_RNA_1ug_B1_T1.CEL


title: patient10_PBMC

description: 20101117_RD_Lankenau_p10_PBMC_RNA_1ug_B1_T1.CEL


title: patient9_PBMC

description: 20101117_RD_Lankenau_p9_PBMC_RNA_1ug_B1_T1.CEL


title: T1_Pre_Male_Young (81422)

description:
EA08017_81422_AGEX_YM_T1_17_H133+.CHP
EA08017_81422_AGEX_YM_T1_17_H133+.CEL


title: T1_Pre_Male_Young (81390)

description:
EA08017_81390_AGEX_YM_T1_9_H133+.CHP
EA08017_81390_AGEX_YM_T1_9_H133+.CEL


title: T1_Pre_Male_Young (81432)

description:
EA08017_81432_AGEX_YM_T1_19_H133+.CHP
EA08017_81432_AGEX_YM_T1_19_H133+.CEL


title: T1_Pre_Male_Young (81379)

description:
EA08017_81379_AGEX_YM_T1_6_H133+.CHP
EA08017_81379_AGEX_YM_T1_6_H133+.CEL


title: patient3_PBMC

description: 20101117_RD_Lankenau_p3_PBMC_RNA_1ug_B1_T1.CEL


title: T3_Pre_OF_13_2A_13F

label_protocol: 5ng of total RNA was labeled using NuGen WT-Ovation RNA Amp v2 kit and protocol

value: old female 13 (OF_13)

value: female

value: Old (85±1y)

tag: fiber type

value: fast-twitch (MHC IIa)


title: T1_Pre_Male_Young (81412)

description:
EA08017_81412_AGEX_YM_T1_14_H133+.CHP
EA08017_81412_AGEX_YM_T1_14_H133+.CEL

value: Young

value: Male

value: Untrained


title: T4_Post_OF_10_2A_10H

value: old female 10 (OF_10)

value: Trained


title: T4_Post_OF_9_2A_9H

value: old female 9 (OF_9)

value: 4hrs post exercise


title: T4_Post_OF_13_2A_13H


title: patient4_PBMC

description: 20101208_RD_Lankenau_p4_PBMC_RNA_1ug_B2_T1

value: Blood

value: PBMC


title: patient5_PBMC

description: 20101117_RD_Lankenau_p5_PBMC_RNA_1ug_B1_T1.CEL


title: T3_Pre_OF_11_2A_11F

value: old female 11 (OF_11)

value: Basal


title: 129S6_BrainStem_Wild-type HSV-1_7d_f (251486827610_1_2)

description: US93503719_251486827610_S01_GE1-v5_95_Feb07_1_2.txt

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505C).

source_name: BrainStem

growth_protocol: Gender-matched, 6- to 8- week old immunocompetent, control 129S6 and 129S6 Stat1 knockout mice were infected corneally with 2x10^6 PFU of either wild type HSV-1, a vhs-null HSV virus, or mock-infected. Brain stems and liver of individual mice were isolated at days 1, 3, 5 and 7 post-inoculation for microarray analysis.

extract_protocol: RNA was isolated using Qiagen RNeasy Mini kits with RNA-Later solution according to the manufacturer’s recommended protocol and purified using RNasy columns (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Brain stems and livers from each animal were harvested and briefly rinse tissue in cold (4ºC) PBS, placed in 0.3 ml of solution D (4 M guanidine thiocyanate, 25 ml of sodium citrate, 0.5% sarcosyl, 0.1 M 2-mercaptoethanol), and stored at −80°C.

value: BrainStem

value: f

tag: sample collection time post infection

tag: virus infection

value: Wild-type HSV-1


title: T2_Post_OF_13_2A_13D

value: old female 13 (OF_13)

value: female

value: Vastus lateralis muscle


title: T4_Post_OF_11_2A_11H

value: Old (85±1y)

value: fast-twitch (MHC IIa)


title: T1_Pre_Male_Young (81373)

description:
EA08017_81373_AGEX_YM_T1_4_H133+.CHP
EA08017_81373_AGEX_YM_T1_4_H133+.CEL

source_name: Vastus lateralis muscle

value: Young

value: Male

value: Untrained


title: 129S6_BrainStem_Wild-type HSV-1_3d_m (251486827141_1_3)

description: US93503719_251486827141_S01_GE1-v5_95_Feb07_1_3.txt

value: m


title: T3_Pre_OF_14_2A_14F

value: old female 14 (OF_14)

value: Trained


title: 129S6_BrainStem_Wild-type HSV-1_7d_m (251486827612_1_4)

description: US93503719_251486827612_S01_GE1-v5_95_Feb07_1_4.txt


title: control9c_Microvesicles

description: 20101118_RD_Lankenau_c9c_Microvesicles_RNA_3ug_B1_T1.CEL

source_name: Microvesicles

value: Blood

value: Microvesicles

value: healthy control


title: patient2_PBMC

description: 20101117_RD_Lankenau_p2_PBMC_RNA_1ug_B1_T1.CEL

value: PBMC

value: ulcerative colitis


title: 129S6_BrainStem_Wild-type HSV-1_3d_f (251486827141_1_1)

description: US93503719_251486827141_S01_GE1-v5_95_Feb07_1_1.txt

value: BrainStem

value: f

value: Wild-type HSV-1


title: 129S6_BrainStem_Wild-type HSV-1_1d_m (251486827619_1_1)

description: US93503719_251486827619_S01_GE1-v5_95_Feb07_1_1.txt


title: 129S6_BrainStem_Wild-type HSV-1_5d_f (251486827613_1_4)

description: US93503719_251486827613_S01_GE1-v5_95_Feb07_1_4.txt


title: control9b_Microvesicles

description: 20101118_RD_Lankenau_c9b_Microvesicles_RNA_3ug_B1_T1.CEL


title: T2_Post_OF_11_2A_11D

value: old female 11 (OF_11)

value: female

value: Vastus lateralis muscle

value: 4hrs post exercise


title: control9a_Microvesicles

description: 20101118_RD_Lankenau_c9a_Microvesicles_RNA_3ug_B1_T1.CEL


title: T3_Pre_OF_10_2A_10F

value: old female 10 (OF_10)

value: Old (85±1y)

value: Basal

value: fast-twitch (MHC IIa)


title: T1_Pre_OF_11_2A_11B

value: Untrained


title: 129S6_BrainStem_Wild-type HSV-1_5d_m (251486827615_1_1)

description: US93503719_251486827615_S01_GE1-v5_95_Feb07_1_1.txt

value: m


title: 129S6_BrainStem_Wild-type HSV-1_1d_m (251486827613_1_3)

description: US93503719_251486827613_S01_GE1-v5_95_Feb07_1_3.txt


title: 129S6_BrainStem_mock_7d_f (251486827140_1_4)

description: US93503719_251486827140_S01_GE1-v5_95_Feb07_1_4.txt

value: mock


title: T2_Post_OF_9_2A_9D

value: old female 9 (OF_9)


title: T4_Post_YF_6_2A_6H

value: young female 6 (YF_6)

value: Young (23±2y)

value: Trained


title: T4_Post_YF_3_2A_3H

value: young female 3 (YF_3)


title: 129S6_BrainStem_mock_7d_m (251486827140_1_2)

description: US93503719_251486827140_S01_GE1-v5_95_Feb07_1_2.txt

value: BrainStem


title: T4_Post_YF_4_2A_4H

value: young female 4 (YF_4)


title: T4_Post_YF_5_2A_5H

value: young female 5 (YF_5)

value: female


title: control16_Microvesicles

description: 20101118_RD_Lankenau_c16_Microvesicles_RNA_3ug_B1_T1.CEL

value: Blood

value: Microvesicles

value: healthy control


title: control19_Microvesicles

description: 20101208_RD_Lankenau_c19_Microvesicles_RNA_3ug_B2_T1


title: 129S6_BrainStem_mock_3d_m (251486827121_1_3)

description: US93503719_251486827121_S01_GE1-v5_95_Feb07_1_3.txt


title: T1_Pre_OF_10_2A_10B

value: old female 10 (OF_10)

value: Old (85±1y)

value: Vastus lateralis muscle

value: Basal


title: control20_Microvesicles

description: 20101118_RD_Lankenau_c20_Microvesicles_RNA_3ug_B1_T1.CEL


title: control17_Microvesicles

description: 20101118_RD_Lankenau_c17_Microvesicles_RNA_3ug_B1_T1.CEL


title: T3_Pre_YF_3_2A_3F

value: fast-twitch (MHC IIa)


title: control14_Microvesicles

description: 20101118_RD_Lankenau_c14_Microvesicles_RNA_3ug_B1_T1.CEL


title: T4_Post_YF_1_2A_1H

value: young female 1 (YF_1)

value: 4hrs post exercise


title: T3_Pre_YF_6_2A_6F

value: young female 6 (YF_6)

value: Young (23±2y)


title: control18_Microvesicles

description: 20101118_RD_Lankenau_c18_Microvesicles_RNA_3ug_B1_T1.CEL


title: 129S6_BrainStem_mock_1d_m (251486827695_1_2)

description: US93503719_251486827695_S01_GE1-v5_95_Feb07_1_2.txt

value: m

value: mock


title: 129S6_BrainStem_mock_1d_m (251486827617_1_2)

description: US93503719_251486827617_S01_GE1-v5_95_Feb07_1_2.txt

value: BrainStem


title: T3_Pre_YF_2_2A_2F

value: young female 2 (YF_2)

value: Trained


title: T3_Pre_YF_1_2A_1F

value: female


title: T2_Post_YF_3_2A_3D

value: young female 3 (YF_3)

value: Untrained


title: T4_Post_YF_2_2A_2H


title: T2_Post_YF_7_2A_7D

value: young female 7 (YF_7)


title: 129S6_BrainStem_mock_5d_f (251486827617_1_3)

description: US93503719_251486827617_S01_GE1-v5_95_Feb07_1_3.txt

value: f


title: T2_Post_YF_2_2A_2D

value: Vastus lateralis muscle


title: T1_Pre_YF_6_2A_6B

value: Basal


title: 129S6_BrainStem_mock_3d_f (251486827139_1_3)

description: US93503719_251486827139_S01_GE1-v5_95_Feb07_1_3.txt


title: 129S6_BrainStem_vhs-null HSV-1_7d_f (251486827610_1_4)

description: US93503719_251486827610_S01_GE1-v5_95_Feb07_1_4.txt

value: vhs-null HSV-1


title: 129S6_BrainStem_mock_5d_m (251486827615_1_3)

description: US93503719_251486827615_S01_GE1-v5_95_Feb07_1_3.txt


title: T3_Pre_YF_5_2A_5F

value: young female 5 (YF_5)

value: fast-twitch (MHC IIa)


title: 129S6_BrainStem_vhs-null HSV-1_7d_m (251486827610_1_3)

description: US93503719_251486827610_S01_GE1-v5_95_Feb07_1_3.txt


title: T3_Pre_YF_8_2A_8F

value: young female 8 (YF_8)


title: T1_Pre_YF_3_2A_3B

value: Young (23±2y)


title: control13_Microvesicles

description: 20101118_RD_Lankenau_c13_Microvesicles_RNA_3ug_B1_T1.CEL

value: Blood

value: Microvesicles

value: healthy control


title: T2_Post_YF_1_2A_1D

value: young female 1 (YF_1)

value: 4hrs post exercise


title: control15_Microvesicles

description: 20101118_RD_Lankenau_c15_Microvesicles_RNA_3ug_B1_T1.CEL


title: T1_Pre_YF_2_2A_2B

value: young female 2 (YF_2)

value: female


title: 129S6_BrainStem_vhs-null HSV-1_5d_m (251486827695_1_3)

description: US93503719_251486827695_S01_GE1-v5_95_Feb07_1_3.txt

value: BrainStem

value: m


title: T1_Pre_YF_1_2A_1B

value: Untrained


title: T4_Post_OF_13_1_13G

value: old female 13 (OF_13)

value: Old (85±1y)

value: Vastus lateralis muscle

value: Trained

value: slow-twitch (MHC I)


title: control12_Microvesicles

description: 20101118_RD_Lankenau_c12_Microvesicles_RNA_3ug_B1_T1.CEL


title: control11_Microvesicles

description: 20101118_RD_Lankenau_c11_Microvesicles_RNA_3ug_B1_T1.CEL


title: control8_Microvesicles

description: 20101118_RD_Lankenau_c8_Microvesicles_RNA_3ug_B1_T1.CEL


title: control10_Microvesicles

description: 20101118_RD_Lankenau_c10_Microvesicles_RNA_3ug_B1_T1.CEL


title: control6_Microvesicles

description: 20101118_RD_Lankenau_c6_Microvesicles_RNA_3ug_B1_T1.CEL


title: T4_Post_OF_12_1_12G

value: old female 12 (OF_12)


title: control7_Microvesicles

description: 20101118_RD_Lankenau_c7_Microvesicles_RNA_3ug_B1_T1.CEL


title: 129S6_BrainStem_vhs-null HSV-1_5d_f (251486827696_1_3)

description: US93503719_251486827696_S01_GE1-v5_95_Feb07_1_3.txt

value: f

value: vhs-null HSV-1


title: 129S6_BrainStem_vhs-null HSV-1_1d_m (251486827692_1_3)

description: US93503719_251486827692_S01_GE1-v5_95_Feb07_1_3.txt


title: T4_Post_OF_11_1_11G

value: old female 11 (OF_11)


title: T4_Post_OF_10_1_10G

value: old female 10 (OF_10)


title: control5_Microvesicles

description: 20101118_RD_Lankenau_c5_Microvesicles_RNA_3ug_B1_T1.CEL

value: Blood

value: Microvesicles

value: healthy control


title: 129S6_BrainStem_vhs-null HSV-1_3d_m (251486827142_1_1)

description: US93503719_251486827142_S01_GE1-v5_95_Feb07_1_1.txt


title: T3_Pre_OF_10_1_10E

value: female

value: Basal


title: 129S6_Liver_Wild-type HSV-1_7d_f (251486831127_1_1)

description: US93503719_251486831127_S01_GE1-v5_95_Feb07_1_1.txt

source_name: Liver

value: Liver

value: Wild-type HSV-1


title: T3_Pre_OF_12_1_12E


title: 129S6_BrainStem_vhs-null HSV-1_3d_f (251486827142_1_4)

description: US93503719_251486827142_S01_GE1-v5_95_Feb07_1_4.txt

value: BrainStem


title: T4_Post_OF_9_1_9G

value: old female 9 (OF_9)

value: Old (85±1y)

value: 4hrs post exercise


title: T3_Pre_OF_11_1_11E

value: Vastus lateralis muscle

value: Trained

value: slow-twitch (MHC I)


title: control4_Microvesicles

description: 20101118_RD_Lankenau_c4_Microvesicles_RNA_3ug_B1_T1.CEL


title: 129S6_Liver_Wild-type HSV-1_7d_m (251486831356_1_3)

description: US93503719_251486831356_S01_GE1-v5_95_Feb07_1_3.txt

value: m


title: T2_Post_OF_9_1_9C

value: Untrained


title: 129S6_Liver_Wild-type HSV-1_5d_m (251486831129_1_1)

description: US93503719_251486831129_S01_GE1-v5_95_Feb07_1_1.txt


title: T2_Post_OF_13_1_13C

value: old female 13 (OF_13)


title: T2_Post_OF_11_1_11C

value: old female 11 (OF_11)


title: T3_Pre_OF_13_1_13E


title: T1_Pre_OF_14_1_14A

value: old female 14 (OF_14)


title: control3_Microvesicles

description: 20101118_RD_Lankenau_c3_Microvesicles_RNA_3ug_B1_T1.CEL

value: Blood

value: Microvesicles

value: healthy control


title: control2_Microvesicles

description: 20101118_RD_Lankenau_c2_Microvesicles_RNA_3ug_B1_T1.CEL


title: 129S6_Liver_Wild-type HSV-1_5d_f (251486831229_1_1)

description: US93503719_251486831229_S01_GE1-v5_95_Feb07_1_1.txt

value: Liver

value: f


title: patient7c_Microvesicles

description: 20101118_RD_Lankenau_p7c_Microvesicles_RNA_3ug_B1_T1.CEL

value: ulcerative colitis


title: control1_Microvesicles

description: 20101118_RD_Lankenau_c1_Microvesicles_RNA_3ug_B1_T1.CEL


title: patient7b_Microvesicles

description: 20101118_RD_Lankenau_p7b_Microvesicles_RNA_3ug_B1_T1.CEL


title: T1_Pre_OF_12_1_12A

value: old female 12 (OF_12)

value: female

value: Basal


title: T4_Post_YF_7_1_7G

value: young female 7 (YF_7)

value: Young (23±2y)

value: Vastus lateralis muscle

value: 4hrs post exercise


title: T1_Pre_OF_11_1_11A

value: Old (85±1y)

value: Untrained

value: slow-twitch (MHC I)


title: T1_Pre_OF_13_1_13A

value: old female 13 (OF_13)


title: T4_Post_YF_2_1_2G

value: young female 2 (YF_2)

value: Trained


title: T4_Post_YF_6_1_6G

value: young female 6 (YF_6)


title: T4_Post_YF_4_1_4G

value: young female 4 (YF_4)


title: T3_Pre_YF_7_1_7E


title: T4_Post_YF_1_1_1G

value: young female 1 (YF_1)


title: T4_Post_YF_3_1_3G

value: young female 3 (YF_3)


title: patient14_Microvesicles

description: 20101118_RD_Lankenau_p14_Microvesicles_RNA_3ug_B1_T1.CEL

value: Blood

value: Microvesicles

value: ulcerative colitis


title: 129S6_Liver_Wild-type HSV-1_3d_m (251486831257_1_4)

description: US93503719_251486831257_S01_GE1-v5_95_Feb07_1_4.txt

value: Liver

value: m

value: Wild-type HSV-1


title: 129S6_Liver_mock_7d_f (251486831226_1_2)

description: US93503719_251486831226_S01_GE1-v5_95_Feb07_1_2.txt

value: f

value: mock


title: 129S6_Liver_Wild-type HSV-1_1d_m (251486831126_1_3)

description: US93503719_251486831126_S01_GE1-v5_95_Feb07_1_3.txt


title: 129S6_Liver_mock_7d_m (251486831257_1_2)

description: US93503719_251486831257_S01_GE1-v5_95_Feb07_1_2.txt


title: patient7a_Microvesicles

description: 20101118_RD_Lankenau_p7a_Microvesicles_RNA_3ug_B1_T1.CEL


title: 129S6_Liver_Wild-type HSV-1_3d_f (251486831126_1_2)

description: US93503719_251486831126_S01_GE1-v5_95_Feb07_1_2.txt


title: 129S6_Liver_Wild-type HSV-1_1d_m (251486831230_1_2)

description: US93503719_251486831230_S01_GE1-v5_95_Feb07_1_2.txt


title: T2_Post_YF_8_1_8C

value: young female 8 (YF_8)

value: female

value: Young (23±2y)

value: Vastus lateralis muscle

value: Untrained

value: 4hrs post exercise


title: T3_Pre_YF_1_1_1E

value: Trained

value: Basal

value: slow-twitch (MHC I)


title: patient21_Microvesicles

description: 20101118_RD_Lankenau_p21_Microvesicles_RNA_3ug_B1_T1.CEL

value: Blood


title: patient20_Microvesicles

description: 20101118_RD_Lankenau_p20_Microvesicles_RNA_3ug_B1_T1.CEL

value: Microvesicles


title: T2_Post_YF_7_1_7C

value: young female 7 (YF_7)


title: T3_Pre_YF_2_1_2E

value: young female 2 (YF_2)


title: T3_Pre_YF_3_1_3E

value: young female 3 (YF_3)


title: T3_Pre_YF_4_1_4E

value: young female 4 (YF_4)


title: T2_Post_YF_6_1_6C

value: young female 6 (YF_6)


title: T2_Post_YF_1_1_1C

value: young female 1 (YF_1)


title: Liver_nash metformin_no.3

city: Kanazawa

first: Hirofumi

last: Misu

address: 13-1 Takaramachi

institute: Kanazawa University

description:
Gene expression data from mouse liver.
Sample name: Met3
GC1973new.CEL

hyb_protocol: After generating the hybridization cocktails, hybridization to the DNA microarray and fluorescent labelling were performed with a GeneChip Hybridization Wash and Stain kit (Affymetrix).

scan_protocol: The microarrays were subsequently scanned with the GeneChip Scanner 3000 MegAllele System (Affymetrix).

data_processing: Data analysis was conducted with the GeneChip Operating System 1.1 (Affymetrix). Detection, signal, signal log ratio, and change were obtained from the GeneChip Operating System (GCOS) with default settings after global normalization was performed to make the average intensity of all probe sets equal to 100.

source_name: Liver, fasting

label_protocol: A total of 2 μg of total RNA was labelled according to the small sample labelling protocol recommended by the manufacturer.

growth_protocol: Hepatic tissues were obtained after the sacrifice and immediately frozen in liquid nitrogen and stored at −80°C until use.

extract_protocol: Total RNA was extracted from each liver using the RNeasy Mini kit (Qiagen, Tokyo, Japan).

treatment_protocol: Eight-week-old C57BL/6 mice were divided into three experimental groups and fed for 8 weeks as follows: a) normal chow (normal), b) methionine- and choline-deficient diet+ high fat diet (NASH), c) MCD + HF diet mixed with 0.1% metformin (nash metformin).

tag: diet

value: liver


title: Liver_nash metformin_no.2

description:
Gene expression data from mouse liver.
Sample name: Met2
GC1972new.CEL

value: MCD + HF diet mixed with 0.1% metformin (nash metformin)


title: Liver_nash metformin_no.4

description:
Gene expression data from mouse liver.
Sample name: Met4
GC1974new.CEL


title: T1_Pre_YF_8_1_8A

value: young female 8 (YF_8)

tag: gender

value: female

value: Young (23±2y)


title: patient19_Microvesicles

description: 20101118_RD_Lankenau_p19_Microvesicles_RNA_3ug_B1_T1.CEL

value: ulcerative colitis


title: patient17_Microvesicles

description: 20101118_RD_Lankenau_p17_Microvesicles_RNA_3ug_B1_T1.CEL


title: 129S6_Liver_mock_5d_f (251486831130_1_2)

description: US93503719_251486831130_S01_GE1-v5_95_Feb07_1_2.txt

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

value: Liver

value: f

value: mock


title: T1_Pre_YF_4_1_4A

tag: age

value: Vastus lateralis muscle

value: Untrained

value: Basal

value: slow-twitch (MHC I)


title: patient15_Microvesicles

description: 20101118_RD_Lankenau_p15_Microvesicles_RNA_3ug_B1_T1.CEL

value: Blood

value: Microvesicles


title: 129S6_Liver_mock_1d_m (251486831257_1_3)

description: US93503719_251486831257_S01_GE1-v5_95_Feb07_1_3.txt

value: m


title: patient18_Microvesicles

description: 20101208_RD_Lankenau_p18_Microvesicles_RNA_3ug_B2_T1


title: Liver_nash metformin_no.1

description:
Gene expression data from mouse liver.
Sample name: Met1
GC1971new.CEL


title: patient13_Microvesicles

description: 20101118_RD_Lankenau_p13_Microvesicles_RNA_3ug_B1_T1.CEL


title: patient16_Microvesicles

description: 20101118_RD_Lankenau_p16_Microvesicles_RNA_3ug_B1_T1.CEL


title: 129S6_Liver_mock_3d_f (251486831387_1_4)

description: US93503719_251486831387_S01_GE1-v5_95_Feb07_1_4.txt


title: Liver_nash_no.4

description:
Gene expression data from mouse liver.
Sample name: NASH4
GC1969new.CEL

value: methionine- and choline-deficient diet+ high fat diet (NASH)


title: 129S6_Liver_mock_5d_m (251486831388_1_2)

description: US93503719_251486831388_S01_GE1-v5_95_Feb07_1_2.txt


title: T1_Pre_YF_2_1_2A

value: young female 2 (YF_2)


title: T2_Post_YF_2_1_2C

value: 4hrs post exercise


title: T1_Pre_YF_6_1_6A

value: young female 6 (YF_6)


title: Liver_nash_no.3

description:
Gene expression data from mouse liver.
Sample name: NASH3
GC1968new.CEL

value: liver


title: T1_Pre_YF_3_1_3A

value: young female 3 (YF_3)

value: female

value: Young (23±2y)


title: 129S6_Liver_mock_1d_m (251486831227_1_1)

description: US93503719_251486831227_S01_GE1-v5_95_Feb07_1_1.txt

value: Liver


title: 129S6_Liver_mock_3d_m (251486831258_1_1)

description: US93503719_251486831258_S01_GE1-v5_95_Feb07_1_1.txt

value: mock


title: 129S6_Liver_vhs-null HSV-1_7d_m (251486831228_1_4)

description: US93503719_251486831228_S01_GE1-v5_95_Feb07_1_4.txt

value: vhs-null HSV-1


title: Hyperinsulinemic Insulin Sensitive 7

city: Helsinki

first: Jarkko

last: Soronen

address: Haartmaninkatu 8

department: Institute for Molecular Medicine Finland (FIMM)

country: Finland

institute: University of Helsinki

hyb_protocol: Affymetrix Fluidics Station 450 and Hybridization Oven 640 under standard conditions

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

source_name: Hyperinsulinemic Insulin Sensitive

extract_protocol: RNeasy Lipid Tissue Mini Kit (Qiagen)

treatment_protocol: Adipose tissue sample was obtained by needle biopsy from female subject after an o/n fast and after 3h of hyperinsulinemic euglycemic clamp

value: subcutaneous adipose

tag: stimulation

value: hyperinsulinemia

tag: resistance status

value: sensitive


title: patient11_Microvesicles

description: 20101118_RD_Lankenau_p11_Microvesicles_RNA_3ug_B1_T1.CEL

value: Blood

value: ulcerative colitis

tag: subject


title: 129S6_Liver_vhs-null HSV-1_7d_f (251486831230_1_1)

description: US93503719_251486831230_S01_GE1-v5_95_Feb07_1_1.txt

tag: tissue

value: f


title: Liver_nash_no.1

description:
Gene expression data from mouse liver.
Sample name: NASH1
GC1966new.CEL

value: methionine- and choline-deficient diet+ high fat diet (NASH)


title: Hyperinsulinemic Insulin Sensitive 4


title: patient9_Microvesicles

description: 20101208_RD_Lankenau_p9_Microvesicles_RNA_3ug_B2_T1

tag: cell type

value: Microvesicles


title: patient10_Microvesicles

description: 20101118_RD_Lankenau_p10_Microvesicles_RNA_3ug_B1_T1.CEL


title: Hyperinsulinemic Insulin Sensitive 5


title: 129S6_Liver_vhs-null HSV-1_5d_f (251486831386_1_1)

description: US93503719_251486831386_S01_GE1-v5_95_Feb07_1_1.txt


title: 129S6_Liver_vhs-null HSV-1_5d_m (251486831127_1_3)

description: US93503719_251486831127_S01_GE1-v5_95_Feb07_1_3.txt

value: m


title: Liver_normal_no.3

description:
Gene expression data from mouse liver.
Sample name: C3
GC1963new.CEL

value: normal chow (normal)


title: 129S6_Liver_vhs-null HSV-1_3d_m (251486831356_1_4)

description: US93503719_251486831356_S01_GE1-v5_95_Feb07_1_4.txt


title: Hyperinsulinemic Insulin Sensitive 13


title: patient6_Microvesicles

description: 20101118_RD_Lankenau_p6_Microvesicles_RNA_3ug_B1_T1.CEL


title: Hyperinsulinemic Insulin Resistant 9

source_name: Hyperinsulinemic Insulin Resistant

value: resistant


title: 129S6_Liver_vhs-null HSV-1_1d_m (251486831258_1_4)

description: US93503719_251486831258_S01_GE1-v5_95_Feb07_1_4.txt


title: 129S6_Liver_vhs-null HSV-1_3d_f (251486831367_1_2)

description: US93503719_251486831367_S01_GE1-v5_95_Feb07_1_2.txt


title: Hyperinsulinemic Insulin Sensitive 3


title: Liver_normal_no.2

description:
Gene expression data from mouse liver.
Sample name: C2
GC1962new.CEL

value: liver


title: KO_WY_rep4

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

data_processing: Expression estimates were calculated using GCRMA (v2.2.0) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.

source_name: heart

label_protocol: The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).

growth_protocol: Pure-bred wild type (129S1/SvImJ) and PPARα-/- (129S4/SvJae) mice, aged 2-6 months, were used. Animals were put on a run-in diet consisting of a modified AIN76A diet (corn oil was replaced with olive oil) two weeks before the start of the experiment.

extract_protocol: Total RNA was prepared from mouse hearts using TRIzol reagent, followed by purification of total RNA using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Starting at 5AM the animals were fasted for 4 hours followed by an intragastric gavage of 400 µL synthetic triolein, trilinolein, trilinolenin, or tridocosahexaenoin. Wy14643 was given as 400 µL of a 10 mg/mL suspension in 0.5% carboxylmethyl cellulose (CMC). CMC only served as control treatment  (400uL). Six hours after the oral gavage, mice were anaesthetized with a mixture of isofluorane (1.5%), nitrous oxide (70%) and oxygen (30%). Blood was collected by orbital puncture, followed by sacrifice of the mice by cervical dislocation. Hearts were removed, snap-frozen in liquid nitrogen and stored at -80ºC.

value: male

value: PPARalpha -/- (129S4/SvJae)

tag: treatment

value: Wy14,643 (aka pirinixic acid) is a synthetic PPARalpha agonist. CAS Number:50892-23-4


title: patient8_Microvesicles

description: 20101118_RD_Lankenau_p8_Microvesicles_RNA_3ug_B1_T1.CEL


title: Liver_normal_no.1

description:
Gene expression data from mouse liver.
Sample name: C1
GC1961new.CEL


title: Hyperinsulinemic Insulin Resistant 20

value: female


title: patient5_Microvesicles

description: 20101118_RD_Lankenau_p5_Microvesicles_RNA_3ug_B1_T1.CEL


title: Liver_normal_no.4

description:
Gene expression data from mouse liver.
Sample name: C4
GC1964new.CEL


title: Hyperinsulinemic Insulin Resistant 21


title: KO_WY_rep5


title: 129S6_BrainStem_Wild-type HSV-1_7d_m (251486827140_1_1)

description: US93503719_251486827140_S01_GE1-v5_95_Feb07_1_1.txt

value: Wild-type

value: BrainStem

value: Wild-type HSV-1


title: 129S6_Liver_vhs-null HSV-1_1d_m (251486831126_1_1)

description: US93503719_251486831126_S01_GE1-v5_95_Feb07_1_1.txt

value: Liver

value: vhs-null HSV-1


title: control9c_platelets

description: 20101122_RD_Lankenau_c9c_Platelet_RNA_1ug_B1_T1.CEL

source_name: platelets

value: Blood

value: platelets

value: healthy control


title: patient3_Microvesicles

description: 20101118_RD_Lankenau_p3_Microvesicles_RNA_3ug_B1_T1.CEL

value: Microvesicles

value: ulcerative colitis


title: patient4_Microvesicles

description: 20101118_RD_Lankenau_p4_Microvesicles_RNA_3ug_B1_T1.CEL


title: 129S6_BrainStem_vhs-null HSV-1_1d_m (251486827662_1_3)

description: US93503719_251486827662_S01_GE1-v5_95_Feb07_1_3.txt

value: m


title: Hyperinsulinemic Insulin Resistant 14

value: subcutaneous adipose

value: hyperinsulinemia

value: resistant


title: 129S6_BrainStem_Wild-type HSV-1_7d_f (251486827611_1_3)

description: US93503719_251486827611_S01_GE1-v5_95_Feb07_1_3.txt

value: f


title: Fasting Insulin Sensitive 7

source_name: Fasting Insulin Sensitive

value: fasting

value: sensitive


title: KO_WY_rep3

value: male

value: PPARalpha -/- (129S4/SvJae)

value: Wy14,643 (aka pirinixic acid) is a synthetic PPARalpha agonist. CAS Number:50892-23-4


title: 129S6_BrainStem_Wild-type HSV-1_5d_f (251486827613_1_2)

description: US93503719_251486827613_S01_GE1-v5_95_Feb07_1_2.txt

value: Wild-type

value: BrainStem

value: Wild-type HSV-1


title: Hyperinsulinemic Insulin Resistant 1

value: female


title: control9b_platelets

description: 20101122_RD_Lankenau_c9b_Platelet_RNA_1ug_B1_T1.CEL

value: Blood

value: platelets

value: healthy control


title: patient2_Microvesicles

description: 20101118_RD_Lankenau_p2_Microvesicles_RNA_3ug_B1_T1.CEL

value: Microvesicles

value: ulcerative colitis


title: 129S6_BrainStem_Wild-type HSV-1_3d_m (251486827141_1_2)

description: US93503719_251486827141_S01_GE1-v5_95_Feb07_1_2.txt

value: m


title: KO_WY_rep1


title: 129S6_BrainStem_Wild-type HSV-1_5d_m (251486827613_1_1)

description: US93503719_251486827613_S01_GE1-v5_95_Feb07_1_1.txt


title: Fasting Insulin Sensitive 5

value: subcutaneous adipose


title: KO_WY_rep2


title: control19_platelets

description: 20101208_RD_Lankenau_c19_Platelet_RNA_500ng_B2_T1.CEL


title: KO_C226TG_rep5

value: tridocosahexaenoin


title: control9a_platelets

description: 20101122_RD_Lankenau_c9a_Platelet_RNA_1ug_B1_T1.CEL


title: Fasting Insulin Sensitive 3

value: fasting


title: Liver_nash_no.2

description:
Gene expression data from mouse liver.
Sample name: NASH2
GC1967new.CEL

value: methionine- and choline-deficient diet+ high fat diet (NASH)

value: liver


title: 129S6_BrainStem_Wild-type HSV-1_3d_f (251486827693_1_1)

description: US93503719_251486827693_S01_GE1-v5_95_Feb07_1_1.txt

value: f


title: Fasting Insulin Sensitive 4

value: sensitive


title: 129S6_BrainStem_Wild-type HSV-1_1d_m (251486827615_1_2)

description: US93503719_251486827615_S01_GE1-v5_95_Feb07_1_2.txt

value: Wild-type


title: KO_C226TG_rep4

value: male

value: PPARalpha -/- (129S4/SvJae)


title: Fasting Insulin Resistant 20

source_name: Fasting Insulin Resistant

value: female

value: resistant


title: Fasting Insulin Sensitive 13


title: KO_C181TG_rep5

value: triolein